2NMY

Crystal structure analysis of HIV-1 protease mutant V82A with a inhibitor saquinavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir.

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

(2007) Proteins 67: 232-242

  • DOI: 10.1002/prot.21304
  • Primary Citation of Related Structures:  
    2NMY, 2NMZ, 2NNK, 2NNP, 3OXC

  • PubMed Abstract: 
  • Saquinavir (SQV), the first antiviral HIV-1 protease (PR) inhibitor approved for AIDS therapy, has been studied in complexes with PR and the variants PR(I) (84V) and PR(V) (82A) containing the single mutations I84V and V82A that provide resistance to all the clinical inhibitors ...

    Saquinavir (SQV), the first antiviral HIV-1 protease (PR) inhibitor approved for AIDS therapy, has been studied in complexes with PR and the variants PR(I) (84V) and PR(V) (82A) containing the single mutations I84V and V82A that provide resistance to all the clinical inhibitors. Atomic resolution crystal structures (0.97-1.25 A) of the SQV complexes were analyzed in comparison to the protease complexes with darunavir, a new drug that targets resistant HIV, in order to understand the molecular basis of drug resistance. PR(I) (84V) and PR(V) (82A) complexes were obtained in both the space groups P2(1)2(1)2 and P2(1)2(1)2(1), which provided experimental limits for the conformational flexibility. The SQV interactions with PR were very similar in the mutant complexes, consistent with the similar inhibition constants. The mutation from bigger to smaller amino acids allows more space to accommodate the large group at P1' of SQV, unlike the reduced interactions observed in darunavir complexes. The residues 79-82 have adjusted to accommodate the large hydrophobic groups of SQV, suggesting that these residues are intrinsically flexible and their conformation depends more on the nature of the inhibitor than on the mutations in this region. This analysis will assist with development of more effective antiviral inhibitors.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASEA, B99Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: gagpol
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROC (Subject of Investigation/LOI)
Query on ROC

Download Ideal Coordinates CCD File 
F [auth A](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
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
C [auth A], G [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ROC BindingDB:  2NMY Ki: min: 0.04, max: 138 (nM) from 29 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 46 assay(s)
ΔH: min: -3.18e+1, max: 43.47 (kJ/mol) from 48 assay(s)
ΔG: min: -6.23e+1, max: -3.55e+1 (kJ/mol) from 41 assay(s)
PDBBind:  2NMY Ki: 4.3 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000454 (ROC)
Query on PRD_000454
F [auth A]SaquinavirPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.988α = 90
b = 87.464β = 90
c = 47.19γ = 90
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
HKL-2000data collection
MAR345data collection
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: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary