Structure of PDB 3ebz Chain B Binding Site BS02

Receptor Information

>3ebz Chain B (length=99) Species: 11720 (Human immunodeficiency virus type 2 (ISOLATE ROD))

PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGI
GGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL

Ligand information

• Ligand ID: IMD
• InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
• InChIKey: RAXXELZNTBOGNW-UHFFFAOYSA-O
• SMILES:
  CACTVS 3.341: [nH]1cc[nH+]c1
  ACDLabs 10.04: c1c[nH+]cn1
  OpenEye OEToolkits 1.5.0: c1c[nH+]c[nH]1
• Formula: C3 H5 N2
• Name: IMIDAZOLE
• PDB chain: 3ebz Chain B Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ebz Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease
• Resolution: 1.2 Å
• Binding residue (original residue number in PDB): D130 M176
• Binding residue (residue number reindexed from 1): D30 M76
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D125 T126 G127
• Catalytic site (residue number reindexed from 1): D25 T26 G27
• Enzyme Commision number: 2.7.7.-
  2.7.7.49: RNA-directed DNA polymerase.
  2.7.7.7: DNA-directed DNA polymerase.
  3.1.-.-
  3.1.13.2: exoribonuclease H.
  3.1.26.13: retroviral ribonuclease H.
  3.4.23.47: HIV-2 retropepsin.

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3ebz, PDBe:3ebz, PDBj:3ebz
• PDBsum: 3ebz
• PubMed: 18834890
• UniProt: P04584|POL_HV2RO Gag-Pol polyprotein (Gene Name=gag-pol)