HIV Protease, pseudo-symmetric inhibitors

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


2-Pyridyl P1'-substituted symmetry-based human immunodeficiency virus protease inhibitors (A-792611 and A-790742) with potential for convenient dosing and reduced side effects.

Degoey, D.A.Grampovnik, D.J.Flentge, C.A.Flosi, W.J.Chen, H.J.Yeung, C.M.Randolph, J.T.Klein, L.L.Dekhtyar, T.Colletti, L.Marsh, K.C.Stoll, V.Mamo, M.Morfitt, D.C.Nguyen, B.Schmidt, J.M.Swanson, S.J.Mo, H.Kati, W.M.Molla, A.Kempf, D.J.

(2009) J Med Chem 52: 2571-2586

  • DOI: https://doi.org/10.1021/jm900044w
  • Primary Citation of Related Structures:  
    3GGA, 3GGV, 3GGX, 3S85

  • PubMed Abstract: 

    A series of symmetry-based HIV protease inhibitors was designed and synthesized. Modification of the core regiochemistry and stereochemistry significantly affected the potency, metabolic stability, and oral bioavailability of the inhibitors, as did the variation of a pendent arylmethyl P3 group. Optimization led to the selection of two compounds, 10c (A-790742) and 9d (A-792611), for advancement to preclinical studies. Both compounds displayed low nanomolar potency against wild type HIV in the presence of human serum, low rates of metabolism in human liver microsomes, and high oral bioavailability in animal models. The compounds were examined in a preclinical model for the hyperbilirubinemia observed with some HIV PIs, and both exhibited less bilirubin elevation than comparator compounds. X-ray crystallographic analyses of the new cores were used to examine differences in their binding modes. The antiviral activity of the compounds against protease inhibitor resistant strains of HIV was also determined.

  • Organizational Affiliation

    Antiviral Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064, USA. David.DeGoey@abbott.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-1 protease
A, B, C, D, E
A, B, C, D, E, F, G, H
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: ORF
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GGX

Download Ideal Coordinates CCD File 
I [auth B],
J [auth C],
K [auth E],
L [auth H]
methyl [(1S)-1-{[(1R,3S,4S)-4-{[(2S)-3,3-dimethyl-2-{3-[(6-methylpyridin-2-yl)methyl]-2-oxo-2,3-dihydro-1H-imidazol-1-yl}butanoyl]amino}-3-hydroxy-5-phenyl-1-(4-pyridin-2-ylbenzyl)pentyl]carbamoyl}-2,2-dimethylpropyl]carbamate
C47 H59 N7 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.654α = 90
b = 195.569β = 91.19
c = 50.371γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2009-05-26 
  • Deposition Author(s): Stoll, V.S.

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance