Structure of PDB 3o9c Chain B Binding Site BS01

Receptor Information

>3o9c Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: K20
• InChI: InChI=1S/C29H38N2O9S/c1-3-19(2)15-31(41(34,35)21-9-10-25-26(14-21)39-18-38-25)16-24(32)23(13-20-7-5-4-6-8-20)30-29(33)40-27-17-37-28-22(27)11-12-36-28/h4-10,14,19,22-24,27-28,32H,3,11-13,15-18H2,1-2H3,(H,30,33)/t19-,22-,23-,24+,27-,28+/m0/s1
• InChIKey: QQGKYOUYWIXTAU-VGOMVBHOSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CC[C@H](C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)c4ccc5c(c4)OCO5
  CACTVS 3.370: CC[C@H](C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@H]3OCC[C@@H]23)[S](=O)(=O)c4ccc5OCOc5c4
  CACTVS 3.370: CC[CH](C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)O[CH]2CO[CH]3OCC[CH]23)[S](=O)(=O)c4ccc5OCOc5c4
  ACDLabs 12.01: O=S(=O)(c2cc1OCOc1cc2)N(CC(C)CC)CC(O)C(NC(=O)OC3COC4OCCC34)Cc5ccccc5
  OpenEye OEToolkits 1.7.0: CCC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2COC3C2CCO3)O)S(=O)(=O)c4ccc5c(c4)OCO5
• Formula: C29 H38 N2 O9 S
• Name: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{(1,3-benzodioxol-5-ylsulfonyl)[(2S)-2-methylbutyl]amino}-1-benzyl-2-hydroxypropyl]carbamate
• ZINC: ZINC000098209065
• PDB chain: 3o9c Chain A Residue 200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3o9c Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): D25 A28 D30 P81 V82
• Binding residue (residue number reindexed from 1): D25 A28 D30 P81 V82
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=12.05,Ki=0.9pM

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: 3.1.26.13: retroviral ribonuclease H.

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3o9c, PDBe:3o9c, PDBj:3o9c
• PDBsum: 3o9c
• PubMed: 24012370
• UniProt: Q90K99