Structure of PDB 9hvp Chain B Binding Site BS01

Receptor Information

>9hvp Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 0E9
• InChI: InChI=1S/C43H52N4O7/c1-29(2)37(46-42(51)53-27-33-21-13-7-14-22-33)40(49)44-35(25-31-17-9-5-10-18-31)39(48)36(26-32-19-11-6-12-20-32)45-41(50)38(30(3)4)47-43(52)54-28-34-23-15-8-16-24-34/h5-24,29-30,35-39,48H,25-28H2,1-4H3,(H,44,49)(H,45,50)(H,46,51)(H,47,52)/t35-,36-,37-,38-/m0/s1
• InChIKey: GEANBHANAKKWSL-ZQWQDMLBSA-N
• SMILES:
  CACTVS 3.352: CC(C)[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](Cc2ccccc2)[C@@H](O)[C@H](Cc3ccccc3)NC(=O)[C@@H](NC(=O)OCc4ccccc4)C(C)C
  CACTVS 3.352: CC(C)[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](Cc2ccccc2)[CH](O)[CH](Cc3ccccc3)NC(=O)[CH](NC(=O)OCc4ccccc4)C(C)C
  ACDLabs 10.04: O=C(OCc1ccccc1)NC(C(=O)NC(Cc2ccccc2)C(O)C(NC(=O)C(NC(=O)OCc3ccccc3)C(C)C)Cc4ccccc4)C(C)C
• Formula: C43 H52 N4 O7
• Name: benzyl [(1R,4S,6S,9R)-4,6-dibenzyl-5-hydroxy-1,9-bis(1-methylethyl)-2,8,11-trioxo-13-phenyl-12-oxa-3,7,10-triazatridec-1-yl]carbamate;
  A-74704
• ChEMBL: CHEMBL307193
• PDB chain: 9hvp Chain A Residue 100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 9hvp Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 G48 P81 I84
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 G48 P81 I84
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.35,Ki=4.5nM

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:9hvp, PDBe:9hvp, PDBj:9hvp
• PDBsum: 9hvp
• PubMed: 2200122
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)