Structure of PDB 2y3i Chain A Binding Site BS01

Receptor Information
>2y3i Chain A (length=414) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLD
NGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGP
EVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRA
SLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALE
SPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNME
IGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQAT
VASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGT
KALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLEL
LEGKVLPGVDALSN
Ligand information
Ligand IDLA8
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m0/s1
InChIKeyXTWYTFMLZFPYCI-DEGSGYPDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1c1nc(c2c(n1)n(cn2)[C@@H]3[C@H]([C@H]([C@@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.352Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.352Nc1ncnc2n(cnc12)[C@H]3O[C@@H](CO[P](O)(=O)O[P](O)(O)=O)[C@H](O)[C@@H]3O
OpenEye OEToolkits 1.6.1c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameL-ADENOSINE-5'-DIPHOSPHATE;
L-ADP
ChEMBL
DrugBank
ZINCZINC000031977053
PDB chain2y3i Chain A Residue 1418 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2y3i Interaction of Human 3-Phosphoglycerate Kinase with its Two Substrates: Is Substrate Antagonism a Kinetic Advantage?
Resolution2.9 Å
Binding residue
(original residue number in PDB)		G213 A214 F291 N336 G340 V341 E343 G372 G373 D374 T375
Binding residue
(residue number reindexed from 1)		G212 A213 F290 N335 G339 V340 E342 G371 G372 D373 T374
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R38 K215 G373 G396
Catalytic site (residue number reindexed from 1) R37 K214 G372 G395
Enzyme Commision number 2.7.2.3: phosphoglycerate kinase.
Gene Ontology
Molecular Function
GO:0004618 phosphoglycerate kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0043531 ADP binding
GO:0047134 protein-disulfide reductase (NAD(P)H) activity
Biological Process
GO:0006094 gluconeogenesis
GO:0006096 glycolytic process
GO:0016310 phosphorylation
GO:0016525 negative regulation of angiogenesis
GO:0030855 epithelial cell differentiation
GO:0031639 plasminogen activation
GO:0061621 canonical glycolysis
GO:0071456 cellular response to hypoxia
Cellular Component
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0045121 membrane raft
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2y3i, PDBe:2y3i, PDBj:2y3i
PDBsum2y3i
PubMed21549713
UniProtP00558|PGK1_HUMAN Phosphoglycerate kinase 1 (Gene Name=PGK1)

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