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(-) Description

Title :  CRYSTAL STRUCTURE OF KIT IN COMPLEX WITH PONATINIB
 
Authors :  T. Zhou, X. Zhu, D. C. Dalgarno
Date :  11 Jul 14  (Deposition) - 08 Oct 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Kit, Receptor Tyrosine Kinase, Inhibitor, Ponatinib, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Garner, J. M. Gozgit, R. Anjum, S. Vodala, A. Schrock, T. Zhou, C. Serrano, G. Eilers, M. Zhu, J. Ketzer, S. Wardwell, Y. Ning, Y. Song, A. Kohlmann, F. Wang, T. Clackson, M. C. Heinrich, J. A. Fletcher, S. Bauer, V. M. Rivera
Ponatinib Inhibits Polyclonal Drug-Resistant Kit Oncoproteins And Shows Therapeutic Potential In Heavily Pretreated Gastrointestinal Stromal Tumor (Gist) Patients.
Clin. Cancer Res. V. 20 5745 2014
PubMed-ID: 25239608  |  Reference-DOI: 10.1158/1078-0432.CCR-14-1397

(-) Compounds

Molecule 1 - MAST/STEM CELL GROWTH FACTOR RECEPTOR KIT,MAST/STEM CELL GROWTH FACTOR RECEPTOR KIT
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 563-693 AND 754-935 LINKED VIA LINKER (THR SER)
    Gene: KIT, SCFR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SCFR,PIEBALD TRAIT PROTEIN,PBT,PROTO-ONCOGENE C-KIT, TYROSINE-PROTEIN KINASE KIT,P145 C-KIT,V-KIT HARDY-ZUCKERMAN 4 FELINE SARCOMA VIRAL ONCOGENE HOMOLOG,SCFR,PIEBALD TRAIT PROTEIN,PBT,PROTO- ONCOGENE C-KIT,TYROSINE-PROTEIN KINASE KIT,P145 C-KIT,V-KIT HARDY- ZUCKERMAN 4 FELINE SARCOMA VIRAL ONCOGENE HOMOLOG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
10LI1Ligand/Ion3-(IMIDAZO[1,2-B]PYRIDAZIN-3-YLETHYNYL)-4-METHYL-N-{4-[(4-METHYLPIPERAZIN-1-YL)METHYL]-3-(TRIFLUOROMETHYL)PHENYL}BENZAMIDE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:595 , ALA A:621 , VAL A:622 , LYS A:623 , GLU A:640 , LEU A:647 , ILE A:653 , VAL A:654 , THR A:670 , GLU A:671 , TYR A:672 , CYS A:673 , CYS A:788 , ILE A:789 , HIS A:790 , ARG A:791 , LEU A:799 , ILE A:808 , CYS A:809 , ASP A:810 , PHE A:811 , HOH A:1204binding site for residue 0LI A 1001
2AC2SOFTWARELYS A:642 , TYR A:675 , HIS A:802 , GLY A:803 , LYS A:913 , HOH A:1138 , HOH A:1188binding site for residue PO4 A 1002
3AC3SOFTWARETHR A:619 , TYR A:672 , CYS A:674 , HIS A:802 , HOH A:1105 , HOH A:1132 , HOH A:1193binding site for residue PO4 A 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U0I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U0I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U0I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U0I)

(-) Exons   (0, 0)

(no "Exon" information available for 4U0I)

(-) Sequences/Alignments

Asymmetric/Biological 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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..hhhhh.hhh.eeeeeeeee...eeeeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee..hhhhh........ee....eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0i A 565 GNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSLALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTN 933
                                   574       584       594       604       617       627       637       647       657       667       677       687    || 766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       
                                                                         612|                                                                         692|                                                                                                                                                                           
                                                                          616                                                                          762
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  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  (0, 0)

(no "SCOP Domain" information available for 4U0I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U0I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U0I)

(-) Gene Ontology  (104, 104)

Asymmetric/Biological Unit(hide GO term definitions)

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  4u0i
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  KIT_HUMAN | P10721
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  2.7.10.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        KIT_HUMAN | P10721: 1pkg 1qzj 1qzk 1r01 1t45 1t46 2e9w 2ec8 2iuh 2vif 3g0e 3g0f 4hvs 4k94 4k9e 4pgz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4U0I)