2AQU

Structure of HIV-1 protease bound to atazanavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Analysis of HIV-1 CRF_01 A/E protease inhibitor resistance: structural determinants for maintaining sensitivity and developing resistance to atazanavir.

Clemente, J.C.Coman, R.M.Thiaville, M.M.Janka, L.K.Jeung, J.A.Nukoolkarn, S.Govindasamy, L.Agbandje-McKenna, M.McKenna, R.Leelamanit, W.Goodenow, M.M.Dunn, B.M.

(2006) Biochemistry 45: 5468-5477

  • DOI: 10.1021/bi051886s
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A series of HIV-1 protease mutants has been designed in an effort to analyze the contribution to drug resistance provided by natural polymorphisms as well as therapy-selective (active and non-active site) mutations in the HIV-1 CRF_01 A/E (AE) protea ...

    A series of HIV-1 protease mutants has been designed in an effort to analyze the contribution to drug resistance provided by natural polymorphisms as well as therapy-selective (active and non-active site) mutations in the HIV-1 CRF_01 A/E (AE) protease when compared to that of the subtype B (B) protease. Kinetic analysis of these variants using chromogenic substrates showed differences in substrate specificity between pretherapy B and AE proteases. Inhibition analysis with ritonavir, indinavir, nelfinavir, amprenavir, saquinavir, lopinavir, and atazanavir revealed that the natural polymorphisms found in A/E can influence inhibitor resistance. It was also apparent that a high level of resistance in the A/E protease, as with B protease, is due to it aquiring a combination of active site and non-active site mutations. Structural analysis of atazanavir bound to a pretherapy B protease showed that the ability of atazanavir to maintain its binding affinity for variants containing some resistance mutations is due to its unique interactions with flap residues. This structure also explains why the I50L and I84V mutations are important in decreasing the binding affinity of atazanavir.


    Organizational Affiliation

    Johnson & Johnson Pharmaceutical Research & Development, LLC, 665 Stockton Drive, Exton, Pennsylvania 19341, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
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 P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DR7
Query on DR7

Download CCD File 
B
(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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DR7Ki:  0.49000000953674316   nM  BindingDB
DR7Ki:  0.23999999463558197   nM  BindingDB
DR7Ki:  0.5600000023841858   nM  BindingDB
DR7Kd:  0.4000000059604645   nM  BindingDB
DR7Ki:  0.5699999928474426   nM  BindingDB
DR7IC50:  0.03999999910593033   nM  BindingDB
DR7Ki :  0.47999998927116394   nM  PDBBind
DR7Ki:  0.699999988079071   nM  BindingDB
DR7Ki:  0.33000001311302185   nM  BindingDB
DR7Ki:  1.100000023841858   nM  BindingDB
DR7Ki:  0.23999999463558197   nM  BindingDB
DR7Ki:  0.47999998927116394   nM  BindingDB
DR7Ki:  0.47999998927116394   nM  Binding MOAD
DR7Ki:  0.009999999776482582   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.411α = 90
b = 62.411β = 90
c = 82.569γ = 120
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance