Crystal Structure of the inhibitor Darunavir (DRV) in complex with a multi-drug resistant HIV-1 protease variant (L10F/G48V/I54V/V64I/V82A) (Refer: FLAP+ in citation.)

Experimental Data Snapshot

  • Resolution: 1.97 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.6 of the entry. See complete history


Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease.

King, N.M.Prabu-Jeyabalan, M.Bandaranayake, R.M.Nalam, M.N.Nalivaika, E.A.Ozen, A.Yilmaz, N.K.Schiffer, C.A.

(2012) ACS Chem Biol 7: 1536-1546

  • DOI: https://doi.org/10.1021/cb300191k
  • Primary Citation of Related Structures:  
    3EKP, 3EKQ, 3EKT, 3EKV, 3EKW, 3EKX, 3EKY, 3EL0, 3EL1, 3EL4, 3EL5, 3EL9

  • PubMed Abstract: 

    The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, profound changes are observed in the binding thermodynamics of a drug-resistant variant compared to wild-type HIV-1 protease, irrespective of the inhibitor bound. This variant (Flap+) has a combination of flap and active site mutations and exhibits extremely large entropy-enthalpy compensation compared to wild-type protease, 5-15 kcal/mol, while losing only 1-3 kcal/mol in total binding free energy for any of six FDA-approved inhibitors. Although entropy-enthalpy compensation has been previously observed for a variety of systems, never have changes of this magnitude been reported. The co-crystal structures of Flap+ protease with four of the inhibitors were determined and compared with complexes of both the wild-type protease and another drug-resistant variant that does not exhibit this energetic compensation. Structural changes conserved across the Flap+ complexes, which are more pronounced for the flaps covering the active site, likely contribute to the thermodynamic compensation. The finding that drug-resistant mutations can profoundly modulate the relative thermodynamic properties of a therapeutic target independent of the inhibitor presents a new challenge for rational drug design.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
99HIV-1 M:B_ARV2/SF2Mutation(s): 6 
Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03369 
Go to UniProtKB:  P03369
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03369
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 017

Download Ideal Coordinates CCD File 
G [auth B],
N [auth D]
C27 H37 N3 O7 S
Query on PO4

Download Ideal Coordinates CCD File 
I [auth C],
J [auth C],
K [auth C],
O [auth D],
P [auth D]
O4 P
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
L [auth C]
M [auth C]
E [auth A],
F [auth A],
H [auth B],
L [auth C],
M [auth C],
Q [auth D],
R [auth D],
S [auth D]
C2 H3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
017 BindingDB:  3EKT Ki: min: 2.00e-4, max: 2 (nM) from 16 assay(s)
Kd: 0.02 (nM) from 1 assay(s)
IC50: min: 0.06, max: 370 (nM) from 10 assay(s)
EC50: min: 0.25, max: 112 (nM) from 5 assay(s)
Binding MOAD:  3EKT Kd: 0.03 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.97 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.013α = 90
b = 92.013β = 90
c = 106.161γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2012-07-25
    Changes: Data collection, Database references
  • Version 1.3: 2012-10-17
    Changes: Database references
  • Version 1.4: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.5: 2021-10-20
    Changes: Advisory, Database references, Derived calculations, Structure summary
  • Version 1.6: 2024-02-21
    Changes: Data collection