Structure of PDB 6urx Chain A Binding Site BS01

Receptor Information

>6urx Chain A (length=259) Species: 3988 (Ricinus communis)

KQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPI
NQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEA
ITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYY
YSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPS
VITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIA
LMVYRCAPP

Ligand information

• Ligand ID: JMG
• InChI: InChI=1S/C11H8O2S/c12-11(13)10-7-6-9(14-10)8-4-2-1-3-5-8/h1-7H,(H,12,13)
• InChIKey: QGMFBCDNJUZQBZ-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)c2ccc(s2)C(=O)O
  ACDLabs 12.01: c2c(c1ccc(C(O)=O)s1)cccc2
  CACTVS 3.385: OC(=O)c1sc(cc1)c2ccccc2
• Formula: C11 H8 O2 S
• Name: 5-phenylthiophene-2-carboxylic acid
• ChEMBL: CHEMBL3951007
• ZINC: ZINC000000158686
• PDB chain: 6urx Chain A Residue 316

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6urx Small Molecule Inhibitors Targeting the Interaction of Ricin Toxin A Subunit with Ribosomes.
• Resolution: 1.99 Å
• Binding residue (original residue number in PDB): Y183 R234 R235 F240
• Binding residue (residue number reindexed from 1): Y180 R231 R232 F237
• Annotation score: 1
• Binding affinity: MOAD: ic50=181uM

Enzymatic activity

• Catalytic site (original residue number in PDB): V81 E177 R180
• Catalytic site (residue number reindexed from 1): V78 E174 R177
• 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:6urx, PDBe:6urx, PDBj:6urx
• PDBsum: 6urx
• PubMed: 32428396
• UniProt: P02879|RICI_RICCO Ricin