2XDE

Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention.

Blair, W.S.Pickford, C.Irving, S.L.Brown, D.G.Anderson, M.Bazin, R.Cao, J.Ciaramella, G.Isaacson, J.Jackson, L.Hunt, R.Kjerrstrom, A.Nieman, J.Patick, A.K.Perros, M.Scott, A.D.Whitby, K.Wu, H.Butler, S.L.

(2010) Plos Pathog. 6: E1220

  • DOI: 10.1371/journal.ppat.1001220

  • PubMed Abstract: 
  • Despite a high current standard of care in antiretroviral therapy for HIV, multidrug-resistant strains continue to emerge, underscoring the need for additional novel mechanism inhibitors that will offer expanded therapeutic options in the clinic. We ...

    Despite a high current standard of care in antiretroviral therapy for HIV, multidrug-resistant strains continue to emerge, underscoring the need for additional novel mechanism inhibitors that will offer expanded therapeutic options in the clinic. We report a new class of small molecule antiretroviral compounds that directly target HIV-1 capsid (CA) via a novel mechanism of action. The compounds exhibit potent antiviral activity against HIV-1 laboratory strains, clinical isolates, and HIV-2, and inhibit both early and late events in the viral replication cycle. We present mechanistic studies indicating that these early and late activities result from the compound affecting viral uncoating and assembly, respectively. We show that amino acid substitutions in the N-terminal domain of HIV-1 CA are sufficient to confer resistance to this class of compounds, identifying CA as the target in infected cells. A high-resolution co-crystal structure of the compound bound to HIV-1 CA reveals a novel binding pocket in the N-terminal domain of the protein. Our data demonstrate that broad-spectrum antiviral activity can be achieved by targeting this new binding site and reveal HIV CA as a tractable drug target for HIV therapy.


    Organizational Affiliation

    Pfizer Global Research and Development, La Jolla Laboratories, San Diego, California, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GAG POLYPROTEIN
A, B
145Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1B0
Query on 1B0

Download SDF File 
Download CCD File 
A, B
N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE
C27 H27 N3 O2
ACDFWSNAQWFRRF-VWLOTQADSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1B0Kd: 3420 nM BINDINGMOAD
1B0Kd: 3420 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.756α = 90.00
b = 71.035β = 90.41
c = 41.419γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references, Version format compliance
  • Version 2.0: 2019-05-22
    Type: Atomic model, Data collection, Other, Refinement description