Structure of PDB 1idb Chain B Binding Site BS01

Receptor Information

>1idb Chain B (length=99) Species: 11709 (Human immunodeficiency virus 2)

PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGI
GGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL

Ligand information

• Ligand ID: 0DO
• InChI: InChI=1S/C35H46N4O6S/c1-24-10-9-11-25(2)33(24)45-23-32(41)37-29(20-26-12-7-6-8-13-26)31(40)22-39-19-16-28(21-30(39)34(42)38-35(3,4)5)46(43,44)27-14-17-36-18-15-27/h6-15,17-18,28-31,40H,16,19-23H2,1-5H3,(H,37,41)(H,38,42)/t28-,29+,30+,31-/m1/s1
• InChIKey: HJVDBHNPRUSMDC-QNRWOPMTSA-N
• SMILES:
  CACTVS 3.370: Cc1cccc(C)c1OCC(=O)N[C@@H](Cc2ccccc2)[C@H](O)CN3CC[C@H](C[C@H]3C(=O)NC(C)(C)C)[S](=O)(=O)c4ccncc4
  CACTVS 3.370: Cc1cccc(C)c1OCC(=O)N[CH](Cc2ccccc2)[CH](O)CN3CC[CH](C[CH]3C(=O)NC(C)(C)C)[S](=O)(=O)c4ccncc4
  ACDLabs 12.01: O=S(=O)(c1ccncc1)C4CC(C(=O)NC(C)(C)C)N(CC(O)C(NC(=O)COc2c(cccc2C)C)Cc3ccccc3)CC4
  OpenEye OEToolkits 1.7.0: Cc1cccc(c1OCC(=O)NC(Cc2ccccc2)C(CN3CCC(CC3C(=O)NC(C)(C)C)S(=O)(=O)c4ccncc4)O)C
  OpenEye OEToolkits 1.7.0: Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C[N@@]3CC[C@H](C[C@H]3C(=O)NC(C)(C)C)S(=O)(=O)c4ccncc4)O)C
• Formula: C35 H46 N4 O6 S
• Name: (2R,4S)-N-tert-butyl-1-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutyl]-4-(pyridin-4-ylsulfonyl)piperidine-2-carboxamide
• ZINC: ZINC000076342586
• PDB chain: 1idb Chain B Residue 100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1idb Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 D30 V47 G49 I50 P81 I82
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 D30 V47 G49 I50 P81 I82
• Annotation score: 1
• Binding affinity: MOAD: ic50=11nM
  PDBbind-CN: -logKd/Ki=7.96,IC50=11nM

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.
  3.4.23.47: HIV-2 retropepsin.

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:1idb, PDBe:1idb, PDBj:1idb
• PDBsum: 1idb
• PubMed: 7743130
• UniProt: P04584|POL_HV2RO Gag-Pol polyprotein (Gene Name=gag-pol)