4Q5M

D30N tethered HIV-1 protease dimer/saquinavir complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.795 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Why Nelfinavir-Resistant D30N Mutant of HIV-1 Protease Remains Susceptible to Saquinavir.

Prashar, V.Bihani, S.C.Ferrer, J.Hosur, M.V.

(2014) Chem.Biol.Drug Des. --: --

  • DOI: 10.1111/cbdd.12494

  • PubMed Abstract: 
  • Although anti-HIV-1 protease drugs nelfinavir (NFV) and saquinavir (SQV) share common functional groups, D30N is a major resistance mutation against NFV but remains susceptible to SQV. We have determined the crystal structure of D30N mutant-tethered ...

    Although anti-HIV-1 protease drugs nelfinavir (NFV) and saquinavir (SQV) share common functional groups, D30N is a major resistance mutation against NFV but remains susceptible to SQV. We have determined the crystal structure of D30N mutant-tethered HIV-1 protease in complex with SQV to 1.79 Å resolution. Structural analysis showed that SQV forms two direct hydrogen bonds with the main chain atoms of the residues Asp29 and Asp30 that are not observed in the D30N-NFV complex. Apart from maintaining these two main chain hydrogen bonds, the P2-asparagine of SQV forms an additional hydrogen bond to the mutated side chain of the residue 30. These could be the reasons why D30N is not a drug resistance mutation against SQV. This structure supports the previous studies showing that the interactions between a potential inhibitor and backbone atoms of the enzyme are important to maintain potency against drug-resistant HIV-1 protease.


    Organizational Affiliation

    Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India.,Institut de Biologie Structurale Jean-Pierre Ebel, Groupe Synchrotron, Commissariat a l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Universite de Grenoble Alpes, Grenoble, 38027, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A
203Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 4 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROC
Query on ROC

Download SDF File 
Download CCD File 
A
(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1-phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide
Fortovase; SAQUINAVIR,RO 31-8959
C38 H50 N6 O5
QWAXKHKRTORLEM-UGJKXSETSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000454 (ROC)
Query on PRD_000454
ASaquinavirPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.795 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.840α = 90.00
b = 62.840β = 90.00
c = 82.490γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
ADSCdata collection
PHENIXmodel building
PHENIXphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Source and taxonomy