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 1JLD | pdb_00001jld

Potent hiv protease inhibitors containing a novel (hydroxyethyl)amide isostere


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 
    0.179 (Depositor) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1JLD

This is version 1.4 of the entry. See complete history. 

Literature

Potent HIV protease inhibitors containing a novel (hydroxyethyl)amide isostere.

Beaulieu, P.L., Wernic, D., Abraham, A., Anderson, P.C., Bogri, T., Bousquet, Y., Croteau, G., Guse, I., Lamarre, D., Liard, F., Paris, W., Thibeault, D., Pav, S., Tong, L.

(1997) J Med Chem 40: 2164-2176

  • DOI: https://doi.org/10.1021/jm9606608
  • Primary Citation Related Structures: 
    1JLD

  • PubMed Abstract: 

    A series of HIV protease inhibitors containing a novel (hydroxyethyl)amidosuccinoyl core has been synthesized. These peptidomimetic structures inhibit viral protease activity at low nanomolar concentrations (IC50 < 10 nM for HIV-1 protease). The inhibition constant (Ki) for inhibitor 19 was determined to be 7.5 pM against HIV-1 and 1.2 nM against HIV-2 proteases, respectively. Several compounds (19-24) inhibited HIV-1 replication in cell culture assays with 50% effective concentrations (EC50) = 3.7-35 nM. This series of inhibitors was found to exhibit poor bioavailability (< 10%) in the rat, following oral administration. The synthesis and biological properties of these compounds are discussed. In addition, an X-ray structure of one of these inhibitors (23) in complex with HIV-2 protease provides insight into the binding mode of this novel class of HIV protease inhibitors.


  • Organizational Affiliation: 
    • Bio-Méga Research Division, Boehringer Ingelheim (Canada) Ltd., Laval (Québec), Canada.

Macromolecule Content 

  • Total Structure Weight: 22.12 kDa 
  • Atom Count: 1,572 
  • Modeled Residue Count: 198 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pol polyprotein
A, B
99Human immunodeficiency virus 2Mutation(s): 0 
Gene Names: pol
UniProt
Find proteins for P04584 (Human immunodeficiency virus type 2 subtype A (isolate ROD))
Explore P04584 
Go to UniProtKB:  P04584
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04584
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0PP

Query on 0PP



Download:Ideal Coordinates CCD File
C [auth A](2S)-2-tert-butyl-N~4~-(1-ethylpropyl)-N~1~-[(2R,3S)-2-hydroxy-4-phenyl-3-{[N-(quinolin-2-ylcarbonyl)-L-threonyl]amino}butyl]butanediamide
C37 H51 N5 O6
LUQGXGNLGWQNMB-BJPNTFJISA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work:  0.179 (Depositor) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.6α = 90
b = 62.6β = 90
c = 115.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 1997-12-03 
  • Deposition Author(s): Tong, L.

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-03
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary