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(-) Description

Title :  KIT KINASE DOMAIN MUTANT D816H IN COMPLEX WITH SUNITINIB
 
Authors :  K. S. Gajiwala, J. C. Wu, E. A. Lunney, G. D. Demetri
Date :  27 Jan 09  (Deposition) - 24 Feb 09  (Release) - 13 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Kit Kinase Domain, Sutent Binding, Drug Resistance, Atp- Binding, Disease Mutation, Glycoprotein, Immunoglobulin Domain, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Polymorphism, Proto-Oncogene, Receptor, Transmembrane, Tyrosine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. S. Gajiwala, J. C. Wu, J. Christensen, G. D. Deshmukh, W. Diehl, J. P. Dinitto, J. M. English, M. J. Greig, Y. A. He, S. L. Jacques, E. A. Lunney, M. Mctigue, D. Molina, T. Quenzer, P. A. Wells, X. Yu, Y. Zhang, A. Zou, M. R. Emmett, A. G. Marshall, H. M. Zhang, G. D. Demetri
Kit Kinase Mutants Show Unique Mechanisms Of Drug Resistance To Imatinib And Sunitinib In Gastrointestinal Stromal Tumor Patients.
Proc. Natl. Acad. Sci. Usa V. 106 1542 2009
PubMed-ID: 19164557  |  Reference-DOI: 10.1073/PNAS.0812413106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAST/STEM CELL GROWTH FACTOR RECEPTOR
    ChainsA, B
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    Expression System Vector TypeVIRUS
    FragmentKINASE DOMAIN - KID DELETED
    GeneKIT
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSCFR, PROTO-ONCOGENE TYROSINE-PROTEIN KINASE KIT, C-KIT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB
Biological Unit 2 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1B492Ligand/IonN-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1B494Ligand/IonN-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1B492Ligand/IonN-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:603 , ALA A:621 , THR A:670 , GLU A:671 , TYR A:672 , CYS A:673 , CYS A:674 , LEU A:799 , CYS A:809BINDING SITE FOR RESIDUE B49 A9001
2AC2SOFTWAREHIS A:630 , LEU A:631 , ARG A:634 , LYS B:826 , GLY B:827BINDING SITE FOR RESIDUE SO4 A 1
3AC3SOFTWARELEU B:595 , VAL B:603 , ALA B:621 , THR B:670 , GLU B:671 , TYR B:672 , CYS B:673 , GLY B:676 , LEU B:799 , CYS B:809 , ASP B:810 , PHE B:811BINDING SITE FOR RESIDUE B49 B9001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G0F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G0F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (19, 38)

Asymmetric Unit (19, 38)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_004104E583KKIT_HUMANDisease (PBT)121913680A/BE583K
02UniProtVAR_033129F584CKIT_HUMANDisease (PBT)28933371A/BF584C
03UniProtVAR_004105F584LKIT_HUMANDisease (PBT)794726671A/BF584L
04UniProtVAR_033130G601RKIT_HUMANDisease (PBT)  ---A/BG601R
05UniProtVAR_033131L656PKIT_HUMANDisease (PBT)  ---A/BL656P
06UniProtVAR_004106G664RKIT_HUMANDisease (PBT)121913679A/BG664R
07UniProtVAR_004107R791GKIT_HUMANDisease (PBT)  ---A/BR791G
08UniProtVAR_033132R796GKIT_HUMANDisease (PBT)121913684A/BR796G
09UniProtVAR_042026R804WKIT_HUMANUnclassified145602440A/BR804W
10UniProtVAR_004108G812VKIT_HUMANDisease (PBT)  ---A/BG812V
11UniProtVAR_033133D816FKIT_HUMANUnclassified  ---A/BH816F
12UniProtVAR_033134D816HKIT_HUMANUnclassified28933969A/BH816H
13UniProtVAR_004109D816VKIT_HUMANUnclassified121913507A/BH816V
14UniProtVAR_023828D816YKIT_HUMANUnclassified121913506A/BH816Y
15UniProtVAR_033135D820GKIT_HUMANPolymorphism121913682A/BD820G
16UniProtVAR_023829N822KKIT_HUMANUnclassified121913514A/BN822K
17UniProtVAR_023830A829PKIT_HUMANUnclassified  ---A/BA829P
18UniProtVAR_033136E839KKIT_HUMANPolymorphism121913509A/BE839K
19UniProtVAR_033137T847PKIT_HUMANDisease (PBT)121913687A/BT847P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (19, 76)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_004104E583KKIT_HUMANDisease (PBT)121913680A/BE583K
02UniProtVAR_033129F584CKIT_HUMANDisease (PBT)28933371A/BF584C
03UniProtVAR_004105F584LKIT_HUMANDisease (PBT)794726671A/BF584L
04UniProtVAR_033130G601RKIT_HUMANDisease (PBT)  ---A/BG601R
05UniProtVAR_033131L656PKIT_HUMANDisease (PBT)  ---A/BL656P
06UniProtVAR_004106G664RKIT_HUMANDisease (PBT)121913679A/BG664R
07UniProtVAR_004107R791GKIT_HUMANDisease (PBT)  ---A/BR791G
08UniProtVAR_033132R796GKIT_HUMANDisease (PBT)121913684A/BR796G
09UniProtVAR_042026R804WKIT_HUMANUnclassified145602440A/BR804W
10UniProtVAR_004108G812VKIT_HUMANDisease (PBT)  ---A/BG812V
11UniProtVAR_033133D816FKIT_HUMANUnclassified  ---A/BH816F
12UniProtVAR_033134D816HKIT_HUMANUnclassified28933969A/BH816H
13UniProtVAR_004109D816VKIT_HUMANUnclassified121913507A/BH816V
14UniProtVAR_023828D816YKIT_HUMANUnclassified121913506A/BH816Y
15UniProtVAR_033135D820GKIT_HUMANPolymorphism121913682A/BD820G
16UniProtVAR_023829N822KKIT_HUMANUnclassified121913514A/BN822K
17UniProtVAR_023830A829PKIT_HUMANUnclassified  ---A/BA829P
18UniProtVAR_033136E839KKIT_HUMANPolymorphism121913509A/BE839K
19UniProtVAR_033137T847PKIT_HUMANDisease (PBT)121913687A/BT847P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (19, 38)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_004104E583KKIT_HUMANDisease (PBT)121913680A/BE583K
02UniProtVAR_033129F584CKIT_HUMANDisease (PBT)28933371A/BF584C
03UniProtVAR_004105F584LKIT_HUMANDisease (PBT)794726671A/BF584L
04UniProtVAR_033130G601RKIT_HUMANDisease (PBT)  ---A/BG601R
05UniProtVAR_033131L656PKIT_HUMANDisease (PBT)  ---A/BL656P
06UniProtVAR_004106G664RKIT_HUMANDisease (PBT)121913679A/BG664R
07UniProtVAR_004107R791GKIT_HUMANDisease (PBT)  ---A/BR791G
08UniProtVAR_033132R796GKIT_HUMANDisease (PBT)121913684A/BR796G
09UniProtVAR_042026R804WKIT_HUMANUnclassified145602440A/BR804W
10UniProtVAR_004108G812VKIT_HUMANDisease (PBT)  ---A/BG812V
11UniProtVAR_033133D816FKIT_HUMANUnclassified  ---A/BH816F
12UniProtVAR_033134D816HKIT_HUMANUnclassified28933969A/BH816H
13UniProtVAR_004109D816VKIT_HUMANUnclassified121913507A/BH816V
14UniProtVAR_023828D816YKIT_HUMANUnclassified121913506A/BH816Y
15UniProtVAR_033135D820GKIT_HUMANPolymorphism121913682A/BD820G
16UniProtVAR_023829N822KKIT_HUMANUnclassified121913514A/BN822K
17UniProtVAR_023830A829PKIT_HUMANUnclassified  ---A/BA829P
18UniProtVAR_033136E839KKIT_HUMANPolymorphism121913509A/BE839K
19UniProtVAR_033137T847PKIT_HUMANDisease (PBT)121913687A/BT847P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KIT_HUMAN595-623
 
  2A:595-623
B:595-623
2RECEPTOR_TYR_KIN_IIIPS00240 Receptor tyrosine kinase class III signature.KIT_HUMAN648-661
 
  2A:648-661
B:648-661
3PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.KIT_HUMAN788-800
 
  2A:788-800
B:788-800
Biological Unit 1 (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KIT_HUMAN595-623
 
  4A:595-623
B:595-623
2RECEPTOR_TYR_KIN_IIIPS00240 Receptor tyrosine kinase class III signature.KIT_HUMAN648-661
 
  4A:648-661
B:648-661
3PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.KIT_HUMAN788-800
 
  4A:788-800
B:788-800
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KIT_HUMAN595-623
 
  2A:595-623
B:595-623
2RECEPTOR_TYR_KIN_IIIPS00240 Receptor tyrosine kinase class III signature.KIT_HUMAN648-661
 
  2A:648-661
B:648-661
3PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.KIT_HUMAN788-800
 
  2A:788-800
B:788-800

(-) Exons   (9, 18)

Asymmetric Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002881351aENSE00001905199chr4:55524085-55524248164KIT_HUMAN1-23230--
1.2aENST000002881352aENSE00001032350chr4:55561678-55561947270KIT_HUMAN23-113910--
1.3ENST000002881353ENSE00001074448chr4:55564450-55564731282KIT_HUMAN113-207950--
1.4ENST000002881354ENSE00001121859chr4:55565796-55565932137KIT_HUMAN207-252460--
1.5ENST000002881355ENSE00001074426chr4:55569890-55570058169KIT_HUMAN253-309570--
1.6ENST000002881356ENSE00001074418chr4:55573264-55573453190KIT_HUMAN309-372640--
1.7ENST000002881357ENSE00001074452chr4:55575590-55575705116KIT_HUMAN372-411400--
1.8ENST000002881358ENSE00001074431chr4:55589750-55589864115KIT_HUMAN411-449390--
1.9bENST000002881359bENSE00001074423chr4:55592023-55592216194KIT_HUMAN449-514660--
1.10ENST0000028813510ENSE00001074410chr4:55593384-55593490107KIT_HUMAN514-549360--
1.11ENST0000028813511ENSE00001074417chr4:55593582-55593708127KIT_HUMAN550-592432A:566-592
B:564-592
27
29
1.12ENST0000028813512ENSE00001074438chr4:55593989-55594093105KIT_HUMAN592-627362A:592-627
B:592-627
36
36
1.13ENST0000028813513ENSE00001074408chr4:55594177-55594287111KIT_HUMAN627-664382A:627-664
B:627-664
38
38
1.14bENST0000028813514bENSE00001074445chr4:55595501-55595651151KIT_HUMAN664-714512A:664-689
B:664-689
26
26
1.15ENST0000028813515ENSE00001074450chr4:55597494-5559758592KIT_HUMAN714-745320--
1.16ENST0000028813516ENSE00001074441chr4:55598037-55598164128KIT_HUMAN745-787432A:764-787
B:764-787
24
24
1.17aENST0000028813517aENSE00001074435chr4:55599236-55599358123KIT_HUMAN788-828412A:788-828
B:788-828
41
41
1.18ENST0000028813518ENSE00001074442chr4:55602664-55602775112KIT_HUMAN829-866382A:829-866
B:829-866
38
38
1.19ENST0000028813519ENSE00001224349chr4:55602887-55602986100KIT_HUMAN866-899342A:866-899
B:866-899
34
34
1.20ENST0000028813520ENSE00001074415chr4:55603341-55603446106KIT_HUMAN899-934362A:899-930
B:899-930
32
32
1.21bENST0000028813521bENSE00001898693chr4:55604595-556068812287KIT_HUMAN935-976420--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:291
 aligned with KIT_HUMAN | P10721 from UniProtKB/Swiss-Prot  Length:976

    Alignment length:365
                                   575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925     
            KIT_HUMAN   566 NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISE 930
               SCOP domains d3g0fa_ A: c-KIT receptor                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -----------3g0fA01 A:577-672 Phosphorylase Kinase; domain 1                                                3g0fA02 A:673-924                                                                           Transferase(Phosphotransferase) domain 1                                                                                                                        ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........hhhhh.hhh.eeeeeeeee...eeeeeeeee.......eeeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee....eehhhhhhhh....--------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhh.eee...hhh.eee.hhh.eee...............eee..eeehhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhh..... Sec.struct. author
             SAPs(SNPs) (1) -----------------KC----------------R------------------------------------------------------P-------R------------------------------------------------------------------------------------------------------------------------------G----G-------W-------V---F---G-K------P---------K-------P----------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------L---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (3)
             SAPs(SNPs) (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (4)
                    PROSITE -----------------------------PROTEIN_KINASE_ATP           ------------------------RECEPTOR_TYR_K------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: A:566-592  ----------------------------------Exon 1.13  PDB: A:627-664             -------------------------------------------------Exon 1.15  PDB: -               ------------------------------------------Exon 1.17a  PDB: A:788-828               Exon 1.18  PDB: A:829-866             --------------------------------Exon 1.20  PDB: A:899-930        Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.12  PDB: A:592-627           ------------------------------------Exon 1.14b  PDB: A:664-689 UniProt: 664-714        ------------------------------Exon 1.16  PDB: A:764-787 UniProt: 745-787 ------------------------------------------------------------------------------Exon 1.19  PDB: A:866-899         ------------------------------- Transcript 1 (2)
                 3g0f A 566 NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSF--------------------------------------------------------------------------LDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARHIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISE 930
                                   575       585       595       605       615       625       635       645       655       665       675       685   |     -         -         -         -         -         -         -       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925     
                                                                                                                                                     689                                                                        764                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:293
 aligned with KIT_HUMAN | P10721 from UniProtKB/Swiss-Prot  Length:976

