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

Experimental Data Snapshot

  • Resolution: 1.74 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

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Discovery of Novel Small-Molecule HIV-1 Replication Inhibitors That Stabilize Capsid Complexes.

Lamorte, L.Titolo, S.Lemke, C.T.Goudreau, N.Mercier, J.F.Wardrop, E.Shah, V.B.von Schwedler, U.K.Langelier, C.Banik, S.S.Aiken, C.Sundquist, W.I.Mason, S.W.

(2013) Antimicrob Agents Chemother 57: 4622-4631

  • DOI: https://doi.org/10.1128/AAC.00985-13
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The identification of novel antiretroviral agents is required to provide alternative treatment options for HIV-1-infected patients. The screening of a phenotypic cell-based viral replication assay led to the identification of a novel class of 4,5-dihydro-1H-pyrrolo[3,4-c]pyrazol-6-one (pyrrolopyrazolone) HIV-1 inhibitors, exemplified by two compounds: BI-1 and BI-2. These compounds inhibited early postentry stages of viral replication at a step(s) following reverse transcription but prior to 2 long terminal repeat (2-LTR) circle formation, suggesting that they may block nuclear targeting of the preintegration complex. Selection of viruses resistant to BI-2 revealed that substitutions at residues A105 and T107 within the capsid (CA) amino-terminal domain (CANTD) conferred high-level resistance to both compounds, implicating CA as the antiviral target. Direct binding of BI-1 and/or BI-2 to CANTD was demonstrated using isothermal titration calorimetry and nuclear magnetic resonance (NMR) chemical shift titration analyses. A high-resolution crystal structure of the BI-1:CANTD complex revealed that the inhibitor bound within a recently identified inhibitor binding pocket (CANTD site 2) between CA helices 4, 5, and 7, on the surface of the CANTD, that also corresponds to the binding site for the host factor CPSF-6. The functional consequences of BI-1 and BI-2 binding differ from previously characterized inhibitors that bind the same site since the BI compounds did not inhibit reverse transcription but stabilized preassembled CA complexes. Hence, this new class of antiviral compounds binds CA and may inhibit viral replication by stabilizing the viral capsid.

  • Organizational Affiliation

    Department of Biological Sciences.

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 Q79791 (Human immunodeficiency virus 1)
Explore Q79791 
Go to UniProtKB:  Q79791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79791
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0OE

Download Ideal Coordinates CCD File 
B [auth A]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
Query on 1JR

Download Ideal Coordinates CCD File 
C [auth A](4S)-3-phenyl-4-(pyridin-3-yl)-4,5-dihydropyrrolo[3,4-c]pyrazol-6(2H)-one
C16 H12 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
1JR PDBBind:  4J93 Kd: 2.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.74 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.779α = 90
b = 42.494β = 90
c = 83.279γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2013-07-10 
  • Deposition Author(s): Lemke, C.T.

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-10-09
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations