9N0V | pdb_00009n0v

Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, KFA-027


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 
    0.309 (Depositor), 0.309 (DCC) 
  • R-Value Work: 
    0.274 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 
    0.277 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Delineating Structural Functionalities of Lenacapavir Amenable to Modifications for Targeting Emerging Drug-Resistant HIV‐1 Capsid Variants.

Adu-Ampratwum, D.Annamalai, A.S.Dinh, T.Lockwood, J.R.Bockbrader, R.H.Haney, R.Kvaratskhelia, M.Fuchs, J.R.

(2025) ACS Med Chem Lett 16: 2007-2014

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00405
  • Primary Citation Related Structures: 
    9N0V

  • PubMed Abstract: 

    Lenacapavir (LEN) is a new, first-in-class, long acting, HIV-1 capsid (CA)-targeting inhibitor for treating multidrug-resistant HIV-1 infections. LEN exhibits high potency against all major HIV-1 subtypes including variants resistant to current antiretroviral therapies providing a life-saving opportunity for heavily treatment-experienced adults with multidrug-resistant HIV-1. Despite this, LEN has a relatively low barrier to viral resistance. Clinical trials identified resistance-associated mutations near LEN binding site, with the M66I variant exhibiting highest level of resistance (>3200-fold). These findings necessitate continuing efforts to develop next-generation inhibitors against emerging LEN-resistant mutation. We focused on identifying LEN structural functionalities amenable to modifications and to develop LEN analogs with improved antiviral activity against the M66I mutant. Here, we report a new LEN analog, KFA-027, with substantially improved antiviral activity (EC 50 ∼ 444 nM, >20-fold) against M66I variant. Overall, these findings suggest a route for developing next-generation LEN analogs against WT and emerging drug-resistant CA mutations.


  • Organizational Affiliation
    • Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States.

Macromolecule Content 

  • Total Structure Weight: 101.27 kDa 
  • Atom Count: 7,064 
  • Modeled Residue Count: 880 
  • Deposited Residue Count: 880 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein p24
A, B, C, D
220Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag-pol
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BUL
(Subject of Investigation/LOI)

Query on A1BUL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth B],
G [auth C],
H [auth D]
N-[(1S)-1-{(3M)-3-[4-chloro-3-(methanesulfonamido)-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl]-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-phenylethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide
C39 H34 Cl F8 N7 O5 S2
VWUUKSNKCUTDKK-WEWMWRJBSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free:  0.309 (Depositor), 0.309 (DCC) 
  • R-Value Work:  0.274 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 0.277 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.32α = 90
b = 153.32β = 90
c = 112.33γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references