3EC0

High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-06579A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease

Kovalevsky, A.Y.Louis, J.M.Aniana, A.Ghosh, A.K.Weber, I.T.

(2008) J Mol Biol 384: 178-192

  • DOI: https://doi.org/10.1016/j.jmb.2008.09.031
  • Primary Citation of Related Structures:  
    3EBZ, 3EC0, 3ECG

  • PubMed Abstract: 

    No drug has been targeted specifically for HIV-2 (human immunodeficiency virus type 2) infection despite its increasing prevalence worldwide. The antiviral HIV-1 (human immunodeficiency virus type 1) protease (PR) inhibitor darunavir and the chemically related GRL98065 and GRL06579A were designed with the same chemical scaffold and different substituents at P2 and P2' to optimize polar interactions for HIV-1 PR (PR1). These inhibitors are also effective antiviral agents for HIV-2-infected cells. Therefore, crystal structures of HIV-2 PR (PR2) complexes with the three inhibitors have been solved at 1.2-A resolution to analyze the molecular basis for their antiviral potency. Unusually, the crystals were grown in imidazole and zinc acetate buffer, which formed interactions with the PR2 and the inhibitors. Overall, the structures were very similar to the corresponding inhibitor complexes of PR1 with an RMSD of 1.1 A on main-chain atoms. Most hydrogen-bond and weaker C-H...O interactions with inhibitors were conserved in the PR2 and PR1 complexes, except for small changes in interactions with water or disordered side chains. Small differences were observed in the hydrophobic contacts for the darunavir complexes, in agreement with relative inhibition of the two PRs. These near-atomic-resolution crystal structures verify the inhibitor potency for PR1 and PR2 and will provide the basis for the development of antiviral inhibitors targeting PR2.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease
A, B
99Human immunodeficiency virus type 2 (ISOLATE ROD)Mutation(s): 0 
EC: 3.4.23.47
UniProt
Find proteins for P04584 (Human immunodeficiency virus type 2 subtype A (isolate ROD))
Explore P04584 
Go to UniProtKB:  P04584
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04584
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GRL
Query on GRL

Download Ideal Coordinates CCD File 
C [auth A](3AS,5R,6AR)-HEXAHYDRO-2H-CYCLOPENTA[B]FURAN-5-YL (2S,3S)-3-HYDROXY-4-(4-(HYDROXYMETHYL)-N-ISOBUTYLPHENYLSULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE
C29 H40 N2 O7 S
VYBDPVQMILRSMK-GRXYLYAXSA-N
IMD
Query on IMD

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D [auth A]
E [auth A]
M [auth B]
N [auth B]
O [auth B]
D [auth A],
E [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
Q [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

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AA [auth B]
BA [auth B]
J [auth A]
K [auth A]
W [auth B]
AA [auth B],
BA [auth B],
J [auth A],
K [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.36α = 90
b = 30.913β = 91.79
c = 55.954γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description