HIV-1 protease in complex with an ethyleneamine inhibitor

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

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This is version 1.4 of the entry. See complete history


Role of hydroxyl group and R/S configuration of isostere in binding properties of HIV-1 protease inhibitors

Petrokova, H.Duskova, J.Dohnalek, J.Skalova, T.Vondrackova-Buchtelova, E.Soucek, M.Konvalinka, J.Brynda, J.Fabry, M.Sedlacek, J.Hasek, J.

(2004) Eur J Biochem 271: 4451-4461

  • DOI: https://doi.org/10.1111/j.1432-1033.2004.04384.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the complex between human immunodeficiency virus type 1 (HIV-1) protease and a peptidomimetic inhibitor of ethyleneamine type has been refined to R factor of 0.178 with diffraction limit 2.5 A. The peptidomimetic inhibitor Boc-Phe-Psi[CH2CH2NH]-Phe-Glu-Phe-NH2 (denoted here as OE) contains the ethyleneamine replacement of the scissile peptide bond. The inhibitor lacks the hydroxyl group which is believed to mimic tetrahedral transition state of proteolytic reaction and thus is suspected to be necessary for good properties of peptidomimetic HIV-1 protease inhibitors. Despite the missing hydroxyl group the inhibition constant of OE is 1.53 nm and it remains in the nanomolar range also towards several available mutants of HIV-1 protease. The inhibitor was found in the active site of protease in an extended conformation with a unique hydrogen bond pattern different from hydroxyethylene and hydroxyethylamine inhibitors. The isostere nitrogen forms a hydrogen bond to one catalytic aspartate only. The other aspartate forms two weak hydrogen bridges to the ethylene group of the isostere. A comparison with other inhibitors of this series containing isostere hydroxyl group in R or S configuration shows different ways of accommodation of inhibitor in the active site. Special attention is devoted to intermolecular contacts between neighbouring dimers responsible for mutual protein adhesion and for a special conformation of Met46 and Phe53 side chains not expected for free protein in water solution.

  • Organizational Affiliation

    Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Praha, Czech Republic. petrokova@imc.cas.cz

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03367
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0ZQ

Download Ideal Coordinates CCD File 
C [auth B]N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide
C38 H49 N5 O7
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
0ZQ BindingDB:  1M0B Ki: min: 1.5, max: 4.1 (nM) from 4 assay(s)
Binding MOAD:  1M0B Ki: 1.53 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.7α = 90
b = 62.7β = 90
c = 82.23γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations