3TOG

HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Monoclinic Crystal form P21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals.

Olajuyigbe, F.M.Demitri, N.De Zorzi, R.Geremia, S.

(2016) Molecules 21: --

  • DOI: 10.3390/molecules21111458
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protease inhibitors are key components in the chemotherapy of HIV infection. However, the appearance of viral mutants routinely compromises their clinical efficacy, creating a constant need for new and more potent inhibitors. Recently, a new class of ...

    Protease inhibitors are key components in the chemotherapy of HIV infection. However, the appearance of viral mutants routinely compromises their clinical efficacy, creating a constant need for new and more potent inhibitors. Recently, a new class of epoxide-based inhibitors of HIV-1 protease was investigated and the configuration of the epoxide carbons was demonstrated to play a crucial role in determining the binding affinity. Here we report the comparison between three crystal structures at near-atomic resolution of HIV-1 protease in complex with the epoxide-based inhibitor, revealing an in-situ epoxide ring opening triggered by a pH change in the mother solution of the crystal. Increased pH in the crystal allows a stereospecific nucleophile attack of an ammonia molecule onto an epoxide carbon, with formation of a new inhibitor containing amino-alcohol functions. The described experiments open a pathway for the development of new stereospecific protease inhibitors from a reactive lead compound.


    Organizational Affiliation

    Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, Basovizza, Trieste 34149, Italy. nicola.demitri@elettra.eu.,Department of Biochemistry, School of Sciences, Federal University of Technology Akure, P.M.B. 704, Akure 340252, Ondo State, Nigeria. folajuyi@futa.edu.ng.,Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste 34127, Italy. folajuyi@futa.edu.ng.,Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste 34127, Italy. nicola.demitri@elettra.eu.,Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste 34127, Italy. sgeremia@units.it.,Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste 34127, Italy. rdezorzi@units.it.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag-Pol polyprotein
A, B, C, D
99Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)Mutation(s): 5 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Go to UniProtKB:  P03367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
079
Query on 079

Download SDF File 
Download CCD File 
A, D
(S)-N-((2S,3S,4R,5R)-4-amino-3,5-dihydroxy-1,6-diphenylhexan-2-yl)-3-methyl-2-(2-phenoxyacetamido)butanamide
C31 H39 N3 O5
ASWZRLFSSZUWDR-UZMSACSVSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001019 (079)
Query on PRD_001019
A,D(S)-N-((2S,3S,4R,5R)-4-AMINO-3,5-DIHYDROXY-1,6-DIPHENYLHEXAN-2-YL)-3-METHYL-2-(2-PHENOXYACETAMIDO)BUTANAMIDEPeptide-like / Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.191α = 90.00
b = 62.136β = 98.73
c = 58.751γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Other
  • Version 1.2: 2014-10-29
    Type: Structure summary
  • Version 1.3: 2017-11-08
    Type: Refinement description
  • Version 1.4: 2019-03-20
    Type: Data collection, Database references