9PGT | pdb_00009pgt

HIV Capsid Hexamer bound to Compound 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.247 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Lenacapavir: First-in-Class Twice-Yearly Capsid Inhibitor for HIV-1 Treatment and Pre-exposure Prophylaxis.

Canales, E.Tse, W.Schroeder, S.D.Chou, C.H.Liu, Q.Zhang, J.Lazerwith, S.E.Morganelli, P.Saito, R.D.Brizgys, G.Li, J.Wu, Q.Graupe, M.Halcomb, R.L.Desai, M.Cannizzaro, C.Hu, E.Perry, J.K.Villasenor, A.G.Somoza, J.R.Ferrao, R.D.Swaminathan, S.Zheng, J.Lu, B.Mwangi, J.Wang, K.Subramanian, R.Smith, B.J.Rhodes, G.Rowe, W.Sauer, D.Lad, L.Papalia, G.A.Clancy, S.Stepan, G.J.Yu, H.Sakowicz, R.Shi, B.Carr, G.Bam, R.A.Tsai, L.K.Singer, E.Hansen, D.Mulato, A.Yant, S.R.Cihlar, T.Link, J.O.

(2025) J Med Chem 68: 21072-21094

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01625
  • Primary Citation of Related Structures:  
    9PGS, 9PGT, 9PGU, 9PGV

  • PubMed Abstract: 

    The HIV capsid is essential to the virus lifecycle, making it a promising target for therapeutic intervention. In 2006, a screening campaign was initiated to identify small molecules capable of disrupting the protein-protein interactions required for self-assembly of the 1500 capsid monomers that form the 37 MDa fullerene cone-shaped capsid. Numerous compound design cycles over many years were undertaken to discover the complex structural elements that together afford the multistage HIV capsid inhibitor lenacapavir. Lenacapavir is the most potent (HIV-1 EC 50 = 105 pM) and longest-acting HIV antiviral to date, with a unique twice-yearly dosing regimen. Clinically, lenacapavir has demonstrated robust efficacy for both HIV-1 treatment and prevention, and, remarkably, achieved 100% protection in women for the first time. These findings represent a significant advancement in treatment and prevention of HIV-1 infection, offering the potential to profoundly impact the global course of the HIV epidemic.


  • Organizational Affiliation
    • Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Dr., Foster City, California 94404, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 capsid
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
232Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag
UniProt
Find proteins for B6DRA0 (Human immunodeficiency virus type 1)
Explore B6DRA0 
Go to UniProtKB:  B6DRA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6DRA0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CH5 (Subject of Investigation/LOI)
Query on A1CH5

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth I],
V [auth J],
W [auth K],
X [auth L]
N-[(1S)-1-[3-(4-chlorophenyl)pyridin-2-yl]-2-(3,5-difluorophenyl)ethyl]-2-(5-hydroxy-1H-indol-3-yl)acetamide
C29 H22 Cl F2 N3 O2
VWDVTOLVWGUBLC-MHZLTWQESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.8α = 90
b = 156.66β = 97.751
c = 118.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Database references
  • Version 1.2: 2025-10-29
    Changes: Database references