4E91

Crystal Structure of the N-Terminal Domain of HIV-1 Capsid in Complex With Inhibitor BD3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Distinct Effects of Two HIV-1 Capsid Assembly Inhibitor Families That Bind the Same Site within the N-Terminal Domain of the Viral CA Protein.

Lemke, C.T.Titolo, S.von Schwedler, U.Goudreau, N.Mercier, J.F.Wardrop, E.Faucher, A.M.Coulombe, R.Banik, S.S.Fader, L.Gagnon, A.Kawai, S.H.Rancourt, J.Tremblay, M.Yoakim, C.Simoneau, B.Archambault, J.Sundquist, W.I.Mason, S.W.

(2012) J.Virol. 86: 6643-6655

  • DOI: 10.1128/JVI.00493-12
  • Primary Citation of Related Structures:  4E92

  • PubMed Abstract: 
  • The emergence of resistance to existing classes of antiretroviral drugs necessitates finding new HIV-1 targets for drug discovery. The viral capsid (CA) protein represents one such potential new target. CA is sufficient to form mature HIV-1 capsids i ...

    The emergence of resistance to existing classes of antiretroviral drugs necessitates finding new HIV-1 targets for drug discovery. The viral capsid (CA) protein represents one such potential new target. CA is sufficient to form mature HIV-1 capsids in vitro, and extensive structure-function and mutational analyses of CA have shown that the proper assembly, morphology, and stability of the mature capsid core are essential for the infectivity of HIV-1 virions. Here we describe the development of an in vitro capsid assembly assay based on the association of CA-NC subunits on immobilized oligonucleotides. This assay was used to screen a compound library, yielding several different families of compounds that inhibited capsid assembly. Optimization of two chemical series, termed the benzodiazepines (BD) and the benzimidazoles (BM), resulted in compounds with potent antiviral activity against wild-type and drug-resistant HIV-1. Nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic analyses showed that both series of inhibitors bound to the N-terminal domain of CA. These inhibitors induce the formation of a pocket that overlaps with the binding site for the previously reported CAP inhibitors but is expanded significantly by these new, more potent CA inhibitors. Virus release and electron microscopic (EM) studies showed that the BD compounds prevented virion release, whereas the BM compounds inhibited the formation of the mature capsid. Passage of virus in the presence of the inhibitors selected for resistance mutations that mapped to highly conserved residues surrounding the inhibitor binding pocket, but also to the C-terminal domain of CA. The resistance mutations selected by the two series differed, consistent with differences in their interactions within the pocket, and most also impaired virus replicative capacity. Resistance mutations had two modes of action, either directly impacting inhibitor binding affinity or apparently increasing the overall stability of the viral capsid without affecting inhibitor binding. These studies demonstrate that CA is a viable antiviral target and demonstrate that inhibitors that bind within the same site on CA can have distinct binding modes and mechanisms of action.


    Related Citations: 
    • A novel inhibitor-binding site on the HIV-1 capsid N-terminal domain leads to improved crystallization via compound-mediated dimerization.
      Lemke, C.T.,Titolo, S.,Goudreau, N.,Faucher, A.M.,Mason, S.W.,Bonneau, P.
      (2013) Acta Crystallogr.,Sect.D 69: 1115


    Organizational Affiliation

    Department of Chemistry, Research & Development, Laval, Quebec, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag protein
A, B
146Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12497
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0OE
Query on 0OE

Download SDF File 
Download CCD File 
A, B
4-{2-[5-(3-chlorophenyl)-1H-pyrazol-4-yl]-1-[3-(1H-imidazol-1-yl)propyl]-1H-benzimidazol-5-yl}benzoic acid
C29 H23 Cl N6 O2
LGXPZODGTPYYBU-UHFFFAOYSA-N
 Ligand Interaction
0OF
Query on 0OF

Download SDF File 
Download CCD File 
A
(3S)-1-ethyl-3-[3-hydroxy-5-(pyridin-3-yl)phenyl]-5-phenyl-7-(trifluoromethyl)-1H-1,5-benzodiazepine-2,4(3H,5H)-dione
C29 H22 F3 N3 O3
XKOABKQMKVLVHH-SANMLTNESA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.220 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.783α = 90.00
b = 65.783β = 90.00
c = 143.323γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
MAR345dtbdata collection
PHENIXphasing
HKL-2000data scaling
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-20 
  • Released Date: 2012-04-25 
  • Deposition Author(s): Lemke, C.T.

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-06-06
    Type: Database references
  • Version 1.2: 2013-06-12
    Type: Database references