    Alignment length:367
                                   573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       
            KIT_HUMAN   564 NGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKQEDHAEAALYKNLLHSKESSCSDSTNEYMDMKPGVSYVVPTKADKRRSVRIGSYIERDVTPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISE 930
               SCOP domains d3g0fb_ B: c-KIT receptor                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------3g0fB01 B:577-672 Phosphorylase Kinase; domain 1                                                3g0fB02 B:673-924                                                                           Transferase(Phosphotransferase) domain 1                                                                                                                        ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee........hhhhh.hhh.eeeeeeeee...eeeeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee....eehhhhhhhh....--------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhh.eee...hhh.eee.hhh.eee...............eee..eeehhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) -------------------KC----------------R------------------------------------------------------P-------R------------------------------------------------------------------------------------------------------------------------------G----G-------W-------V---F---G-K------P---------K-------P----------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------L---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (3)
             SAPs(SNPs) (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (4)
                    PROSITE -------------------------------PROTEIN_KINASE_ATP           ------------------------RECEPTOR_TYR_K------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: B:564-592    ----------------------------------Exon 1.13  PDB: B:627-664             -------------------------------------------------Exon 1.15  PDB: -               ------------------------------------------Exon 1.17a  PDB: B:788-828               Exon 1.18  PDB: B:829-866             --------------------------------Exon 1.20  PDB: B:899-930        Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.12  PDB: B:592-627           ------------------------------------Exon 1.14b  PDB: B:664-689 UniProt: 664-714        ------------------------------Exon 1.16  PDB: B:764-787 UniProt: 745-787 ------------------------------------------------------------------------------Exon 1.19  PDB: B:866-899         ------------------------------- Transcript 1 (2)
                 3g0f B 564 NGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSF--------------------------------------------------------------------------LDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARHIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISE 930
                                   573       583       593       603       613       623       633       643       653       663       673       683     |   -         -         -         -         -         -         -         -|      773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       
                                                                                                                                                       689                                                                        764                                                                                                                                                                      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G0F)

(-) Gene Ontology  (104, 104)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KIT_HUMAN | P10721)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0019955    cytokine binding    Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0046934    phosphatidylinositol-4,5-bisphosphate 3-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0004716    signal transducer, downstream of receptor, with protein tyrosine kinase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
    GO:0005020    stem cell factor receptor activity    Combining with stem cell factor (SCF) and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate. Stem cell factor is a cytokine that stimulates mast cell growth and differentiation.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
biological process
    GO:0038093    Fc receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of an immunoglobulin to an Fc receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0038109    Kit signaling pathway    A series of molecular signals that starts with the binding of stem cell factor to the tyrosine kinase receptor KIT on the surface of a cell, and ends with regulation of a downstream cellular process, e.g. transcription. Stem cell factor (KIT ligand) binding to the receptor Kit mediates receptor dimerization, activation of its intrinsic tyrosine kinase activity and autophosphorylation. The activated receptor then phosphorylates various substrates, thereby activating distinct signaling cascades within the cell that trigger a change in state or activity of the cell.
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0097067    cellular response to thyroid hormone stimulus    A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0002371    dendritic cell cytokine production    Any process that contributes to cytokine production by a dendritic cell.
    GO:0050910    detection of mechanical stimulus involved in sensory perception of sound    The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal.
    GO:0048066    developmental pigmentation    The developmental process that results in the deposition of coloring matter in an organism, tissue or cell.
    GO:0048565    digestive tract development    The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
    GO:0035234    ectopic germ cell programmed cell death    Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo.
    GO:0035162    embryonic hemopoiesis    The stages of blood cell formation that take place within the embryo.
    GO:0050673    epithelial cell proliferation    The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances.
    GO:0030218    erythrocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
    GO:0038162    erythropoietin-mediated signaling pathway    A series of molecular signals initiated by the binding of erythropoietin (EPO) to the erythropoietin receptor (EPO-R) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0008354    germ cell migration    The orderly movement of a cell specialized to produce haploid gametes through the embryo from its site of production to the place where the gonads will form.
    GO:0006687    glycosphingolipid metabolic process    The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.
    GO:0035701    hematopoietic stem cell migration    The orderly movement of a hematopoietic stem cell from one site to another. A hematopoietic stem cell is a cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    GO:0002327    immature B cell differentiation    The process in which a precursor cell type acquires the specialized features of an immature B cell.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0002320    lymphoid progenitor cell differentiation    The process in which a precursor cell type acquires the specialized features of a lymphoid progenitor cell. Lymphoid progenitor cells include progenitor cells for any of the lymphoid lineages.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0002551    mast cell chemotaxis    The movement of a mast cell in response to an external stimulus.
    GO:0032762    mast cell cytokine production    Any process that contributes to cytokine production by a mast cell.
    GO:0043303    mast cell degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine, serotonin, and neutral proteases by a mast cell.
    GO:0060374    mast cell differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation.
    GO:0070662    mast cell proliferation    The expansion of a mast cell population by cell division.
    GO:0035855    megakaryocyte development    The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow.
    GO:0097326    melanocyte adhesion    The attachment of a melanocyte to another cell via adhesion molecules.
    GO:0030318    melanocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a melanocyte.
    GO:0097324    melanocyte migration    The orderly movement of melanocytes from one site to another, often during the development of a multicellular organism. A melanocyte is a pigment cell derived from the neural crest. It contains melanin-filled pigment granules, which give a brown to black appearance.
    GO:0002573    myeloid leukocyte differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage.
    GO:0002318    myeloid progenitor cell differentiation    The process in which a precursor cell type acquires the specialized features of a myeloid progenitor cell. Myeloid progenitor cells include progenitor cells for any of the myeloid lineages.
    GO:0043069    negative regulation of programmed cell death    Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
    GO:0001541    ovarian follicle development    The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0046854    phosphatidylinositol phosphorylation    The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043473    pigmentation    The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0046427    positive regulation of JAK-STAT cascade    Any process that activates or increases the frequency, rate or extent of the JAK-STAT signaling pathway activity.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0045747    positive regulation of Notch signaling pathway    Any process that activates or increases the frequency, rate or extent of the Notch signaling pathway.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0048170    positive regulation of long-term neuronal synaptic plasticity    A process that increases long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
    GO:0043552    positive regulation of phosphatidylinositol 3-kinase activity    Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0010863    positive regulation of phospholipase C activity    Any process that increases the rate of phospholipase C activity.
    GO:0031274    positive regulation of pseudopodium assembly    Any process that activates or increases the frequency, rate or extent of the assembly of pseudopodia.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:1905065    positive regulation of vascular smooth muscle cell differentiation    Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell differentiation.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0048070    regulation of developmental pigmentation    Any process that modulates the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism.
    GO:0014066    regulation of phosphatidylinositol 3-kinase signaling    Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0009314    response to radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0048103    somatic stem cell division    The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line.
    GO:0035019    somatic stem cell population maintenance    Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
    GO:0007286    spermatid development    The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0048863    stem cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:0019827    stem cell population maintenance    The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0008542    visual learning    Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0042629    mast cell granule    Coarse, bluish-black staining cytoplasmic granules, bounded by a plasma membrane and found in mast cells and basophils. Contents include histamine, heparin, chondroitin sulfates, chymase and tryptase.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KIT_HUMAN | P107211pkg 1qzj 1qzk 1r01 1t45 1t46 2e9w 2ec8 2iuh 2vif 3g0e 4hvs 4k94 4k9e 4pgz 4u0i

(-) Related Entries Specified in the PDB File

3g0e KIT KINASE DOMAIN IN COMPLEX WITH SUNITINIB