1EBZ

HIV-1 protease in complex with the inhibitor BEA388


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • Primary Citation of Related Structures:  

  • 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 patt ...

    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.




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
BEC
Query on BEC

Download SDF File 
Download CCD File 
B
[5-(2-HYDROXY-INDAN-1-YLCARBAMOYL)-3,4-DIHYDROXY-2,5-[DIBENZYL-OXY]-PENTANOYL]-VALINYL-AMIDO-METHANE
INHIBITOR BEA388
C35 H43 N3 O8
VZNNJZGVQVNHCM-CDNLURBZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BECKi: .4 nM (98) BINDINGDB
BECKi: 0.4 nM BINDINGMOAD
BECKi: 0.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.840α = 90.00
b = 86.660β = 90.00
c = 46.870γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
DENZOdata reduction
X-PLORmodel building
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-01-25 
  • Released Date: 2002-06-26 
  • Deposition Author(s): Unge, T.

Revision History 

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