Structure of PDB 5m6z Chain A Binding Site BS01

Receptor Information
>5m6z Chain A (length=416) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCL
DNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVG
PEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFR
ASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLIKKELNYFAKAL
ESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNM
EIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQA
TVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARG
TKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLE
LLEGKVLPGVDALSNI
Ligand information
Ligand IDADP
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-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(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 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5m6z Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5m6z The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		A214 K219 G238 L256 G312 L313 G340 V341 E343 D374
Binding residue
(residue number reindexed from 1)		A214 K219 G238 L256 G312 L313 G340 V341 E343 D374
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R38 K215 G373 G396
Catalytic site (residue number reindexed from 1) R38 K215 G373 G396
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:5m6z, PDBe:5m6z, PDBj:5m6z
PDBsum5m6z
PubMed29995887
UniProtP00558|PGK1_HUMAN Phosphoglycerate kinase 1 (Gene Name=PGK1)

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