Structure of PDB 5nzo Chain B Binding Site BS01

Receptor Information

>5nzo Chain B (length=195) Species: 9606 (Homo sapiens)

NGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLG
ILGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPL
CDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRAL
QSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSR

Ligand information

• Ligand ID: 9EZ
• InChI: InChI=1S/C10H11N3/c1-13-10(11)7-9(12-13)8-5-3-2-4-6-8/h2-7H,11H2,1H3
• InChIKey: KCYRMURRLLYLPU-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: Cn1c(cc(n1)c2ccccc2)N
  CACTVS 3.385: Cn1nc(cc1N)c2ccccc2
• Formula: C10 H11 N3
• Name: 2-methyl-5-phenyl-pyrazol-3-amine
• ChEMBL: CHEMBL4084029
• ZINC: ZINC000000095216
• PDB chain: 5nzo Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5nzo Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer.
• Resolution: 1.29 Å
• Binding residue (original residue number in PDB): Y174 P176 T207 P208 T213
• Binding residue (residue number reindexed from 1): Y75 P77 T108 P109 T114
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=2.24,Kd=5.8mM
  BindingDB: Kd=5800000nM

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:0051287 NAD binding

External links

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