Structure of PDB 1rhm Chain D Binding Site BS01

Receptor Information

>1rhm Chain D (length=91) Species: 9606 (Homo sapiens)

KIPVEADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHI
LTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYFY

Ligand information

• Ligand ID: NA4
• InChI: InChI=1S/C17H14N2O6/c20-9-14(6-15(21)22)19-16(23)13-5-12(7-18-8-13)10-1-3-11(4-2-10)17(24)25/h1-5,7-9,14H,6H2,(H,19,23)(H,21,22)(H,24,25)/t14-/m0/s1
• InChIKey: JNRAPROKLOUIRA-AWEZNQCLSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)CC(C=O)NC(=O)c2cncc(c1ccc(C(=O)O)cc1)c2
  CACTVS 3.341: OC(=O)C[CH](NC(=O)c1cncc(c1)c2ccc(cc2)C(O)=O)C=O
  OpenEye OEToolkits 1.5.0: c1cc(ccc1c2cc(cnc2)C(=O)NC(CC(=O)O)C=O)C(=O)O
  CACTVS 3.341: OC(=O)C[C@H](NC(=O)c1cncc(c1)c2ccc(cc2)C(O)=O)C=O
  OpenEye OEToolkits 1.5.0: c1cc(ccc1c2cc(cnc2)C(=O)N[C@@H](CC(=O)O)C=O)C(=O)O
• Formula: C17 H14 N2 O6
• Name: 4-[5-(2-CARBOXY-1-FORMYL-ETHYLCARBAMOYL)-PYRIDIN-3-YL]-BENZOIC ACID
• ChEMBL: CHEMBL310554
• DrugBank: DB08251
• ZINC: ZINC000000026888
• PDB chain: 1rhm Chain C Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1rhm Reducing the Peptidyl Features of Caspase-3 Inhibitors: A Structural Analysis.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): Y838 S839 W840 R841 S881C
• Binding residue (residue number reindexed from 1): Y19 S20 W21 R22 S66
• Annotation score: 1
• Binding affinity: BindingDB: IC50=1735nM

Enzymatic activity

• Enzyme Commision number: 3.4.22.56: caspase-3.

Gene Ontology

Molecular Function

• GO:0004197 cysteine-type endopeptidase activity
• GO:0008234 cysteine-type peptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:1rhm, PDBe:1rhm, PDBj:1rhm
• PDBsum: 1rhm
• PubMed: 15115390
• UniProt: P42574|CASP3_HUMAN Caspase-3 (Gene Name=CASP3)