1EBW

HIV-1 protease in complex with the inhibitor BEA322

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.191 

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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

  • DOI: 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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 PROTEASEA, B99Human immunodeficiency virus 1Mutation(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)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEI
Query on BEI
Download Ideal Coordinates CCD File 
C [auth A]N,N-[2,5-O-[DIBENZYL]-GLUCARYL]-DI-[ISOLEUCYL-AMIDO-METHANE]
C34 H50 N4 O8
GLKONBHDVMFJNJ-XAOMMOPXSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BEI Binding MOAD:  1EBW Ki: 0.9 (nM) from 1 assay(s)
PDBBind:  1EBW Ki: 0.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.04α = 90
b = 86.83β = 90
c = 46.98γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2000-01-25 
  • 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