Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.25 kDa 
• Atom Count: 1677 
• Residue Count: 198 
• Unique protein chains: 1

1EBW

HIV-1 protease in complex with the inhibitor BEA322

• DOI: 10.2210/pdb1EBW/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 12694187 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 PROTEASE	A, B	99	Human immunodeficiency virus 1	Mutation(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)) Go to UniProtKB:  P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEI	A	N,N-[2,5-O-[DIBENZYL]-GLUCARYL]-DI-[ISOLEUCYL-AMIDO-METHANE] C34 H50 N4 O8 GLKONBHDVMFJNJ-XAOMMOPXSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BEI	Ki:  0.8999999761581421   nM  Binding MOAD
BEI	Ki :  0.8999999761581421   nM  PDBBind

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 = 59.04	α = 90
b = 86.83	β = 90
c = 46.98	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
CNS	refinement
X-PLOR	phasing

Structure Validation

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance