6V2F

Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, GS-6207


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Clinical targeting of HIV capsid protein with a long-acting small molecule.

Link, J.O.Rhee, M.S.Tse, W.C.Zheng, J.Somoza, J.R.Rowe, W.Begley, R.Chiu, A.Mulato, A.Hansen, D.Singer, E.Tsai, L.K.Bam, R.A.Chou, C.H.Canales, E.Brizgys, G.Zhang, J.R.Li, J.Graupe, M.Morganelli, P.Liu, Q.Wu, Q.Halcomb, R.L.Saito, R.D.Schroeder, S.D.Lazerwith, S.E.Bondy, S.Jin, D.Hung, M.Novikov, N.Liu, X.Villasenor, A.G.Cannizzaro, C.E.Hu, E.Y.Anderson, R.L.Appleby, T.C.Lu, B.Mwangi, J.Liclican, A.Niedziela-Majka, A.Papalia, G.A.Wong, M.H.Leavitt, S.A.Xu, Y.Koditek, D.Stepan, G.J.Yu, H.Pagratis, N.Clancy, S.Ahmadyar, S.Cai, T.Z.Sellers, S.Wolckenhauer, S.A.Ling, J.Callebaut, C.Margot, N.Ram, R.R.Liu, Y.P.Hyland, R.Sinclair, G.I.Ruane, P.J.Crofoot, G.E.McDonald, C.K.Brainard, D.M.Lad, L.Swaminathan, S.Sundquist, W.I.Sakowicz, R.Chester, A.E.Lee, W.E.Daar, E.S.Yant, S.R.Cihlar, T.

(2020) Nature 

  • DOI: 10.1038/s41586-020-2443-1
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Oral antiretroviral agents provide life-saving treatments for millions of people living with HIV, and can prevent new infections via pre-exposure prophylaxis 1-5 . However, some people living with HIV who are heavily treatment-experienced ...

    Oral antiretroviral agents provide life-saving treatments for millions of people living with HIV, and can prevent new infections via pre-exposure prophylaxis 1-5 . However, some people living with HIV who are heavily treatment-experienced have limited or no treatment options, owing to multidrug resistance 6 . In addition, suboptimal adherence to oral daily regimens can negatively affect the outcome of treatment-which contributes to virologic failure, resistance generation and viral transmission-as well as of pre-exposure prophylaxis, leading to new infections 1,2,4,7-9 . Long-acting agents from new antiretroviral classes can provide much-needed treatment options for people living with HIV who are heavily treatment-experienced, and additionally can improve adherence 10 . Here we describe GS-6207, a small molecule that disrupts the functions of HIV capsid protein and is amenable to long-acting therapy owing to its high potency, low in vivo systemic clearance and slow release kinetics from the subcutaneous injection site. Drawing on X-ray crystallographic information, we designed GS-6207 to bind tightly at a conserved interface between capsid protein monomers, where it interferes with capsid-protein-mediated interactions between proteins that are essential for multiple phases of the viral replication cycle. GS-6207 exhibits antiviral activity at picomolar concentrations against all subtypes of HIV-1 that we tested, and shows high synergy and no cross-resistance with approved antiretroviral drugs. In phase-1 clinical studies, monotherapy with a single subcutaneous dose of GS-6207 (450 mg) resulted in a mean log 10 -transformed reduction of plasma viral load of 2.2 after 9 days, and showed sustained plasma exposure at antivirally active concentrations for more than 6 months. These results provide clinical validation for therapies that target the functions of HIV capsid protein, and demonstrate the potential of GS-6207 as a long-acting agent to treat or prevent infection with HIV.


    Organizational Affiliation

    Gilead Sciences, Foster City, CA, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 capsidA, B, C, D, E, F232Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag
Find proteins for B6DRA0 (Human immunodeficiency virus 1)
Explore B6DRA0 
Go to UniProtKB:  B6DRA0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QNG
Query on QNG

Download CCD File 
A, B, C, D, E, F
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.301α = 90
b = 158.301β = 90
c = 55.648γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references