4YHQ

Crystal structure of multidrug resistant clinical isolate PR20 with GRL-5010A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Substituted Bis-THF Protease Inhibitors with Improved Potency against Highly Resistant Mature HIV-1 Protease PR20.

Agniswamy, J.Louis, J.M.Shen, C.H.Yashchuk, S.Ghosh, A.K.Weber, I.T.

(2015) J Med Chem 58: 5088-5095

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00474
  • Primary Citation of Related Structures:  
    4YE3, 4YHQ

  • PubMed Abstract: 

    An extremely drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with two potent antiviral investigational inhibitors. GRL-5010A and GRL-4410A were designed to introduce hydrogen bond interactions with the flexible flaps of the PR by incorporating gem-difluorines and alkoxy, respectively, at the C4 position of the bis-THF of darunavir. PR20 provides an excellent model for high level resistance, since clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme. GRL-5010A and GRL-4410A show inhibition constants of 4.3 ± 7.0 and 1.7 ± 1.8 nM, respectively, for PR20, compared to the binding affinity of 41 ± 1 nM measured for darunavir. Crystal structures of PR20 in complexes with the two inhibitors confirmed the new hydrogen bond interactions with Gly 48 in the flap of the enzyme. The two new compounds are more effective than darunavir in inhibiting mature PR20 and show promise for further development of antiviral agents targeting highly resistant PR mutants.


  • Organizational Affiliation

    †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease
A, B
99Human immunodeficiency virus type 1 BH10Mutation(s): 22 
Gene Names: gag-pol
EC: 3.4.23.16
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G10
Query on G10

Download Ideal Coordinates CCD File 
C [auth A](3R,3aS,6aS)-4,4-difluorohexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[(4-aminophenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate
C27 H35 F2 N3 O7 S
UQYAKJSDOQPRAX-YCXOGWGTSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Y1
Query on Y1

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
K [auth B],
L [auth B]
YTTRIUM ION
Y
KAJPZYFHSCFBCI-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
G10 Binding MOAD:  4YHQ Ki: 1.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.303α = 90
b = 60.303β = 90
c = 86.141γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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 StatesGM062920
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM053386

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Database references
  • Version 2.0: 2018-12-05
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2022-03-23
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 2.2: 2023-09-27
    Changes: Data collection, Refinement description