6G3Y

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH5675


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.

Visnes, T.Cazares-Korner, A.Hao, W.Wallner, O.Masuyer, G.Loseva, O.Mortusewicz, O.Wiita, E.Sarno, A.Manoilov, A.Astorga-Wells, J.Jemth, A.S.Pan, L.Sanjiv, K.Karsten, S.Gokturk, C.Grube, M.Homan, E.J.Hanna, B.M.F.Paulin, C.B.J.Pham, T.Rasti, A.Berglund, U.W.von Nicolai, C.Benitez-Buelga, C.Koolmeister, T.Ivanic, D.Iliev, P.Scobie, M.Krokan, H.E.Baranczewski, P.Artursson, P.Altun, M.Jensen, A.J.Kalderen, C.Ba, X.Zubarev, R.A.Stenmark, P.Boldogh, I.Helleday, T.

(2018) Science 362: 834-839

  • DOI: 10.1126/science.aar8048
  • Primary Citation of Related Structures:  
    6G3Y, 6G3X

  • PubMed Abstract: 
  • The onset of inflammation is associated with reactive oxygen species and oxidative damage to macromolecules like 7,8-dihydro-8-oxoguanine (8-oxoG) in DNA. Because 8-oxoguanine DNA glycosylase 1 (OGG1) binds 8-oxoG and because Ogg1 -deficient mice are resistant to acute and systemic inflammation, we hypothesized that OGG1 inhibition may represent a strategy for the prevention and treatment of inflammation ...

    The onset of inflammation is associated with reactive oxygen species and oxidative damage to macromolecules like 7,8-dihydro-8-oxoguanine (8-oxoG) in DNA. Because 8-oxoguanine DNA glycosylase 1 (OGG1) binds 8-oxoG and because Ogg1 -deficient mice are resistant to acute and systemic inflammation, we hypothesized that OGG1 inhibition may represent a strategy for the prevention and treatment of inflammation. We developed TH5487, a selective active-site inhibitor of OGG1, which hampers OGG1 binding to and repair of 8-oxoG and which is well tolerated by mice. TH5487 prevents tumor necrosis factor-α-induced OGG1-DNA interactions at guanine-rich promoters of proinflammatory genes. This, in turn, decreases DNA occupancy of nuclear factor κB and proinflammatory gene expression, resulting in decreased immune cell recruitment to mouse lungs. Thus, we present a proof of concept that targeting oxidative DNA repair can alleviate inflammatory conditions in vivo.


    Organizational Affiliation

    Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-glycosylase/DNA lyase ABC318Mus musculusMutation(s): 0 
Gene Names: Ogg1
EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
Find proteins for O08760 (Mus musculus)
Explore O08760 
Go to UniProtKB:  O08760
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ELB
Query on ELB

Download Ideal Coordinates CCD File 
A, B, C
4-(4-azanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide
C19 H20 I N5 O2
MCANHWLZFZFTAQ-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.817α = 90
b = 81.357β = 90
c = 169.157γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Derived calculations