Structure of PDB 1il5 Chain A Binding Site BS01

Receptor Information

>1il5 Chain A (length=264) Species: 3988 (Ricinus communis)

IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVHEIPVLPNRVGL
PINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDA
EAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISAL
YYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPD
PSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPI
IALMVYRCAPPPQF

Ligand information

• Ligand ID: DDP
• InChI: InChI=1S/C4H6N4O2/c5-1-2(9)7-4(6)8-3(1)10/h5H2,(H4,6,7,8,9,10)
• InChIKey: HWSJQFCTYLBBOF-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1(c(nc(nc1O)N)O)N
  ACDLabs 10.04: Oc1nc(nc(O)c1N)N
  CACTVS 3.341: Nc1nc(O)c(N)c(O)n1
• Formula: C4 H6 N4 O2
• Name: 2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE
• ChEMBL: CHEMBL175083
• DrugBank: DB02037
• ZINC: ZINC000018156496
• PDB chain: 1il5 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1il5 Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): Y80 N122 Y123 R180
• Binding residue (residue number reindexed from 1): Y79 N121 Y122 R179
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=2.66,IC50=2.2mM

Enzymatic activity

• Catalytic site (original residue number in PDB): V81 E177 R180
• Catalytic site (residue number reindexed from 1): V80 E176 R179
• 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:1il5, PDBe:1il5, PDBj:1il5
• PDBsum: 1il5
• PubMed: 11754581
• UniProt: P02879|RICI_RICCO Ricin