Structure of PDB 1iiq Chain A Binding Site BS01

Receptor Information

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

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 0ZR
• InChI: InChI=1S/C38H50N6O7/c1-38(2,3)51-37(50)44-29(21-25-13-7-4-8-14-25)32(45)24-41-31(23-27-17-11-6-12-18-27)36(49)42-28(19-20-33(39)46)35(48)43-30(34(40)47)22-26-15-9-5-10-16-26/h4-18,28-32,41,45H,19-24H2,1-3H3,(H2,39,46)(H2,40,47)(H,42,49)(H,43,48)(H,44,50)/t28-,29-,30-,31-,32-/m0/s1
• InChIKey: SSPOMXWWHDMCTH-XDIGFQIYSA-N
• SMILES:
  ACDLabs 12.01: O=C(N)C(NC(=O)C(NC(=O)C(NCC(O)C(NC(=O)OC(C)(C)C)Cc1ccccc1)Cc2ccccc2)CCC(=O)N)Cc3ccccc3
  CACTVS 3.370: CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)CN[C@@H](Cc2ccccc2)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](Cc3ccccc3)C(N)=O
  OpenEye OEToolkits 1.7.0: CC(C)(C)OC(=O)NC(Cc1ccccc1)C(CNC(Cc2ccccc2)C(=O)NC(CCC(=O)N)C(=O)NC(Cc3ccccc3)C(=O)N)O
  OpenEye OEToolkits 1.7.0: CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)[C@H](CN[C@@H](Cc2ccccc2)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](Cc3ccccc3)C(=O)N)O
  CACTVS 3.370: CC(C)(C)OC(=O)N[CH](Cc1ccccc1)[CH](O)CN[CH](Cc2ccccc2)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](Cc3ccccc3)C(N)=O
• Formula: C38 H50 N6 O7
• Name: N-{(2R,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L-glutaminyl-L-phenylalaninamide
• ChEMBL: CHEMBL386758
• ZINC: ZINC000049781952
• PDB chain: 1iiq Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1iiq Hydroxyethylamine isostere of an HIV-1 protease inhibitor prefers its amine to the hydroxy group in binding to catalytic aspartates. A synchrotron study of HIV-1 protease in complex with a peptidomimetic inhibitor.
• Resolution: 1.83 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 D30 I47 G48 G49 I50 F53 P81
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 D30 I47 G48 G49 I50 F53 P81
• Annotation score: 1
• Binding affinity: MOAD: Ki=33nM
  PDBbind-CN: -logKd/Ki=7.48,Ki=33nM

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:1iiq, PDBe:1iiq, PDBj:1iiq
• PDBsum: 1iiq
• PubMed: 11906284
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)