The Influence of I47A Mutation on Reduced Susceptibility to the Protease Inhibitor Lopinavir

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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Enzymatic and structural analysis of the I47A mutation contributing to the reduced susceptibility to HIV protease inhibitor lopinavir.

Saskova, K.G.Kozisek, M.Lepsik, M.Brynda, J.Rezacova, P.Vaclavikova, J.Kagan, R.M.Machala, L.Konvalinka, J.

(2008) Protein Sci 17: 1555-1564

  • DOI: https://doi.org/10.1110/ps.036079.108
  • Primary Citation of Related Structures:  
    2QHC, 2Z54

  • PubMed Abstract: 

    Lopinavir (LPV) is a second-generation HIV protease inhibitor (PI) designed to overcome resistance development in patients undergoing long-term antiviral therapy. The mutation of isoleucine at position 47 of the HIV protease (PR) to alanine is associated with a high level of resistance to LPV. In this study, we show that recombinant PR containing a single I47A substitution has the inhibition constant (K(i) ) value for lopinavir by two orders of magnitude higher than for the wild-type PR. The addition of the I47A substitution to the background of a multiply mutated PR species from an AIDS patient showed a three-order-of-magnitude increase in K(i) in vitro relative to the patient PR without the I47A mutation. The crystal structure of I47A PR in complex with LPV showed the loss of van der Waals interactions in the S2/S2' subsites. This is caused by the loss of three side-chain methyl groups due to the I47A substitution and by structural changes in the A47 main chain that lead to structural changes in the flap antiparallel beta-strand. Furthermore, we analyzed possible interaction of the I47A mutation with secondary mutations V32I and I54V. We show that both mutations in combination with I47A synergistically increase the relative resistance to LPV in vitro. The crystal structure of the I47A/I54V PR double mutant in complex with LPV shows that the I54V mutation leads to a compaction of the flap, and molecular modeling suggests that the introduction of the I54V mutation indirectly affects the strain of the bound inhibitor in the PR binding cleft.

  • Organizational Affiliation

    Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Protease
A, B
99Human immunodeficiency virus type 1 (BH5 ISOLATE)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5))
Explore P04587 
Go to UniProtKB:  P04587
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04587
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AB1

Download Ideal Coordinates CCD File 
C37 H48 N4 O5
Query on BME

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C2 H6 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
AB1 BindingDB:  2Z54 Ki: min: 5.00e-3, max: 16 (nM) from 7 assay(s)
Kd: 1.30e-3 (nM) from 1 assay(s)
IC50: min: 2.5, max: 25 (nM) from 2 assay(s)
EC50: 1160 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.254α = 90
b = 62.254β = 90
c = 82.15γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata 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: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-04-21
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2021-11-10
    Changes: Database references
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description