Structure of PDB 3me3 Chain B Binding Site BS01

Receptor Information
>3me3 Chain B (length=498) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKE
MIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALD
TKGPEIRTGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDD
GLISLQVDFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGV
EQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEI
LEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLES
MIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAR
EAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTK
SGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWA
EDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP
Ligand information
Ligand ID3SZ
InChIInChI=1S/C19H23N3O6S2/c20-15-3-1-4-16(13-15)29(23,24)21-7-2-8-22(10-9-21)30(25,26)17-5-6-18-19(14-17)28-12-11-27-18/h1,3-6,13-14H,2,7-12,20H2
InChIKeyGMHIOMMKSMSRLY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc(cc(c1)S(=O)(=O)N2CCCN(CC2)S(=O)(=O)c3ccc4c(c3)OCCO4)N
OpenEye OEToolkits 1.7.0c1cc(cc(c1)S(=O)(=O)[N@]2CCC[N@](CC2)S(=O)(=O)c3ccc4c(c3)OCCO4)N
ACDLabs 12.01O=S(=O)(c1cc(N)ccc1)N2CCCN(CC2)S(=O)(=O)c3ccc4OCCOc4c3
CACTVS 3.370Nc1cccc(c1)[S](=O)(=O)N2CCCN(CC2)[S](=O)(=O)c3ccc4OCCOc4c3
FormulaC19 H23 N3 O6 S2
Name3-{[4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)-1,4-diazepan-1-yl]sulfonyl}aniline
ChEMBLCHEMBL1089334
DrugBank
ZINCZINC000036382543
PDB chain3me3 Chain A Residue 540 [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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PDB3me3 Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		F26 L27 Y390 Q393 L394
Binding residue
(residue number reindexed from 1)		F13 L14 Y357 Q360 L361
Annotation score1
Binding affinityBindingDB: EC50=38nM
Enzymatic activity
Catalytic site (original residue number in PDB) R73 R120 K270 T328
Catalytic site (residue number reindexed from 1) R60 R107 K237 T295
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:3me3, PDBe:3me3, PDBj:3me3
PDBsum3me3
PubMed22922757
UniProtP14618|KPYM_HUMAN Pyruvate kinase PKM (Gene Name=PKM)

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