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

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.231 

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Monitoring Binding of HIV-1 Capsid Assembly Inhibitors Using (19) F Ligand-and (15) N Protein-Based NMR and X-ray Crystallography: Early Hit Validation of a Benzodiazepine Series.

Goudreau, N.Coulombe, R.Faucher, A.M.Grand-Maitre, C.Lacoste, J.E.Lemke, C.T.Malenfant, E.Bousquet, Y.Fader, L.Simoneau, B.Mercier, J.F.Titolo, S.Mason, S.W.

(2013) ChemMedChem 8: 405-414

  • DOI: https://doi.org/10.1002/cmdc.201200580
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The emergence of resistance to existing classes of antiretroviral drugs underlines the need to find novel human immunodeficiency virus (HIV)-1 targets for drug discovery. The viral capsid protein (CA) represents one such potential target. Recently, a series of benzodiazepine inhibitors was identified via high-throughput screening using an in vitro capsid assembly assay (CAA). Here, we demonstrate how a combination of NMR and X-ray co-crystallography allowed for the rapid characterization of the early hits from this inhibitor series. Ligand-based (19)F NMR was used to confirm inhibitor binding specificity and reversibility as well as to identify the N-terminal domain of the capsid (CA(NTD)) as its molecular target. Protein-based NMR ((1)H and (15)N chemical shift perturbation analysis) identified key residues within the CA(NTD) involved in inhibitor binding, while X-ray co-crystallography confirmed the inhibitor binding site and its binding mode. Based on these results, two conformationally restricted cyclic inhibitors were designed to further validate the possible binding modes. These studies were crucial to early hit confirmation and subsequent lead optimization.

  • Organizational Affiliation

    Dept. of Chemistry and Biological Sciences, Research & Development, Boehringer Ingelheim (Canada) Ltd, 2100 Cunard Street, Laval, Québec, H7S 2G5, Canada. nathalie.goudreau@boehringer-ingelheim.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag protein146Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag
Find proteins for A9PKC6 (Human immunodeficiency virus 1)
Explore A9PKC6 
Go to UniProtKB:  A9PKC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9PKC6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1F6

Download Ideal Coordinates CCD File 
B [auth A](3Z)-3-{[(2-methoxyethyl)amino]methylidene}-1-methyl-5-phenyl-7-(trifluoromethyl)-1H-1,5-benzodiazepine-2,4(3H,5H)-dione
C21 H20 F3 N3 O3
Query on NA

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
1F6 PDBBind:  4INB IC50: 890 (nM) from 1 assay(s)
Binding MOAD:  4INB IC50: 890 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.231 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.95α = 90
b = 89.21β = 90
c = 39.27γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2013-02-27 
  • Deposition Author(s): Coulombe, R.

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations