Structure of PDB 6oxo Chain B Binding Site BS01

Receptor Information

>6oxo Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: NJM
• InChI: InChI=1S/C28H38N2O8S/c1-19(2)15-30(39(34,35)22-10-8-21(17-31)9-11-22)16-25(32)24(14-20-6-4-3-5-7-20)29-28(33)38-26-18-37-27-23(26)12-13-36-27/h3-11,19,23-27,31-32H,12-18H2,1-2H3,(H,29,33)/t23-,24-,25+,26-,27+/m0/s1
• InChIKey: VSKFMILERNHCAA-UIPNDDLNSA-N
• SMILES:
  ACDLabs 12.01: C(C(Cc1ccccc1)NC(OC2C3C(OC2)OCC3)=O)(CN(CC(C)C)S(c4ccc(cc4)CO)(=O)=O)O
  OpenEye OEToolkits 2.0.7: CC(C)CN(C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)c4ccc(cc4)CO
  CACTVS 3.385: CC(C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)O[CH]2CO[CH]3OCC[CH]23)[S](=O)(=O)c4ccc(CO)cc4
  OpenEye OEToolkits 2.0.7: CC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2COC3C2CCO3)O)S(=O)(=O)c4ccc(cc4)CO
  CACTVS 3.385: CC(C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@H]3OCC[C@@H]23)[S](=O)(=O)c4ccc(CO)cc4
• Formula: C28 H38 N2 O8 S
• Name: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-3-hydroxy-4-[{[4-(hydroxymethyl)phenyl]sulfonyl}(2-methylpropyl)amino]-1-phenylbutan-2-yl}carbamate
• PDB chain: 6oxo Chain A Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6oxo HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands To Optimize Hydrogen Bonding in the Substrate Envelope.
• Resolution: 2.003 Å
• Binding residue (original residue number in PDB): D25 A28 D30 P81 I84
• Binding residue (residue number reindexed from 1): D25 A28 D30 P81 I84
• 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:6oxo, PDBe:6oxo, PDBj:6oxo
• PDBsum: 6oxo
• PubMed: 31386368
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)