Structure of PDB 6vod Chain B Binding Site BS01

Receptor Information

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

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: T1R
• InChI: InChI=1S/C30H40N2O8S/c1-19(2)16-32(41(35,36)23-11-9-22(37-3)10-12-23)17-26(33)25(13-20-7-5-4-6-8-20)31-30(34)40-27-14-21-18-38-29-24(21)15-28(27)39-29/h4-12,19,21,24-29,33H,13-18H2,1-3H3,(H,31,34)/t21-,24-,25+,26-,27-,28+,29-/m1/s1
• InChIKey: NEABZPBSTVJYAP-HBDWHRTCSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CN(C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@@H]2C[C@@H]3CO[C@H]4[C@@H]3C[C@@H]2O4)O)S(=O)(=O)c5ccc(cc5)OC
  ACDLabs 12.01: c1c(ccc(c1)OC)S(=O)(N(CC(C)C)CC(O)C(NC(OC3C4CC2C(OCC2C3)O4)=O)Cc5ccccc5)=O
  OpenEye OEToolkits 2.0.7: CC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2CC3COC4C3CC2O4)O)S(=O)(=O)c5ccc(cc5)OC
  CACTVS 3.385: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](Cc2ccccc2)NC(=O)O[CH]3C[CH]4CO[CH]5O[CH]3C[CH]45
  CACTVS 3.385: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)O[C@@H]3C[C@@H]4CO[C@@H]5O[C@H]3C[C@H]45
• Formula: C30 H40 N2 O8 S
• Name: (1R,3aS,5R,6S,7aR)-octahydro-1,6-epoxy-2-benzofuran-5-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate
• PDB chain: 6vod Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vod Structure-Based Design of Highly Potent HIV-1 Protease Inhibitors Containing New Tricyclic Ring P2-Ligands: Design, Synthesis, Biological, and X-ray Structural Studies.
• Resolution: 1.25 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 D30 V32 I47 G48 G49 I50
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 D30 V32 I47 G48 G49 I50
• Annotation score: 1
• Binding affinity: MOAD: ic50=38nM

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:6vod, PDBe:6vod, PDBj:6vod
• PDBsum: 6vod
• PubMed: 32348139
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)