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

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

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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: https://doi.org/10.1371/journal.ppat.1001220
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
145Human immunodeficiency virus 1Mutation(s): 0 
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1B0

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C27 H27 N3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
1B0 Binding MOAD:  2XDE Kd: 3420 (nM) from 1 assay(s)
PDBBind:  2XDE Kd: 3420 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.756α = 90
b = 71.035β = 90.41
c = 41.419γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata 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: 2010-12-22
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references, Version format compliance
  • Version 2.0: 2019-05-22
    Changes: Atomic model, Data collection, Other, Refinement description
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description