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

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    2XDE

  • 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GAG POLYPROTEINA, B145Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16 (UniProt), 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 P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1B0 (Subject of Investigation/LOI)
Query on 1B0

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE
C27 H27 N3 O2
ACDFWSNAQWFRRF-VWLOTQADSA-N
 Ligand Interaction
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

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

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