HIV-1 protease in complex with the inhibitor BEA409

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors

Andersson, H.O.Fridborg, K.Lowgren, S.Alterman, M.Muhlman, A.Bjorsne, M.Garg, N.Kvarnstrom, I.Schaal, W.Classon, B.Karlen, A.Danielsson, U.H.Ahlsen, G.Nillroth, U.Vrang, L.Oberg, B.Samuelsson, B.Hallberg, A.Unge, T.

(2003) Eur J Biochem 270: 1746-1758

  • DOI: https://doi.org/10.1046/j.1432-1033.2003.03533.x
  • Primary Citation of Related Structures:  
    1D4H, 1D4I, 1D4J, 1EBW, 1EBY, 1EBZ, 1EC1, 1EC2, 1EC3

  • PubMed Abstract: 

    HIV-1 protease is an important target for treatment of AIDS, and efficient drugs have been developed. However, the resistance and negative side effects of the current drugs has necessitated the development of new compounds with different binding patterns. In this study, nine C-terminally duplicated HIV-1 protease inhibitors were cocrystallised with the enzyme, the crystal structures analysed at 1.8-2.3 A resolution, and the inhibitory activity of the compounds characterized in order to evaluate the effects of the individual modifications. These compounds comprise two central hydroxy groups that mimic the geminal hydroxy groups of a cleavage-reaction intermediate. One of the hydroxy groups is located between the delta-oxygen atoms of the two catalytic aspartic acid residues, and the other in the gauche position relative to the first. The asymmetric binding of the two central inhibitory hydroxyls induced a small deviation from exact C2 symmetry in the whole enzyme-inhibitor complex. The study shows that the protease molecule could accommodate its structure to different sizes of the P2/P2' groups. The structural alterations were, however, relatively conservative and limited. The binding capacity of the S3/S3' sites was exploited by elongation of the compounds with groups in the P3/P3' positions or by extension of the P1/P1' groups. Furthermore, water molecules were shown to be important binding links between the protease and the inhibitors. This study produced a number of inhibitors with Ki values in the 100 picomolar range.

  • Organizational Affiliation

    Institute of Cell and Molecular Biology, Uppsala University, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
EC: (PDB Primary Data), (UniProt), (UniProt), (UniProt), (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
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 BEE

Download Ideal Coordinates CCD File 
C40 H50 N4 O8 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
BEE Binding MOAD:  1EC1 Ki: 1.2 (nM) from 1 assay(s)
PDBBind:  1EC1 Ki: 1.2 (nM) from 1 assay(s)
BindingDB:  1EC1 Ki: min: 1.2, max: 1.2 (nM) from 2 assay(s)
Kd: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.12α = 90
b = 86.11β = 90
c = 46.11γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2002-06-26 
  • Deposition Author(s): Unge, T.

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance