2FXD

X-ray crystal structure of HIV-1 protease IRM mutant complexed with atazanavir (BMS-232632)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

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This is version 1.3 of the entry. See complete history


Literature

X-ray crystal structures of human immunodeficiency virus type 1 protease mutants complexed with atazanavir.

Klei, H.E.Kish, K.Lin, P.F.Guo, Q.Friborg, J.Rose, R.E.Zhang, Y.Goldfarb, V.Langley, D.R.Wittekind, M.Sheriff, S.

(2007) J Virol 81: 9525-9535

  • DOI: 10.1128/JVI.02503-05
  • Primary Citation of Related Structures:  
    2FXD, 2FXE

  • PubMed Abstract: 
  • Atazanavir, which is marketed as REYATAZ, is the first human immunodeficiency virus type 1 (HIV-1) protease inhibitor approved for once-daily administration. As previously reported, atazanavir offers improved inhibitory profiles against several common variants of HIV-1 protease over those of the other peptidomimetic inhibitors currently on the market ...

    Atazanavir, which is marketed as REYATAZ, is the first human immunodeficiency virus type 1 (HIV-1) protease inhibitor approved for once-daily administration. As previously reported, atazanavir offers improved inhibitory profiles against several common variants of HIV-1 protease over those of the other peptidomimetic inhibitors currently on the market. This work describes the X-ray crystal structures of complexes of atazanavir with two HIV-1 protease variants, namely, (i) an enzyme optimized for resistance to autolysis and oxidation, referred to as the cleavage-resistant mutant (CRM); and (ii) the M46I/V82F/I84V/L90M mutant of the CRM enzyme, which is resistant to all approved HIV-1 protease inhibitors, referred to as the inhibitor-resistant mutant. In these two complexes, atazanavir adopts distinct bound conformations in response to the V82F substitution, which may explain why this substitution, at least in isolation, has yet to be selected in vitro or in the clinic. Because of its nearly symmetrical chemical structure, atazanavir is able to make several analogous contacts with each monomer of the biological dimer.


    Organizational Affiliation

    Macromolecular Crystallography, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA. herbert.klei@bms.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
pol proteinA, B99Human immunodeficiency virus 1Mutation(s): 13 
Gene Names: pol
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 3.1.26.13 (UniProt)
UniProt
Find proteins for Q90HG9 (Human immunodeficiency virus 1)
Explore Q90HG9 
Go to UniProtKB:  Q90HG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ90HG9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DR7
Query on DR7

Download Ideal Coordinates CCD File 
E [auth A](3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)-8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4-(2-PYRIDINYL)PHENYL]METHYL]-2,5, 6,10,13-PENTAAZATETRADECANEDIOIC ACID DIMETHYL ESTER
C38 H52 N6 O7
AXRYRYVKAWYZBR-GASGPIRDSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DR7 BindingDB:  2FXD Ki: min: 9.00e-3, max: 50 (nM) from 13 assay(s)
Kd: 0.4 (nM) from 1 assay(s)
IC50: min: 0.04, max: 40 (nM) from 4 assay(s)
EC50: 0.7 (nM) from 1 assay(s)
Binding MOAD:  2FXD IC50: 12 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.381α = 90
b = 58.214β = 90
c = 61.278γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
CNXrefinement
HKL-2000data 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: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary