1PRO

HIV-1 PROTEASE DIMER COMPLEXED WITH A-98881


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A novel, picomolar inhibitor of human immunodeficiency virus type 1 protease.

Sham, H.L.Zhao, C.Stewart, K.D.Betebenner, D.A.Lin, S.Park, C.H.Kong, X.P.Rosenbrook Jr., W.Herrin, T.Madigan, D.Vasavanonda, S.Lyons, N.Molla, A.Saldivar, A.Marsh, K.C.McDonald, E.Wideburg, N.E.Denissen, J.F.Robins, T.Kempf, D.J.Plattner, J.J.Norbeck, D.W.

(1996) J Med Chem 39: 392-397

  • DOI: 10.1021/jm9507183
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The design, synthesis, and molecular modeling studies of a novel series of azacyclic ureas, which are inhibitors of human immunodeficiency virus type 1 (HIV-1) protease that incorporate different ligands for the S1', S2, and S2' substrate-binding sit ...

    The design, synthesis, and molecular modeling studies of a novel series of azacyclic ureas, which are inhibitors of human immunodeficiency virus type 1 (HIV-1) protease that incorporate different ligands for the S1', S2, and S2' substrate-binding sites of HIV-1 protease are described. The synthesis of this series is highly flexible in the sense that the P1', P2, and P2' residues of the inhibitors can be changed independently. Molecular modeling studies on the phenyl ring of the P2 and P2' ligand suggested incorporation of hydrogen-bonding donor/acceptor groups at the 3' and 4-positions of the phenyl ring should increase binding potency. This led to the discovery of compound 7f (A-98881), which possesses high potency in the HIV-1 protease inhibition assay and the in vitro MT-4 cell culture assay (Ki = approximately 5 pM and EC50 = 0.002 microM). This compares well with the symmetrical cyclic urea 1 pioneered at DuPont Merck.


    Organizational Affiliation

    Pharmaceutical Products Division, Abbott Laboratories, Abbott Park, Illinois 60064-3500.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASEA, B99Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
Explore P12499 
Go to UniProtKB:  P12499
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A88
Query on A88

Download CCD File 
A
(5R,6R)-2,4-BIS-(4-HYDROXY-3-METHOXYBENZYL)-1,5-DIBENZYL-3-OXO-6-HYDROXY-1,2,4-TRIAZACYCLOHEPTANE
C34 H37 N3 O6
PMBZSBGCSQGJAQ-GRKNLSHJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A88Ki:  0.005000000353902578   nM  Binding MOAD
A88Ki:  0   nM  BindingDB
A88Ki :  0.005000000353902578   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.08α = 90
b = 63.08β = 90
c = 83.68γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance