Structure of PDB 8pqd Chain A Binding Site BS01

Receptor Information
>8pqd Chain A (length=297) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAQGLIKSD
AAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGP
TLVITEYCCYGDLLNFLRRKRDEFVPKDFLTLEHLLSFSYQVAKGMAFLA
SKNCIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVK
WMAPESIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIK
EGFRMSSPEYAPAEMYDIMKTCWDADPDKRPTFKQIVQDIEKQISES
Ligand information
Ligand ID9VV
InChIInChI=1S/C28H29FN10O/c1-19(40)35-28(2,22-4-6-24(29)7-5-22)23-14-30-27(31-15-23)38-10-8-37(9-11-38)26-25-12-20(17-39(25)34-18-32-26)21-13-33-36(3)16-21/h4-7,12-18H,8-11H2,1-3H3,(H,35,40)/t28-/m0/s1
InChIKeyJWBYZGLZBJQWBU-NDEPHWFRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(=O)N[C@@](C)(c1ccc(cc1)F)c2cnc(nc2)N3CCN(CC3)c4c5cc(cn5ncn4)c6cnn(c6)C
CACTVS 3.385Cn1cc(cn1)c2cn3ncnc(N4CCN(CC4)c5ncc(cn5)[C](C)(NC(C)=O)c6ccc(F)cc6)c3c2
CACTVS 3.385Cn1cc(cn1)c2cn3ncnc(N4CCN(CC4)c5ncc(cn5)[C@@](C)(NC(C)=O)c6ccc(F)cc6)c3c2
OpenEye OEToolkits 2.0.7CC(=O)NC(C)(c1ccc(cc1)F)c2cnc(nc2)N3CCN(CC3)c4c5cc(cn5ncn4)c6cnn(c6)C
FormulaC28 H29 F N10 O
Name~{N}-[(1~{S})-1-(4-fluorophenyl)-1-[2-[4-[6-(1-methylpyrazol-4-yl)pyrrolo[2,1-f][1,2,4]triazin-4-yl]piperazin-1-yl]pyrimidin-5-yl]ethyl]ethanamide
ChEMBL
DrugBank
ZINC
PDB chain8pqd Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8pqd Avapritinib-based SAR studies reveal a binding pocket in KIT and PDGFRA
Resolution1.5 Å
Binding residue
(original residue number in PDB)		L595 G596 G598 G601 K602 V603 K623 M624 L625 Y672 C673 G676 L799 D810
Binding residue
(residue number reindexed from 1)		L30 G31 G33 G36 K37 V38 K58 M59 L60 Y107 C108 G111 L165 D176
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0004714 transmembrane receptor protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway

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Molecular Function
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Biological Process
External links
PDB RCSB:8pqd, PDBe:8pqd, PDBj:8pqd
PDBsum8pqd
PubMed38167404
UniProtP10721|KIT_HUMAN Mast/stem cell growth factor receptor Kit (Gene Name=KIT)

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