4Q5M

D30N tethered HIV-1 protease dimer/saquinavir complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


This is version 1.3 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.L.Hosur, M.V.

(2015) Chem Biol Drug Des 86: 302-308

  • DOI: https://doi.org/10.1111/cbdd.12494
  • Primary Citation of Related Structures:  
    4Q5M

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease203HIV-1 M:B_HXB2RMutation(s): 4 
Gene Names: gag-pol
EC: 3.4.23.16
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ROC
Query on ROC

Download Ideal Coordinates CCD File 
B [auth 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
C38 H50 N6 O5
QWAXKHKRTORLEM-UGJKXSETSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ROC BindingDB:  4Q5M Ki: min: 0.04, max: 117 (nM) from 16 assay(s)
Kd: min: 0.31, max: 67 (nM) from 3 assay(s)
IC50: min: 0.2, max: 270 (nM) from 16 assay(s)
-TΔS: min: -7.74e+1, max: -2.80e+1 (kJ/mol) from 28 assay(s)
ΔH: min: -3.18e+1, max: 35.53 (kJ/mol) from 27 assay(s)
ΔG: min: -6.23e+1, max: -4.18e+1 (kJ/mol) from 26 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.84α = 90
b = 62.84β = 90
c = 82.49γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Source and taxonomy
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description