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BioLiP

Structure of PDB 5np8 Chain A Binding Site BS01

Receptor Information
>5np8 Chain A (length=404) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNG
AKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEV
EKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASL
SKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESP
ERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIG
TSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVA
SGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKA
LMDEVVKATSRGCITIIGKWNTEDKVSHVSTGGGASLELLEGKVLPGVDA
LSNI
Ligand information
Ligand ID93T
InChIInChI=1S/C17H16BrN3O2/c1-10-14(7-8-17(22)23)11(2)21-16(19-10)9-15(20-21)12-3-5-13(18)6-4-12/h3-6,9H,7-8H2,1-2H3,(H,22,23)
InChIKeySJELVUFWTXHLTJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1nc2cc(nn2c(C)c1CCC(O)=O)c3ccc(Br)cc3
OpenEye OEToolkits 2.0.6Cc1c(c(n2c(n1)cc(n2)c3ccc(cc3)Br)C)CCC(=O)O
FormulaC17 H16 Br N3 O2
Name3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain5np8 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5np8 A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G238 G239 L257 F292 L314 V342
Binding residue
(residue number reindexed from 1)		G234 G235 L253 F288 L310 V338
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R39 K216 G397
Catalytic site (residue number reindexed from 1) R35 K212 G384
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
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Cellular Component
External links
PDB RCSB:5np8, PDBe:5np8, PDBj:5np8
PDBsum5np8
PubMed31401411
UniProtP00558|PGK1_HUMAN Phosphoglycerate kinase 1 (Gene Name=PGK1)

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