Structure of PDB 4jpg Chain D Binding Site BS02

Receptor Information
>4jpg Chain D (length=512) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKE
MIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALD
TKGPEIRTGLITAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKV
VEVGSKIYVDDGLISLQVKQKDFLVTEVENGGSLGSKKGVNLPGAAVDLP
AVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIIS
KIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNR
AGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGD
YPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEA
SFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGI
FPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGS
GFTNTMRVVPVP
Ligand information
Ligand ID1OX
InChIInChI=1S/C16H12N4O/c21-16-9-12(18-15-7-3-4-8-20(15)16)10-19-11-17-13-5-1-2-6-14(13)19/h1-9,11H,10H2
InChIKeyBCWFSHAZZLFCIE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C2C=C(N=C1C=CC=CN12)Cn3c4ccccc4nc3
OpenEye OEToolkits 1.7.6c1ccc2c(c1)ncn2CC3=CC(=O)N4C=CC=CC4=N3
CACTVS 3.370O=C1C=C(Cn2cnc3ccccc23)N=C4C=CC=CN14
FormulaC16 H12 N4 O
Name2-(1H-benzimidazol-1-ylmethyl)-4H-pyrido[1,2-a]pyrimidin-4-one
ChEMBLCHEMBL2386916
DrugBank
ZINC
PDB chain4jpg Chain D Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4jpg Discovery of 2-((1H-benzo[d]imidazol-1-yl)methyl)-4H-pyrido[1,2-a]pyrimidin-4-ones as novel PKM2 activators.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		F26 K311 Q393
Binding residue
(residue number reindexed from 1)		F13 K292 Q374
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R73 R120 K270 T328
Catalytic site (residue number reindexed from 1) R60 R107 K251 T309
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine kinase.
2.7.11.1: non-specific serine/threonine protein kinase.
2.7.1.40: pyruvate kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003824 catalytic activity
GO:0004713 protein tyrosine kinase activity
GO:0004743 pyruvate kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0023026 MHC class II protein complex binding
GO:0030955 potassium ion binding
GO:0045296 cadherin binding
GO:0046872 metal ion binding
Biological Process
GO:0006096 glycolytic process
GO:0006417 regulation of translation
GO:0012501 programmed cell death
GO:0016310 phosphorylation
GO:0032869 cellular response to insulin stimulus
GO:0061621 canonical glycolysis
GO:1903672 positive regulation of sprouting angiogenesis
GO:2000767 positive regulation of cytoplasmic translation
Cellular Component
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005791 rough endoplasmic reticulum
GO:0005829 cytosol
GO:0005929 cilium
GO:0031982 vesicle
GO:0034774 secretory granule lumen
GO:0062023 collagen-containing extracellular matrix
GO:0070062 extracellular exosome
GO:1903561 extracellular vesicle
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4jpg, PDBe:4jpg, PDBj:4jpg
PDBsum4jpg
PubMed23622982
UniProtP14618|KPYM_HUMAN Pyruvate kinase PKM (Gene Name=PKM)

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