8VQ2

HSV1 polymerase ternary complex with dsDNA and compound 44


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.83 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of Broad-Spectrum Herpes Antiviral Oxazolidinone Amide Derivatives and Their Structure-Activity Relationships.

Plotkin, M.A.Labroli, M.Schubert, J.Shaw, A.Schlegel, K.S.Berger, R.Cooke, A.J.Hayes, R.P.Armacost, K.A.Kinek, K.Krosky, P.Burlein, C.Meng, S.DiNunzio, E.Murray, E.M.Agrawal, S.Madeira, M.Flattery, A.Yao, H.Leithead, A.Rose 2nd, W.A.Cox, C.Tellers, D.M.McKenna, P.M.Raheem, I.

(2024) ACS Med Chem Lett 15: 1232-1241

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00117
  • Primary Citation of Related Structures:  
    8VQ2

  • PubMed Abstract: 

    Herpesvirus infections are ubiquitous, with over 95% of the adult population infected by at least one strain. While most of these infections resolve without treatment in healthy individuals, they can cause significant morbidity and mortality in immunocompromised, stem cell, or organ transplant patients. Current nucleoside standards of care provide meaningful benefit but are limited due to poor tolerability, resistance, and generally narrow spectrum of activity. Herpesviruses share a conserved DNA polymerase, the inhibition of which is validated as an effective strategy to disrupt viral replication. By utilizing a non-nucleoside inhibitor of the viral DNA polymerase, we sought to develop agents covering multiple herpesviruses (e.g., CMV, VZV, HSV1/2, EBV, and HHV6). Herein is described the invention of an oxazolidinone class of broad-spectrum non-nucleoside herpes antiviral inhibitors. A lead compound ( 42 ) with potent biochemical and broad-spectrum cellular activity was found to be efficacious in murine models against both HSV-1 and CMV infection.


  • Organizational Affiliation

    Discovery Chemistry, Merck & Co., Inc., West Point, Pennsylvania 19486, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymeraseA,
D [auth B]
1,163Human alphaherpesvirus 1Mutation(s): 1 
EC: 2.7.7.7
UniProt
Find proteins for I7GY94 (Human herpesvirus 1)
Explore I7GY94 
Go to UniProtKB:  I7GY94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7GY94
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*T)-3')B [auth C],
E
15synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')C [auth D],
F
13synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AC6 (Subject of Investigation/LOI)
Query on A1AC6

Download Ideal Coordinates CCD File 
G [auth C],
H [auth E]
2-(4-bromophenyl)-N-(3-methoxy-4-{[(4S)-2-oxo-1,3-oxazolidin-4-yl]methyl}phenyl)acetamide
C19 H19 Br N2 O4
GVSSEJUGEJTADP-INIZCTEOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.83 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.628α = 90
b = 180.628β = 90
c = 231.875γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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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: 2024-08-28
    Type: Initial release