Structure of PDB 6urw Chain A Binding Site BS01

Receptor Information

>6urw Chain A (length=260) Species: 3988 (Ricinus communis)

PKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLP
INQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAE
AITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALY
YYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDP
SVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPII
ALMVYRCAPP

Ligand information

• Ligand ID: R7T
• InChI: InChI=1S/C12H10O2S/c13-12(14)10-5-3-9(4-6-10)8-11-2-1-7-15-11/h1-7H,8H2,(H,13,14)
• InChIKey: OAIBKSRZDOMJKZ-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: OC(=O)c1ccc(cc1)Cc2cccs2
  OpenEye OEToolkits 2.0.7: c1cc(sc1)Cc2ccc(cc2)C(=O)O
  CACTVS 3.385: OC(=O)c1ccc(Cc2sccc2)cc1
• Formula: C12 H10 O2 S
• Name: 4-[(thiophen-2-yl)methyl]benzoic acid
• ZINC: ZINC000034936268
• PDB chain: 6urw Chain A Residue 324

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6urw Small Molecule Inhibitors Targeting the Interaction of Ricin Toxin A Subunit with Ribosomes.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): Y183 R234 R235 F240 I251
• Binding residue (residue number reindexed from 1): Y181 R232 R233 F238 I249
• Annotation score: 1
• Binding affinity: MOAD: ic50=32uM

Enzymatic activity

• Catalytic site (original residue number in PDB): V81 E177 R180
• Catalytic site (residue number reindexed from 1): V79 E175 R178
• Enzyme Commision number: 3.2.2.22: rRNA N-glycosylase.

Gene Ontology

Molecular Function

• GO:0030598 rRNA N-glycosylase activity

Biological Process

• GO:0017148 negative regulation of translation

External links

• PDB: RCSB:6urw, PDBe:6urw, PDBj:6urw
• PDBsum: 6urw
• PubMed: 32428396
• UniProt: P02879|RICI_RICCO Ricin