1M0B

HIV-1 protease in complex with an ethyleneamine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1111/j.1432-1033.2004.04384.x

  • 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 Bo ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASE RETROPEPSIN
A, B
99Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
0ZQ
Query on 0ZQ

Download SDF File 
Download CCD File 
B
N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide
C38 H49 N5 O7
CBWQRQVEXJTNOT-ZLESDFJESA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000383 (0ZQ)
Query on PRD_000383
BBOC-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2Peptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0ZQKi: 1.5 - 4.1 nM (100) BINDINGDB
0ZQKi: 1.53 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.178 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.700α = 90.00
b = 62.700β = 90.00
c = 82.230γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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