2QD8

HIV-1 Protease Mutant I84V with potent Antiviral inhibitor GRL-98065

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.130 

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This is version 1.3 of the entry. See complete history. 


Literature

Potent new antiviral compound shows similar inhibition and structural interactions with drug resistant mutants and wild type HIV-1 protease.

Wang, Y.F., Tie, Y., Boross, P.I., Tozser, J., Ghosh, A.K., Harrison, R.W., Weber, I.T.

(2007) J Med Chem 50: 4509-4515

  • DOI: 10.1021/jm070482q
  • Primary Citation of Related Structures:  
    2QCI, 2QD6, 2QD7, 2QD8, 2Z4O

  • PubMed Abstract: 

    • The potent new antiviral inhibitor GRL-98065 (1) of HIV-1 protease (PR) has been studied with PR variants containing the single mutations D30N, I50V, V82A, and I84V that provide resistance to the major clinical inhibitors. Compound 1 had inhibition constants of 17-fold, 8-fold, 3-fold, and 3-fold, respectively, for PR(D30N), PR(I50V), PR(V82A), and PR(I84V) relative to wild type PR ...

    The potent new antiviral inhibitor GRL-98065 (1) of HIV-1 protease (PR) has been studied with PR variants containing the single mutations D30N, I50V, V82A, and I84V that provide resistance to the major clinical inhibitors. Compound 1 had inhibition constants of 17-fold, 8-fold, 3-fold, and 3-fold, respectively, for PR(D30N), PR(I50V), PR(V82A), and PR(I84V) relative to wild type PR. The chemically related darunavir had similar relative inhibition, except for PR(D30N), where inhibitor 1 was approximately 3-fold less potent. The high resolution (1.11-1.60 Angstrom) crystal structures of PR mutant complexes with inhibitor 1 showed small changes relative to the wild type enzyme. PR(D30N) and PR(V82A) showed compensating interactions with inhibitor 1 relative to those of PR, while reduced hydrophobic contacts were observed with PR(I50V) and PR(I84V). Importantly, inhibitor 1 complexes showed fewer changes relative to wild type enzyme than reported for darunavir complexes. Therefore, inhibitor 1 is a valuable addition to the antiviral inhibitors with high potency against resistant strains of HIV.

    Organizational Affiliation: 

    Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseA, B99Human immunodeficiency virus 1Mutation(s): 6 
EC: 3.4.23.16 (PDB Primary Data), 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)
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
065 (Subject of Investigation/LOI)
Query on 065
Download Ideal Coordinates CCD File 
H [auth B](3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(2S,3R)-3-HYDROXY-4-(N-ISOBUTYLBENZO[D][1,3]DIOXOLE-5-SULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE
C28 H36 N2 O9 S
HNEIRZJZTYYDES-VPZBFSRCSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
F [auth B], G [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A], E [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
65 PDBBind:  2QD8 Ki: 0.85 (nM) from 1 assay(s)
065 BindingDB:  2QD8 Ki: min: 0.27, max: 14 (nM) from 2 assay(s)
Binding MOAD:  2QD8 Ki: 0.85 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.130 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.423α = 90
b = 86.182β = 90
c = 45.986γ = 90
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-09-13
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations, Structure summary