1HPS

RATIONAL DESIGN, SYNTHESIS AND CRYSTALLOGRAPHIC ANALYSIS OF A HYDROXYETHYLENE-BASED HIV-1 PROTEASE INHIBITOR CONTAINING A HETEROCYCLIC P1'-P2' AMIDE BOND ISOSTERE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Rational design, synthesis, and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor containing a heterocyclic P1'--P2' amide bond isostere.

Thompson, S.K.Murthy, K.H.Zhao, B.Winborne, E.Green, D.W.Fisher, S.M.DesJarlais, R.L.Tomaszek Jr., T.A.Meek, T.D.Gleason, J.G.Abdel-Meguid, S.S.

(1994) J.Med.Chem. 37: 3100-3107


  • PubMed Abstract: 
  • The rational design and synthesis of a highly potent inhibitor of HIV-1 protease have been accomplished. The inhibitor, SB 206343, is based on a model derived from the structure of the MVT-101/HIV-1 protease complex and contains a 4(5)-acylimidazole ...

    The rational design and synthesis of a highly potent inhibitor of HIV-1 protease have been accomplished. The inhibitor, SB 206343, is based on a model derived from the structure of the MVT-101/HIV-1 protease complex and contains a 4(5)-acylimidazole ring as an isosteric replacement for the P1'--P2' amide bond. It is a competitive inhibitor with an apparent inhibition constant of 0.6 nM at pH 6.0. The three-dimensional structure of SB 206343 bound in the active site of HIV-1 protease has been determined at 2.3 A resolution by X-ray diffraction techniques and refined to a crystallographic discrepancy factor, R (= sigma parallel Fo magnitude of/Fc parallel/sigma magnitude of), of 0.194. The inhibitor is held in the enzyme by a set of hydrophobic and polar interactions. N-3 of the imidazole ring participates in a novel hydrogen-bonding interaction with the bound water molecule, demonstrating the effectiveness of the imidazole ring as an isosteric replacement for the P1'--P2' amide bond in hydroxyethylene-based HIV-1 protease inhibitors. Also present are hydrogen-bonding interactions between N-1 of the imidazole ring and the carbonyl of Gly-127 as well as between the imidazole acyl carbonyl oxygen and the amide nitrogen of Asp-129, exemplifying the peptidomimetic nature of the 4(5)-acylimidazole isostere. All of these interactions are in qualitative agreement with those predicted by the model.


    Organizational Affiliation

    Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RUN
Query on RUN

Download SDF File 
Download CCD File 
B
2-[(1R,3S,4S)-1-BENZYL-4-[N-(BENZYLOXYCARBONYL)-L-VALYL]AMINO-3-PHENYLPENTYL]-4(5)-(2-METHYLPROPIONYL)IMIDAZOLE
SB206343
C38 H46 N4 O5
RQAVEWKEUKIFLD-LVPKLHHISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RUNKi: 0.6 nM (98) BINDINGDB
RUNKi: 0.6 nM BINDINGMOAD
RUNKi: 0.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 63.000α = 90.00
b = 63.000β = 90.00
c = 83.300γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-22
    Type: Database references
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other