3S56

HIV-1 protease triple mutants V32I, I47V, V82I with antiviral drug saquinavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Critical differences in HIV-1 and HIV-2 protease specificity for clinical inhibitors.

Tie, Y.Wang, Y.F.Boross, P.I.Chiu, T.Y.Ghosh, A.K.Tozser, J.Louis, J.M.Harrison, R.W.Weber, I.T.

(2012) Protein Sci 21: 339-350

  • DOI: 10.1002/pro.2019
  • Primary Citation of Related Structures:  
    3S43, 3S45, 3S53, 3S54, 3S56

  • PubMed Abstract: 
  • Clinical inhibitor amprenavir (APV) is less effective on HIV-2 protease (PR₂) than on HIV-1 protease (PR₁). We solved the crystal structure of PR₂ with APV at 1.5 Å resolution to identify structural changes associated with the lowered inhibition. Furthermore, we analyzed the PR₁ mutant (PR(1M) ) with substitutions V32I, I47V, and V82I that mimic the inhibitor binding site of PR₂ ...

    Clinical inhibitor amprenavir (APV) is less effective on HIV-2 protease (PR₂) than on HIV-1 protease (PR₁). We solved the crystal structure of PR₂ with APV at 1.5 Å resolution to identify structural changes associated with the lowered inhibition. Furthermore, we analyzed the PR₁ mutant (PR(1M) ) with substitutions V32I, I47V, and V82I that mimic the inhibitor binding site of PR₂. PR(1M) more closely resembled PR₂ than PR₁ in catalytic efficiency on four substrate peptides and inhibition by APV, whereas few differences were seen for two other substrates and inhibition by saquinavir (SQV) and darunavir (DRV). High resolution crystal structures of PR(1M) with APV, DRV, and SQV were compared with available PR₁ and PR₂ complexes. Val/Ile32 and Ile/Val47 showed compensating interactions with SQV in PR(1M) and PR₁, however, Ile82 interacted with a second SQV bound in an extension of the active site cavity of PR(1M). Residues 32 and 82 maintained similar interactions with DRV and APV in all the enzymes, whereas Val47 and Ile47 had opposing effects in the two subunits. Significantly diminished interactions were seen for the aniline of APV bound in PR₁ (M) and PR₂ relative to the strong hydrogen bonds observed in PR₁, consistent with 15- and 19-fold weaker inhibition, respectively. Overall, PR(1M) partially replicates the specificity of PR₂ and gives insight into drug resistant mutations at residues 32, 47, and 82. Moreover, this analysis provides a structural explanation for the weaker antiviral effects of APV on HIV-2.


    Organizational Affiliation

    Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseA, B99Human immunodeficiency virus 1Mutation(s): 8 
Gene Names: pol
EC: 3.4.23.16
UniProt
Find proteins for Q7SSI0 (Human immunodeficiency virus 1)
Explore Q7SSI0 
Go to UniProtKB:  Q7SSI0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROC (Subject of Investigation/LOI)
Query on ROC

Download Ideal Coordinates CCD File 
C [auth A], D [auth B](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
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ROC Binding MOAD:  3S56 Ki: 0.24 (nM) from 1 assay(s)
BindingDB:  3S56 Ki: min: 0.04, max: 138 (nM) from 25 assay(s)
Kd: min: 0.31, max: 67 (nM) from 6 assay(s)
IC50: min: 0.2, max: 270 (nM) from 16 assay(s)
-TΔS: min: -8.03e+1, max: -2.80e+1 (kJ/mol) from 42 assay(s)
ΔH: min: -3.18e+1, max: 43.47 (kJ/mol) from 43 assay(s)
ΔG: min: -6.23e+1, max: -3.55e+1 (kJ/mol) from 39 assay(s)
PDBBind:  3S56 Ki: 0.24 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000454 (ROC)
Query on PRD_000454
C [auth A], D [auth B]SaquinavirPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.203α = 90
b = 67.416β = 90
c = 92.751γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Other