2FXE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    2FXE, 2FXD

  • 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 commo ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
pol proteinAB99Human immunodeficiency virus 1Mutation(s): 9 
Gene Names: POL
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P05959 (Human immunodeficiency virus type 1 group M subtype B (isolate RF/HAT3))
Explore P05959 
Go to UniProtKB:  P05959
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DR7
Query on DR7

Download CCD File 
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 CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DR7Ki:  0.009999999776482582   nM  BindingDB
DR7Ki:  2.700000047683716   nM  BindingDB
DR7Ki:  0.33000001311302185   nM  BindingDB
DR7Ki:  0.49000000953674316   nM  BindingDB
DR7Ki:  0.47999998927116394   nM  BindingDB
DR7IC50:  0.03999999910593033   nM  BindingDB
DR7IC50:  40   nM  BindingDB
DR7Ki:  50   nM  BindingDB
DR7Ki:  0.23999999463558197   nM  BindingDB
DR7Ki:  0.5   nM  BindingDB
DR7Ki:  0.699999988079071   nM  BindingDB
DR7Ki:  0.5600000023841858   nM  BindingDB
DR7Kd:  0.4000000059604645   nM  BindingDB
DR7Ki:  1.100000023841858   nM  BindingDB
DR7IC50:  4   nM  BindingDB
DR7Ki:  0.019999999552965164   nM  BindingDB
DR7EC50:  0.699999988079071   nM  BindingDB
DR7Ki:  0.5699999928474426   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.186α = 90
b = 58.207β = 90
c = 61.285γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
CNXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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: Non-polymer description, Version format compliance