Structure of PDB 3gr4 Chain D Binding Site BS01

Receptor Information
>3gr4 Chain D (length=509) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKE
MIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALD
TKGPEIRTGLIVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEV
GSKIYVDDGLISLQVKQKDFLVTEVENGGSLGSKKGVNLPGAAVDLPAVS
EKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIE
NHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGK
PVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPL
EAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFK
CCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPV
LCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFT
NTMRVVPVP
Ligand information
Ligand IDDYY
InChIInChI=1S/C18H18F2N2O6S2/c19-14-2-1-3-15(20)18(14)30(25,26)22-8-6-21(7-9-22)29(23,24)13-4-5-16-17(12-13)28-11-10-27-16/h1-5,12H,6-11H2
InChIKeySHWNKRPMUBFWKE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c(c(c1)F)S(=O)(=O)N2CCN(CC2)S(=O)(=O)c3ccc4c(c3)OCCO4)F
ACDLabs 10.04Fc1cccc(F)c1S(=O)(=O)N2CCN(CC2)S(=O)(=O)c3ccc4OCCOc4c3
CACTVS 3.341Fc1cccc(F)c1[S](=O)(=O)N2CCN(CC2)[S](=O)(=O)c3ccc4OCCOc4c3
FormulaC18 H18 F2 N2 O6 S2
Name1-[(2,6-difluorophenyl)sulfonyl]-4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)piperazine
ChEMBLCHEMBL1090777
DrugBankDB07692
ZINC
PDB chain3gr4 Chain D Residue 550 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gr4 Activator-Bound Structures of Human Pyruvate Kinase M2
Resolution1.6 Å
Binding residue
(original residue number in PDB)		F26 N318 D354 Y390 Q393 L394 E397
Binding residue
(residue number reindexed from 1)		F13 N296 D332 Y368 Q371 L372 E375
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R73 R120 K270 T328
Catalytic site (residue number reindexed from 1) R60 R107 K248 T306
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:3gr4, PDBe:3gr4, PDBj:3gr4
PDBsum3gr4
PubMed
UniProtP14618|KPYM_HUMAN Pyruvate kinase PKM (Gene Name=PKM)

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