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 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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. mamuka.kvaratskhelia@cuanschutz.edu francisco.asturias@cuanschutz.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein p24A, B, C231Human 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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]
N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-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 H32 Cl F10 N7 O5 S2
BRYXUCLEHAUSDY-WEWMWRJBSA-N
 Ligand Interaction
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • 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 



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