Structure of PDB 3kfn Chain A Binding Site BS02

Receptor Information

>3kfn Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 4DX
• InChI: InChI=1S/C7H14O/c1-6-4-2-3-5-7(6)8/h6-8H,2-5H2,1H3/t6-,7-/m0/s1
• InChIKey: NDVWOBYBJYUSMF-BQBZGAKWSA-N
• SMILES:
  ACDLabs 11.02: OC1CCCCC1C
  OpenEye OEToolkits 1.7.0: CC1CCCCC1O
  CACTVS 3.352: C[CH]1CCCC[CH]1O
  CACTVS 3.352
  OpenEye OEToolkits 1.7.0: C[C@H]1CCCC[C@@H]1O
• Formula: C7 H14 O
• Name: (1S,2S)-2-methylcyclohexanol;
  trans-2-methylcyclohexanol
• ZINC: ZINC000001701830
• PDB chain: 3kfn Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kfn Fragment-based screen against HIV protease.
• Resolution: 1.77 Å
• Binding residue (original residue number in PDB): K14 I15 G17 L63 I64
• Binding residue (residue number reindexed from 1): K14 I15 G17 L63 I64
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• 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.
  3.4.23.16: HIV-1 retropepsin.

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3kfn, PDBe:3kfn, PDBj:3kfn
• PDBsum: 3kfn
• PubMed: 20659109
• UniProt: P12499|POL_HV1Z2 Gag-Pol polyprotein (Gene Name=gag-pol)