Structure of PDB 1ida Chain A Binding Site BS01

Receptor Information

>1ida Chain A (length=99) Species: 11709 (Human immunodeficiency virus 2)

PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGI
GGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL

Ligand information

• Ligand ID: 0PO
• InChI: InChI=1S/C41H52N6O4S/c1-27(2)37(45-38(49)33-18-17-30-15-9-10-16-32(30)43-33)40(51)44-34(22-28-12-7-6-8-13-28)36(48)25-47-21-19-31(52-26-29-14-11-20-42-24-29)23-35(47)39(50)46-41(3,4)5/h6-18,20,24,27,31,34-37,48H,19,21-23,25-26H2,1-5H3,(H,44,51)(H,45,49)(H,46,50)/t31-,34+,35+,36-,37+/m1/s1
• InChIKey: IMPWGYVYFQPDFN-SZNOJMITSA-N
• SMILES:
  ACDLabs 12.01: O=C(c1nc2c(cc1)cccc2)NC(C(=O)NC(C(O)CN4C(C(=O)NC(C)(C)C)CC(SCc3cccnc3)CC4)Cc5ccccc5)C(C)C
  CACTVS 3.370: CC(C)[CH](NC(=O)c1ccc2ccccc2n1)C(=O)N[CH](Cc3ccccc3)[CH](O)CN4CC[CH](C[CH]4C(=O)NC(C)(C)C)SCc5cccnc5
  CACTVS 3.370: CC(C)[C@H](NC(=O)c1ccc2ccccc2n1)C(=O)N[C@@H](Cc3ccccc3)[C@H](O)CN4CC[C@H](C[C@H]4C(=O)NC(C)(C)C)SCc5cccnc5
  OpenEye OEToolkits 1.7.0: CC(C)C(C(=O)NC(Cc1ccccc1)C(CN2CCC(CC2C(=O)NC(C)(C)C)SCc3cccnc3)O)NC(=O)c4ccc5ccccc5n4
  OpenEye OEToolkits 1.7.0: CC(C)[C@@H](C(=O)N[C@@H](Cc1ccccc1)[C@@H](C[N@@]2CC[C@H](C[C@H]2C(=O)NC(C)(C)C)SCc3cccnc3)O)NC(=O)c4ccc5ccccc5n4
• Formula: C41 H52 N6 O4 S
• Name: N-[(1R)-1-{[(1S,2S)-1-benzyl-3-{(2R,4S)-2-(tert-butylcarbamoyl)-4-[(pyridin-3-ylmethyl)sulfanyl]piperidin-1-yl}-2-hydroxypropyl]carbamoyl}-2-methylpropyl]quinoline-2-carboxamide
• ZINC: ZINC000076342387
• PDB chain: 1ida Chain B Residue 100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ida Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): R8 D25 D30 G48 G49 P81
• Binding residue (residue number reindexed from 1): R8 D25 D30 G48 G49 P81
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.70,IC50<=2.0nM

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