HIV-1 Protease NL4-3 V82F, I84V Mutant in complex with darunavir

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance.

Henes, M.Lockbaum, G.J.Kosovrasti, K.Leidner, F.Nachum, G.S.Nalivaika, E.A.Lee, S.K.Spielvogel, E.Zhou, S.Swanstrom, R.Bolon, D.N.A.Kurt Yilmaz, N.Schiffer, C.A.

(2019) ACS Chem Biol 14: 2441-2452

  • DOI: https://doi.org/10.1021/acschembio.9b00370
  • Primary Citation of Related Structures:  
    6OPS, 6OPT, 6OPU, 6OPV, 6OPW, 6OPX, 6OPY, 6OPZ

  • PubMed Abstract: 

    Drug resistance continues to be a growing global problem. The efficacy of small molecule inhibitors is threatened by pools of genetic diversity in all systems, including antibacterials, antifungals, cancer therapeutics, and antivirals. Resistant variants often include combinations of active site mutations and distal "secondary" mutations, which are thought to compensate for losses in enzymatic activity. HIV-1 protease is the ideal model system to investigate these combinations and underlying molecular mechanisms of resistance. Darunavir (DRV) binds wild-type (WT) HIV-1 protease with a potency of <5 pM, but we have identified a protease variant that loses potency to DRV 150 000-fold, with 11 mutations in and outside the active site. To elucidate the roles of these mutations in DRV resistance, we used a multidisciplinary approach, combining enzymatic assays, crystallography, and molecular dynamics simulations. Analysis of protease variants with 1, 2, 4, 8, 9, 10, and 11 mutations showed that the primary active site mutations caused ∼50-fold loss in potency (2 mutations), while distal mutations outside the active site further decreased DRV potency from 13 nM (8 mutations) to 0.76 μM (11 mutations). Crystal structures and simulations revealed that distal mutations induce subtle changes that are dynamically propagated through the protease. Our results reveal that changes remote from the active site directly and dramatically impact the potency of the inhibitor. Moreover, we find interdependent effects of mutations in conferring high levels of resistance. These mechanisms of resistance are likely applicable to many other quickly evolving drug targets, and the insights may have implications for the design of more robust inhibitors.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease NL4-3A [auth B],
B [auth A]
99Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: pol
Find proteins for Q7ZCI0 (Human immunodeficiency virus 1)
Explore Q7ZCI0 
Go to UniProtKB:  Q7ZCI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZCI0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
017 (Subject of Investigation/LOI)
Query on 017

Download Ideal Coordinates CCD File 
C27 H37 N3 O7 S
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
017 BindingDB:  6OPT Ki: min: 2.00e-4, max: 2 (nM) from 30 assay(s)
Kd: 0.02 (nM) from 1 assay(s)
IC50: min: 0.06, max: 370 (nM) from 11 assay(s)
EC50: min: 0.15, max: 112 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.774α = 90
b = 57.852β = 90
c = 61.543γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
Cootmodel building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01-GM109767

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary