Structure of PDB 2qi4 Chain A Binding Site BS01

Receptor Information

>2qi4 Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: MZ6
• InChI: InChI=1S/C29H33N3O5S2/c1-3-20(2)17-32(39(36,37)24-12-13-25-28(16-24)38-19-30-25)18-27(34)26(14-21-8-5-4-6-9-21)31-29(35)22-10-7-11-23(33)15-22/h4-13,15-16,19-20,26-27,33-34H,3,14,17-18H2,1-2H3,(H,31,35)/t20-,26-,27+/m0/s1
• InChIKey: OIOKJSPMDFSKEA-SQMFLSJESA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCC(C)CN(CC(C(Cc1ccccc1)NC(=O)c2cccc(c2)O)O)S(=O)(=O)c3ccc4c(c3)scn4
  OpenEye OEToolkits 1.5.0: CC[C@H](C)C[N@@](C[C@H]([C@H](Cc1ccccc1)NC(=O)c2cccc(c2)O)O)S(=O)(=O)c3ccc4c(c3)scn4
  CACTVS 3.341: CC[C@H](C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)c2cccc(O)c2)[S](=O)(=O)c3ccc4ncsc4c3
  ACDLabs 10.04: O=C(c1cccc(O)c1)NC(Cc2ccccc2)C(O)CN(CC(C)CC)S(=O)(=O)c3ccc4ncsc4c3
  CACTVS 3.341: CC[CH](C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)c2cccc(O)c2)[S](=O)(=O)c3ccc4ncsc4c3
• Formula: C29 H33 N3 O5 S2
• Name: N-[(1S,2R)-3-{(1,3-BENZOTHIAZOL-6-YLSULFONYL)[(2S)-2-METHYLBUTYL]AMINO}-1-BENZYL-2-HYDROXYPROPYL]-3-HYDROXYBENZAMIDE
• ZINC: ZINC000016052448
• PDB chain: 2qi4 Chain A Residue 200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2qi4 HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): D25 G27 D29 D30 I50 V82
• Binding residue (residue number reindexed from 1): D25 G27 D29 D30 I50 V82
• Annotation score: 1
• Binding affinity: MOAD: Ki=0.036nM
  PDBbind-CN: -logKd/Ki=10.44,Ki=0.036nM

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:2qi4, PDBe:2qi4, PDBj:2qi4
• PDBsum: 2qi4
• PubMed: 18412349
• UniProt: P03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)