7SLR

HIV Reverse Transcriptase with compound Pyr01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Potent targeted activator of cell kill molecules eliminate cells expressing HIV-1.

Balibar, C.J.Klein, D.J.Zamlynny, B.Diamond, T.L.Fang, Z.Cheney, C.A.Kristoff, J.Lu, M.Bukhtiyarova, M.Ou, Y.Xu, M.Ba, L.Carroll, S.S.El Marrouni, A.Fay, J.F.Forster, A.Goh, S.L.Gu, M.Krosky, D.Rosenbloom, D.I.S.Sheth, P.Wang, D.Wu, G.Zebisch, M.Zhao, T.Zuck, P.Grobler, J.Hazuda, D.J.Howell, B.J.Converso, A.

(2023) Sci Transl Med 15: eabn2038-eabn2038

  • DOI: https://doi.org/10.1126/scitranslmed.abn2038
  • Primary Citation of Related Structures:  
    7SLR, 7SLS

  • PubMed Abstract: 

    Antiretroviral therapy inhibits HIV-1 replication but is not curative due to establishment of a persistent reservoir after virus integration into the host genome. Reservoir reduction is therefore an important HIV-1 cure strategy. Some HIV-1 nonnucleoside reverse transcriptase inhibitors induce HIV-1 selective cytotoxicity in vitro but require concentrations far exceeding approved dosages. Focusing on this secondary activity, we found bifunctional compounds with HIV-1-infected cell kill potency at clinically achievable concentrations. These targeted activator of cell kill (TACK) molecules bind the reverse transcriptase-p66 domain of monomeric Gag-Pol and act as allosteric modulators to accelerate dimerization, resulting in HIV-1 + cell death through premature intracellular viral protease activation. TACK molecules retain potent antiviral activity and selectively eliminate infected CD4 + T cells isolated from people living with HIV-1, supporting an immune-independent clearance strategy.


  • Organizational Affiliation

    Infectious Disease and Vaccines, Merck & Co. Inc., Rahway, NJ 07065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse transcriptase/ribonuclease H
A, B
561Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9QI (Subject of Investigation/LOI)
Query on 9QI

Download Ideal Coordinates CCD File 
C [auth A]5-(difluoromethyl)-3-({1-[(5-fluoro-2-oxo-1,2-dihydropyridin-3-yl)methyl]-6-oxo-4-(1,1,2,2-tetrafluoroethyl)-1,6-dihydropyrimidin-5-yl}oxy)-2-methylbenzonitrile
C21 H13 F7 N4 O3
VZPBEVWOYXRBLB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.427α = 90
b = 154.243β = 90
c = 155.561γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
BUSTERphasing

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: 2022-11-23
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references