6DJ2

HIV-1 protease with single mutation L76V in complex with Lopinavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.196 
  • R-Value Observed: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease.

Wong-Sam, A.Wang, Y.F.Zhang, Y.Ghosh, A.K.Harrison, R.W.Weber, I.T.

(2018) ACS Omega 3: 12132-12140

  • DOI: 10.1021/acsomega.8b01683
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Four HIV-1 protease (PR) inhibitors, clinical inhibitors lopinavir and tipranavir, and two investigational compounds 4 and 5 , were studied for their effect on the structure and activity of PR with drug-resistant mutation L76V (PR

    Four HIV-1 protease (PR) inhibitors, clinical inhibitors lopinavir and tipranavir, and two investigational compounds 4 and 5 , were studied for their effect on the structure and activity of PR with drug-resistant mutation L76V (PR L76V ). Compound 5 exhibited the best K i value of 1.9 nM for PR L76V , whereas the other three inhibitors had K i values of 4.5-7.6 nM, 2-3 orders of magnitude worse than for wild-type enzymes. Crystal structures showed only minor differences in interactions of inhibitors with PR L76V compared to wild-type complexes. The shorter side chain of Val76 in the mutant lost hydrophobic interactions with Lys45 and Ile47 in the flap, and with Asp30 and Thr74 in the protein core, consistent with decreased stability. Inhibitors forming additional polar interactions with the flaps or dimer interface of PR L76V were unable to compensate for the decrease in internal hydrophobic contacts. These structures provide insights for inhibitor design.


    Organizational Affiliation

    Department of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 proteaseA, B99Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: 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 P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AB1
Query on AB1

Download CCD File 
B
N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE
C37 H48 N4 O5
KJHKTHWMRKYKJE-SUGCFTRWSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AB1Ki:  4.5   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.196 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.011α = 90
b = 85.377β = 90
c = 46.43γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM062920

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence