Structure of PDB 5ofv Chain B Binding Site BS01

Receptor Information
>5ofv Chain B (length=195) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLG
ILGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPL
CDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRAL
QSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSR
Ligand information
Ligand ID9TZ
InChIInChI=1S/C8H7FO2/c1-5-2-3-6(9)4-7(5)8(10)11/h2-4H,1H3,(H,10,11)
InChIKeyJVBLXLBINTYFPR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(F)cc1C(O)=O
OpenEye OEToolkits 2.0.6Cc1ccc(cc1C(=O)O)F
FormulaC8 H7 F O2
Name5-fluoranyl-2-methyl-benzoic acid
ChEMBLCHEMBL5285114
DrugBank
ZINCZINC000000167088
PDB chain5ofv Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ofv Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		Y174 P176 T207 T213
Binding residue
(residue number reindexed from 1)		Y75 P77 T108 T114
Annotation score1
Binding affinityMOAD: Kd=26.2mM
PDBbind-CN: -logKd/Ki=1.58,Kd=26.2mM
Enzymatic activity
Catalytic site (original residue number in PDB) N102 R236 D260 E265 H283
Catalytic site (residue number reindexed from 1) N3 R137 D161 E166 H184
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
1.1.1.399: 2-oxoglutarate reductase.
1.1.1.95: phosphoglycerate dehydrogenase.
Gene Ontology
Molecular Function
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding

View graph for
Molecular Function
External links
PDB RCSB:5ofv, PDBe:5ofv, PDBj:5ofv
PDBsum5ofv
PubMed29568346
UniProtO43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase (Gene Name=PHGDH)

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