Structure of PDB 5x1w Chain D Binding Site BS01

Receptor Information
>5x1w Chain D (length=511) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKE
MIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALD
TKGPEIRTGAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEV
GSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPA
VSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISK
IENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRA
GKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDY
PLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEAS
FKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIF
PVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSG
FTNTMRVVPVP
Ligand information
Ligand ID7Y0
InChIInChI=1S/C28H22Cl4N4O4/c1-35-13-15(25(37)17-5-3-7-19(29)23(17)31)11-21(35)27(39)33-9-10-34-28(40)22-12-16(14-36(22)2)26(38)18-6-4-8-20(30)24(18)32/h3-8,11-14H,9-10H2,1-2H3,(H,33,39)(H,34,40)
InChIKeyJORSMLRHZLRFBN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1cc(cc1C(=O)NCCNC(=O)c2cc(cn2C)C(=O)c3cccc(Cl)c3Cl)C(=O)c4cccc(Cl)c4Cl
OpenEye OEToolkits 2.0.6Cn1cc(cc1C(=O)NCCNC(=O)c2cc(cn2C)C(=O)c3cccc(c3Cl)Cl)C(=O)c4cccc(c4Cl)Cl
FormulaC28 H22 Cl4 N4 O4
Name4-[2,3-bis(chloranyl)phenyl]carbonyl-N-[2-[[4-[2,3-bis(chloranyl)phenyl]carbonyl-1-methyl-pyrrol-2-yl]carbonylamino]ethyl]-1-methyl-pyrrole-2-carboxamide
ChEMBLCHEMBL4070458
DrugBank
ZINC
PDB chain5x1w Chain C Residue 601 [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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PDB5x1w Discovery and structure-guided fragment-linking of 4-(2,3-dichlorobenzoyl)-1-methyl-pyrrole-2-carboxamide as a pyruvate kinase M2 activator
Resolution3.0 Å
Binding residue
(original residue number in PDB)		F26 L353 Y390 Q393 L394 E397
Binding residue
(residue number reindexed from 1)		F13 L333 Y370 Q373 L374 E377
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R73 R120 K270 T328
Catalytic site (residue number reindexed from 1) R60 R107 K250 T308
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:5x1w, PDBe:5x1w, PDBj:5x1w
PDBsum5x1w
PubMed28511909
UniProtP14618|KPYM_HUMAN Pyruvate kinase PKM (Gene Name=PKM)

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