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(-) Description

Title :  PI3KDELTA IN COMPLEX WITH THE INHIBITOR GS-643624
 
Authors :  J. R. Somoza, A. Villasenor
Date :  04 Sep 16  (Deposition) - 28 Dec 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pi3Kdelta Phosphatidylinositol-3-Kinase Pi(3)K, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Patel, J. Chandrasekhar, J. Evarts, K. Forseth, A. Haran, C. Ip, A. Kashishian, M. Kim, D. Koditek, S. Koppenol, L. Lad, E. -I. Lepist, M. E. Mcgrath, S. Perreault, K. Puri, A. Villasenor, J. R. Somoza, B. Steiner, J. Therrien, J. Trilberg, G. Phillips
The Discovery Of Gs-9901: A Potent, Selective And Metabolically Stable Inhibitor Of Pi3Kd
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM
    Chains: A, B
    EC Number: 2.7.1.153
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 106-1043
    Gene: PIK3CD
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PTDINS-3-KINASE SUBUNIT DELTA,PHOSPHATIDYLINOSITOL 4,5- BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT DELTA,P110DELTA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
176C2Ligand/Ion2,4-BIS(AZANYL)-6-[[(1~{S})-1-[5-CHLORANYL-3-(5-FLUORANYL-4-METHYL-PYRIDIN-3-YL)-4-OXIDANYLIDENE-QUINAZOLIN-2-YL]ETHYL]AMINO]PYRIMIDINE-5-CARBONITRILE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
176C1Ligand/Ion2,4-BIS(AZANYL)-6-[[(1~{S})-1-[5-CHLORANYL-3-(5-FLUORANYL-4-METHYL-PYRIDIN-3-YL)-4-OXIDANYLIDENE-QUINAZOLIN-2-YL]ETHYL]AMINO]PYRIMIDINE-5-CARBONITRILE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
176C1Ligand/Ion2,4-BIS(AZANYL)-6-[[(1~{S})-1-[5-CHLORANYL-3-(5-FLUORANYL-4-METHYL-PYRIDIN-3-YL)-4-OXIDANYLIDENE-QUINAZOLIN-2-YL]ETHYL]AMINO]PYRIMIDINE-5-CARBONITRILE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:750 , PHE A:751 , MET A:752 , PRO A:758 , TRP A:760 , ILE A:777 , TYR A:813 , ILE A:825 , GLU A:826 , VAL A:828 , SER A:831 , ASP A:832 , THR A:833 , MET A:900 , ILE A:910 , HOH A:1229binding site for residue 76C A 1101
2AC2SOFTWARETHR B:750 , PHE B:751 , MET B:752 , PRO B:758 , TRP B:760 , ILE B:777 , TYR B:813 , ILE B:825 , GLU B:826 , VAL B:828 , SER B:831 , ASP B:832 , THR B:833 , MET B:900 , ILE B:910 , HOH B:1222binding site for residue 76C B 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T7F)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:367 -Glu A:368
2Thr A:434 -Gly A:435
3Ser B:367 -Glu B:368
4Thr B:434 -Gly B:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T7F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T7F)

(-) Exons   (0, 0)

(no "Exon" information available for 5T7F)

(-) 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:819
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.......eeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhh..hhh.eeeee.....ee....hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhh.........eeeeeeeee......eeeeeeeee.........ee...ee........eeeeeeee.hhh....eeeeeeeee..eeeeeeeee...........eeeee.ee....................eeeee..........hhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eee..eeeeee.ee.hhhhee.......eeeeee...hhhhhh.eeeeee...hhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....eeehhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee...............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5t7f A  109 VKKLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQLGWVEWLQYSFPLQLEPRALLVNVKFEGSEESFTFQVSTKDMPLALMACALRKKATVFRQQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNLWSLEQPFSIELIEGRKVNAMKLVVQAGLFHGNEMLCKTVSSSEVNVCSEPVWKQRLEFDISVCDLPRMARLCFALYAVVDCPIAWANLMLFDYKDQLKTGERCLYMWPSVLLNPAGTVRGNPNTESAAALVIYLPEVAPVYFPALEKILELLREILERELYEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLHSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNRVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRES 1026
                                   118       128       138       148       158       168    || 192       202       212       222       236       246       256       266       276       286    || 320       330    || 343       353       363       373       383       393    || 419       429       439     ||455       465       475   ||  487      |513   ||  527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917||     937       947       957       967       977       987       997      1007      1017         
                                                                                          173|                                       230|                                                     291|                335|                                                        398|                           445|                        479|         494|   517|                                                                                                                                                                                                                                                                                                                                                                                                         918|                                                                                                 
                                                                                           188                                        235                                                      316                 339                                                         415                            452                         482          511    522                                                                                                                                                                                                                                                                                                                                                                                                          929                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:816
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.......eeeeeeee......eeeeee...hhhhhhhhhhhhhhhhh..hhh.eeeee.....ee....hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhh........eeeeee........eeeeeeeeee..ee.........ee..........eeeeee.hhh....eeeeeeeee..eeeeeeeee...........eee...ee......................eee..........hhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eee..eeeeee.ee.hhhhee.......eeeeee..........eeeeee...hhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....eeehhhhh...........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........eeee....eee...............hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5t7f B  109 VKKLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQLGWVEWLQYSFPLQLEPRALLVNVKFEGSEESFTFQVSTKDMPLALMACALRKKATVFRQQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNLWSLEQPFSIELIEGRKVNMKLVVQAGLFHGNEMLCKTVSSSEVNVCSEPVWKQRLEFDISVCDLPRMARLCFALYAVVDCPIAWANLMLFDYKDQLKTGERCLYMWPSVLLNPAGTVRGNPNTESAAALVIYLPEVAPVYFPALEKILELGEQLQLREILEYEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLHSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNRVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEA 1022
                                   118       128       138       148       158       168    || 192       202       212       222       236       246       256       266       276       286    || 320       330   ||  344       354       364       374       384       394   ||  420       430       440    || 456       466       476  ||   488      |509      |526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916 ||    936       946       956       966       976       986       996      1006      1016      
                                                                                          173|                                       230|                                                     291|               334|                                                        398|                           445|                        479|          495|      516|                                                                                                                                                                                                                                                                                                                                                                                                       918|                                                                                             
                                                                                           188                                        235                                                      316                339                                                         415                            452                         482           507       524                                                                                                                                                                                                                                                                                                                                                                                                        929
   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  (0, 0)

(no "SCOP Domain" information available for 5T7F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T7F)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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  PK3CD_MOUSE | O35904
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  2.7.1.153
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 Related Entries

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

UniProtKB/Swiss-Prot
        PK3CD_MOUSE | O35904: 2wxf 2wxg 2wxh 2wxi 2wxj 2wxk 2wxl 2wxm 2wxn 2wxo 2wxp 2wxq 2wxr 2x38 4ajw 4v0i 4xe0 5ae8 5ae9 5i4u 5i6u 5is5 5l72 5ncy 5ncz 5t27 5t28 5t2b 5t2d 5t2g 5t2i 5t2l 5t2m 5t8i

(-) Related Entries Specified in the PDB File

5t8i