Structure of PDB 3o9d Chain B Binding Site BS01

Receptor Information

>3o9d Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: K19
• InChI: InChI=1S/C29H37N3O7S2/c1-3-19(2)15-32(41(35,36)21-9-10-23-27(14-21)40-18-30-23)16-25(33)24(13-20-7-5-4-6-8-20)31-29(34)39-26-17-38-28-22(26)11-12-37-28/h4-10,14,18-19,22,24-26,28,33H,3,11-13,15-17H2,1-2H3,(H,31,34)/t19-,22-,24-,25+,26-,28+/m0/s1
• InChIKey: COTBSCQKHDXTHH-RPEWIUDZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CCC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2COC3C2CCO3)O)S(=O)(=O)c4ccc5c(c4)scn5
  ACDLabs 12.01: O=C(OC1C2CCOC2OC1)NC(Cc3ccccc3)C(O)CN(CC(C)CC)S(=O)(=O)c4ccc5ncsc5c4
  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)c4ccc5ncsc5c4
  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)scn5
  CACTVS 3.370: CC[CH](C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)O[CH]2CO[CH]3OCC[CH]23)[S](=O)(=O)c4ccc5ncsc5c4
• Formula: C29 H37 N3 O7 S2
• Name: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{(1,3-benzothiazol-6-ylsulfonyl)[(2S)-2-methylbutyl]amino}-1-benzyl-2-hydroxypropyl]carbamate
• ZINC: ZINC000098209064
• PDB chain: 3o9d Chain A Residue 200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3o9d 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 G48 P81 V82
• Binding residue (residue number reindexed from 1): D25 A28 D30 G48 P81 V82
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=10.72,Ki=19pM

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:3o9d, PDBe:3o9d, PDBj:3o9d
• PDBsum: 3o9d
• PubMed: 24012370
• UniProt: Q90K99