Structure of PDB 3o9b Chain B Binding Site BS01

Receptor Information

>3o9b Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: K2A
• InChI: InChI=1S/C29H40N2O8S/c1-3-20(2)16-31(40(35,36)23-11-9-22(18-32)10-12-23)17-26(33)25(15-21-7-5-4-6-8-21)30-29(34)39-27-19-38-28-24(27)13-14-37-28/h4-12,20,24-28,32-33H,3,13-19H2,1-2H3,(H,30,34)/t20-,24-,25-,26+,27-,28+/m0/s1
• InChIKey: ALWBGUNCNDFMFE-QKULBLGOSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CCC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2COC3C2CCO3)O)S(=O)(=O)c4ccc(cc4)CO
  ACDLabs 12.01: O=S(=O)(c1ccc(cc1)CO)N(CC(C)CC)CC(O)C(NC(=O)OC2COC3OCCC23)Cc4ccccc4
  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)c4ccc(cc4)CO
  CACTVS 3.370: CC[CH](C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)O[CH]2CO[CH]3OCC[CH]23)[S](=O)(=O)c4ccc(CO)cc4
  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)c4ccc(CO)cc4
• Formula: C29 H40 N2 O8 S
• Name: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-({[4-(hydroxymethyl)phenyl]sulfonyl}[(2S)-2-methylbutyl]amino)propyl]carbamate
• ChEMBL: CHEMBL4532385
• ZINC: ZINC000098209066
• PDB chain: 3o9b Chain A Residue 200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3o9b Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.
• Resolution: 1.5 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=12.30,Ki=0.5pM

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:3o9b, PDBe:3o9b, PDBj:3o9b
• PDBsum: 3o9b
• PubMed: 24012370
• UniProt: Q90K99