Structure of PDB 2x13 Chain A Binding Site BS01

Receptor Information
>2x13 Chain A (length=408) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLD
NGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGP
EVEKACANPAAGSVILLENLRFHVEEEGKGKKAEPAKIEAFRASLSKLGD
VYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFL
AILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFD
EEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPA
GWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEV
VKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLP
GVDALSNI
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 chain2x13 Chain A Residue 1420 [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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PDB2x13 The Structure of Human Phosphoglycerate Kinase in its Fully Active Conformation with Ground State Analogues
Resolution1.74 Å
Binding residue
(original residue number in PDB)		G214 A215 K220 G238 G239 N337 G341 V342 E344 G373 D375 T376
Binding residue
(residue number reindexed from 1)		G205 A206 K211 G229 G230 N328 G332 V333 E335 G364 D366 T367
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R39 K216 G374 G397
Catalytic site (residue number reindexed from 1) R37 K207 G365 G388
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2x13, PDBe:2x13, PDBj:2x13
PDBsum2x13
PubMed39106858
UniProtP00558|PGK1_HUMAN Phosphoglycerate kinase 1 (Gene Name=PGK1)

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