1D4I

HIV-1 protease in complex with the inhibitor BEA425


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.092 

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.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: 10.1046/j.1432-1033.2003.03533.x
  • Structures With Same Primary Citation

  • 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 PROTEASEA, B99Human immunodeficiency virusMutation(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 P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEG
Query on BEG

Download CCD File 
A
2,5-DIBENZYLOXY-3-HYDROXY-HEXANEDIOIC ACID BIS-[(2-HYDROXY-INDAN-1-YL)-AMIDE]
C38 H40 N2 O7
AHAVBKNGKPWROK-UMFPTGFGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BEGKi :  1.399999976158142   nM  PDBBind
BEGKi:  1.399999976158142   nM  Binding MOAD
BEGKi:  1.399999976158142   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.092 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.619α = 90
b = 86.315β = 90
c = 46.686γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1999-10-04 
  • 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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance