9FNV | pdb_00009fnv

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH12163


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.252 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Giving an Enzyme Scissors: Serotonin Derivatives as Potent Organocatalytic Switches for DNA Repair Enzyme OGG1.

Varga, M.Ortis, F.Del Prado, A.Eddershaw, A.Scaletti Hutchinson, E.Hank, E.C.Zhou, K.Rudolfova, N.Dodaro, A.Wiita, E.Almlof, I.Karsten, S.Mamonov, K.Ahmed, S.H.Bentley, K.Wallner, O.Homan, E.J.Scobie, M.Helleday, T.Prejano, M.Stenmark, P.de Vega, M.Watson, A.J.B.Michel, M.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01454
  • Primary Citation of Related Structures:  
    9FNU, 9FNV

  • PubMed Abstract: 

    The base excision repair enzyme 8-oxoguanine DNA glycosylase 1 (OGG1) plays a central role in maintaining genome integrity and mediating cellular responses to oxidative stress. As such, it represents an attractive target for pharmaceutical modulation. Small-molecule organocatalytic switches (ORCAs) greatly enhance the rate of OGG1-catalyzed cleavage of DNA abasic sites, thereby accelerating DNA repair. Here, we present the discovery and hit-to-lead optimization of a novel class of highly potent serotonin-derived ORCAs with greatly improved pharmacokinetic properties. Biochemical assays, X-ray crystallography, and molecular dynamics simulations point toward a water-mediated mechanism of activation, distinct from previously proposed Brønsted base-assisted models. These findings establish serotonin-based ORCAs as promising chemical probes and potential leads for therapeutic modulation of OGG1 in oxidative stress-driven diseases.


  • Organizational Affiliation
    • EaStCHEM, School of Chemistry, University of St Andrews, St Andrews KY16 9ST, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-glycosylase/DNA lyase
A, B, C
318Mus musculusMutation(s): 0 
Gene Names: Ogg1
EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for O08760 (Mus musculus)
Explore O08760 
Go to UniProtKB:  O08760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08760
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.252 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.39α = 90
b = 81.48β = 90
c = 170.19γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Database references, Structure summary