Structure of PDB 5ofw Chain A Binding Site BS01

Receptor Information

>5ofw Chain A (length=195) Species: 9606 (Homo sapiens)

NGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLG
ILGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPL
CDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRAL
QSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSR

Ligand information

• Ligand ID: 9TW
• InChI: InChI=1S/C7H5ClFNO/c8-5-3-4(7(10)11)1-2-6(5)9/h1-3H,(H2,10,11)
• InChIKey: AEYMQEMBMKCNEG-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1cc(c(cc1C(=O)N)Cl)F
  CACTVS 3.385: NC(=O)c1ccc(F)c(Cl)c1
• Formula: C7 H5 Cl F N O
• Name: 3-chloranyl-4-fluoranyl-benzamide
• ChEMBL: CHEMBL4074617
• ZINC: ZINC000000152711
• PDB chain: 5ofw Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ofw Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): G152 Y174 P176 T207 S212 T213 L216
• Binding residue (residue number reindexed from 1): G53 Y75 P77 T108 S113 T114 L117
• Annotation score: 1
• Binding affinity: MOAD: Kd=1.6mM
  BindingDB: Kd=1500000nM

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

External links

• PDB: RCSB:5ofw, PDBe:5ofw, PDBj:5ofw
• PDBsum: 5ofw
• PubMed: 29568346
• UniProt: O43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase (Gene Name=PHGDH)