6VKV

Co-crystal structure of GS-6207 bound to HIV-1 capsid hexamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 
    0.269 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QNGClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Structural and mechanistic bases for a potent HIV-1 capsid inhibitor.

Bester, S.M.Wei, G.Zhao, H.Adu-Ampratwum, D.Iqbal, N.Courouble, V.V.Francis, A.C.Annamalai, A.S.Singh, P.K.Shkriabai, N.Van Blerkom, P.Morrison, J.Poeschla, E.M.Engelman, A.N.Melikyan, G.B.Griffin, P.R.Fuchs, J.R.Asturias, F.J.Kvaratskhelia, M.

(2020) Science 370: 360-364

  • DOI: https://doi.org/10.1126/science.abb4808
  • Primary Citation of Related Structures:  
    6VKV, 6VWS

  • PubMed Abstract: 

    The potent HIV-1 capsid inhibitor GS-6207 is an investigational principal component of long-acting antiretroviral therapy. We found that GS-6207 inhibits HIV-1 by stabilizing and thereby preventing functional disassembly of the capsid shell in infected cells. X-ray crystallography, cryo-electron microscopy, and hydrogen-deuterium exchange experiments revealed that GS-6207 tightly binds two adjoining capsid subunits and promotes distal intra- and inter-hexamer interactions that stabilize the curved capsid lattice. In addition, GS-6207 interferes with capsid binding to the cellular HIV-1 cofactors Nup153 and CPSF6 that mediate viral nuclear import and direct integration into gene-rich regions of chromatin. These findings elucidate structural insights into the multimodal, potent antiviral activity of GS-6207 and provide a means for rationally developing second-generation therapies.


  • Organizational Affiliation

    Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein p24
A, B, C
231Human immunodeficiency virus 1Mutation(s): 4 
Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12493 
Go to UniProtKB:  P12493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12493
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QNG (Subject of Investigation/LOI)
Query on QNG

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B],
R [auth C]
Lenacapavir
C39 H32 Cl F10 N7 O5 S2
BRYXUCLEHAUSDY-WEWMWRJBSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
M [auth B],
S [auth C]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
N [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free:  0.269 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.05α = 90
b = 160.05β = 90
c = 57.526γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QNGClick on this verticalbar to view details

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: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.3: 2024-11-06
    Changes: Structure summary
  • Version 1.4: 2024-12-25
    Changes: Derived calculations, Structure summary