2O4K

Crystal Structure of HIV-1 Protease (Q7K) in Complex with Atazanavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Unique thermodynamic response of tipranavir to human immunodeficiency virus type 1 protease drug resistance mutations.

Muzammil, S.Armstrong, A.A.Kang, L.W.Jakalian, A.Bonneau, P.R.Schmelmer, V.Amzel, L.M.Freire, E.

(2007) J Virol 81: 5144-5154

  • DOI: 10.1128/JVI.02706-06
  • Primary Citation of Related Structures:  
    2O4N, 2O4L, 2O4K, 2O4S, 2O4P

  • PubMed Abstract: 
  • Drug resistance is a major problem affecting the clinical efficacy of antiretroviral agents, including protease inhibitors, in the treatment of infection with human immunodeficiency virus type 1 (HIV-1)/AIDS. Consequently, the elucidation of the mech ...

    Drug resistance is a major problem affecting the clinical efficacy of antiretroviral agents, including protease inhibitors, in the treatment of infection with human immunodeficiency virus type 1 (HIV-1)/AIDS. Consequently, the elucidation of the mechanisms by which HIV-1 protease inhibitors maintain antiviral activity in the presence of mutations is critical to the development of superior inhibitors. Tipranavir, a nonpeptidic HIV-1 protease inhibitor, has been recently approved for the treatment of HIV infection. Tipranavir inhibits wild-type protease with high potency (K(i) = 19 pM) and demonstrates durable efficacy in the treatment of patients infected with HIV-1 strains containing multiple common mutations associated with resistance. The high potency of tipranavir results from a very large favorable entropy change (-TDeltaS = -14.6 kcal/mol) combined with a favorable, albeit small, enthalpy change (DeltaH = -0.7 kcal/mol, 25 degrees C). Characterization of tipranavir binding to wild-type protease, active site mutants I50V and V82F/I84V, the multidrug-resistant mutant L10I/L33I/M46I/I54V/L63I/V82A/I84V/L90M, and the tipranavir in vitro-selected mutant I13V/V32L/L33F/K45I/V82L/I84V was performed by isothermal titration calorimetry and crystallography. Thermodynamically, the good response of tipranavir arises from a unique behavior: it compensates for entropic losses by actual enthalpic gains or by sustaining minimal enthalpic losses when facing the mutants. The net result is a small loss in binding affinity. Structurally, tipranavir establishes a very strong hydrogen bond network with invariant regions of the protease, which is maintained with the mutants, including catalytic Asp25 and the backbone of Asp29, Asp30, Gly48 and Ile50. Moreover, tipranavir forms hydrogen bonds directly to Ile50, while all other inhibitors do so by being mediated by a water molecule.


    Organizational Affiliation

    Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
proteaseAB99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: gag-pol
EC: 3.4.23.16 (UniProt), 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 P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Find proteins for Q903J0 (Human immunodeficiency virus 1)
Explore Q903J0 
Go to UniProtKB:  Q903J0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 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
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DR7Ki:  0.5   nM  BindingDB
DR7Ki:  0.33000001311302185   nM  BindingDB
DR7Kd :  0.03500000014901161   nM  PDBBind
DR7Ki:  0.699999988079071   nM  BindingDB
DR7Ki:  50   nM  BindingDB
DR7Ki:  1.100000023841858   nM  BindingDB
DR7Ki:  0.009999999776482582   nM  BindingDB
DR7Ki:  0.47999998927116394   nM  BindingDB
DR7Ki:  0.5600000023841858   nM  BindingDB
DR7Ki:  0.49000000953674316   nM  BindingDB
DR7Ki:  2.700000047683716   nM  BindingDB
DR7Ki:  0.23999999463558197   nM  BindingDB
DR7Ki:  0.5699999928474426   nM  BindingDB
DR7IC50:  0.03999999910593033   nM  BindingDB
DR7EC50:  0.699999988079071   nM  BindingDB
DR7IC50:  40   nM  BindingDB
DR7IC50:  4   nM  BindingDB
DR7Kd:  0.03500000014901161   nM  Binding MOAD
DR7Ki:  0.019999999552965164   nM  BindingDB
DR7Ki:  0.23999999463558197   nM  BindingDB
DR7Kd:  0.4000000059604645   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.741α = 90
b = 85.805β = 90
c = 46.242γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    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
  • Version 1.3: 2017-10-18
    Changes: Refinement description