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 1.3 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: https://doi.org/10.1021/jm9507183
  • Primary Citation of Related Structures:  
    1PRO

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16
UniProt
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
Explore P12499 
Go to UniProtKB:  P12499
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12499
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A88
Query on A88

Download Ideal Coordinates CCD File 
C [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
A88 PDBBind:  1PRO Ki: 5.00e-3 (nM) from 1 assay(s)
BindingDB:  1PRO Ki: 5.00e-3 (nM) from 1 assay(s)
Binding MOAD:  1PRO Ki: 5.00e-3 (nM) from 1 assay(s)
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  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Other