4N1T

Structure of human MTH1 in complex with TH287


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.

Gad, H.Koolmeister, T.Jemth, A.S.Eshtad, S.Jacques, S.A.Strom, C.E.Svensson, L.M.Schultz, N.Lundback, T.Einarsdottir, B.O.Saleh, A.Gokturk, C.Baranczewski, P.Svensson, R.Berntsson, R.P.Gustafsson, R.Stromberg, K.Sanjiv, K.Jacques-Cordonnier, M.C.Desroses, M.Gustavsson, A.L.Olofsson, R.Johansson, F.Homan, E.J.Loseva, O.Brautigam, L.Johansson, L.Hoglund, A.Hagenkort, A.Pham, T.Altun, M.Gaugaz, F.Z.Vikingsson, S.Evers, B.Henriksson, M.Vallin, K.S.Wallner, O.A.Hammarstrom, L.G.Wiita, E.Almlof, I.Kalderen, C.Axelsson, H.Djureinovic, T.Puigvert, J.C.Haggblad, M.Jeppsson, F.Martens, U.Lundin, C.Lundgren, B.Granelli, I.Jensen, A.J.Artursson, P.Nilsson, J.A.Stenmark, P.Scobie, M.Berglund, U.W.Helleday, T.

(2014) Nature 508: 215-221

  • DOI: https://doi.org/10.1038/nature13181
  • Primary Citation of Related Structures:  
    4N1T, 4N1U

  • PubMed Abstract: 

    Cancers have dysfunctional redox regulation resulting in reactive oxygen species production, damaging both DNA and free dNTPs. The MTH1 protein sanitizes oxidized dNTP pools to prevent incorporation of damaged bases during DNA replication. Although MTH1 is non-essential in normal cells, we show that cancer cells require MTH1 activity to avoid incorporation of oxidized dNTPs, resulting in DNA damage and cell death. We validate MTH1 as an anticancer target in vivo and describe small molecules TH287 and TH588 as first-in-class nudix hydrolase family inhibitors that potently and selectively engage and inhibit the MTH1 protein in cells. Protein co-crystal structures demonstrate that the inhibitors bind in the active site of MTH1. The inhibitors cause incorporation of oxidized dNTPs in cancer cells, leading to DNA damage, cytotoxicity and therapeutic responses in patient-derived mouse xenografts. This study exemplifies the non-oncogene addiction concept for anticancer treatment and validates MTH1 as being cancer phenotypic lethal.


  • Organizational Affiliation

    1] Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
7,8-dihydro-8-oxoguanine triphosphatase159Homo sapiensMutation(s): 0 
Gene Names: NUDT1MTH1
EC: 3.6.1.55 (PDB Primary Data), 3.6.1.56 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens)
Explore P36639 
Go to UniProtKB:  P36639
PHAROS:  P36639
GTEx:  ENSG00000106268 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36639
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
2GD BindingDB:  4N1T IC50: min: 0.8, max: 20 (nM) from 5 assay(s)
Binding MOAD:  4N1T IC50: 0.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.378α = 90
b = 66.321β = 90
c = 36.136γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2015-08-05
    Changes: Structure summary
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description