Structure of PDB 5y2i Chain B Binding Site BS01

Receptor Information
>5y2i Chain B (length=233) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AYKLVLIRHGESAWNLENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEF
DICFTSVQKRAIRTLWTVLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAE
TAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPS
CESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSE
EAIMELNLPTGIPIVYELDKNLKPIKPMQFLGD
Ligand information
Ligand ID8KX
InChIInChI=1S/C21H12F3NO6S/c22-21(23,24)10-5-7-11(8-6-10)25-32(30,31)15-9-14-16(20(29)19(15)28)18(27)13-4-2-1-3-12(13)17(14)26/h1-9,25,28-29H
InChIKeyXKVNBCMGEUDKNP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2c(c1)C(=O)c3cc(c(c(c3C2=O)O)O)S(=O)(=O)Nc4ccc(cc4)C(F)(F)F
CACTVS 3.385Oc1c(O)c(cc2C(=O)c3ccccc3C(=O)c12)[S](=O)(=O)Nc4ccc(cc4)C(F)(F)F
FormulaC21 H12 F3 N O6 S
Name3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)-~{N}-[4-(trifluoromethyl)phenyl]anthracene-2-sulfonamide
ChEMBLCHEMBL3335789
DrugBank
ZINCZINC000072194202
PDB chain5y2i Chain B Residue 301 [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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PDB5y2i Phosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor PGMI-004A
Resolution1.917 Å
Binding residue
(original residue number in PDB)		E19 N20 F22 R90 L95 W115 R116 P123
Binding residue
(residue number reindexed from 1)		E17 N18 F20 R88 L93 W113 R114 P121
Annotation score1
Binding affinityBindingDB: IC50=13100nM,Ki=3910nM
Enzymatic activity
Catalytic site (original residue number in PDB) H11 R62 E89 H186
Catalytic site (residue number reindexed from 1) H9 R60 E87 H184
Enzyme Commision number 5.4.2.11: phosphoglycerate mutase (2,3-diphosphoglycerate-dependent).
5.4.2.4: bisphosphoglycerate mutase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004082 bisphosphoglycerate mutase activity
GO:0004619 phosphoglycerate mutase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016853 isomerase activity
GO:0016868 intramolecular phosphotransferase activity
GO:0019901 protein kinase binding
GO:0046538 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity
Biological Process
GO:0006094 gluconeogenesis
GO:0006096 glycolytic process
GO:0061621 canonical glycolysis
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
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:5y2i, PDBe:5y2i, PDBj:5y2i
PDBsum5y2i
PubMed
UniProtP18669|PGAM1_HUMAN Phosphoglycerate mutase 1 (Gene Name=PGAM1)

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