Structure of PDB 5n53 Chain B Binding Site BS01

Receptor Information

>5n53 Chain B (length=195) Species: 9606 (Homo sapiens)

NGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLG
ILGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPL
CDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRAL
QSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSR

Ligand information

• Ligand ID: 8NB
• InChI: InChI=1S/C9H10ClNO2/c1-6(12)11-7-3-4-9(13-2)8(10)5-7/h3-5H,1-2H3,(H,11,12)
• InChIKey: WNOVNNUWOUKIOL-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(=O)Nc1ccc(c(c1)Cl)OC
  CACTVS 3.385: COc1ccc(NC(C)=O)cc1Cl
• Formula: C9 H10 Cl N O2
• Name: ~{N}-(3-chloranyl-4-methoxy-phenyl)ethanamide
• ChEMBL: CHEMBL4094048
• ZINC: ZINC000000133498
• PDB chain: 5n53 Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5n53 Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer.
• Resolution: 1.48 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: MOAD: Kd=2.8mM
  PDBbind-CN: -logKd/Ki=2.55,Kd=2.8mM
  BindingDB: Kd=2800000nM

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:5n53, PDBe:5n53, PDBj:5n53
• PDBsum: 5n53
• PubMed: 29568346
• UniProt: O43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase (Gene Name=PHGDH)