6US2

MTH1 in complex with compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Literature

Discovery of Potent and Selective MTH1 Inhibitors for Oncology: Enabling Rapid Target (In)Validation.

Farand, J.Kropf, J.E.Blomgren, P.Xu, J.Schmitt, A.C.Newby, Z.E.Wang, T.Murakami, E.Barauskas, O.Sudhamsu, J.Feng, J.Y.Niedziela-Majka, A.Schultz, B.E.Schwartz, K.Viatchenko-Karpinski, S.Kornyeyev, D.Kashishian, A.Fan, P.Chen, X.Lansdon, E.B.Ports, M.O.Currie, K.S.Watkins, W.J.Notte, G.T.

(2020) ACS Med Chem Lett 11: 358-364

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00420
  • Primary Citation of Related Structures:  
    6US2, 6US3, 6US4

  • PubMed Abstract: 

    We describe the discovery of three structurally differentiated potent and selective MTH1 inhibitors and their subsequent use to investigate MTH1 as an oncology target, culminating in target (in)validation. Tetrahydronaphthyridine 5 was rapidly identified as a highly potent MTH1 inhibitor (IC 50 = 0.043 nM). Cocrystallization of 5 with MTH1 revealed the ligand in a Φ- cis - N -(pyridin-2-yl)acetamide conformation enabling a key intramolecular hydrogen bond and polar interactions with residues Gly34 and Asp120. Modification of literature compound TH287 with O - and N -linked aryl and alkyl aryl substituents led to the discovery of potent pyrimidine-2,4,6-triamine 25 (IC 50 = 0.49 nM). Triazolopyridine 32 emerged as a highly selective lead compound with a suitable in vitro profile and desirable pharmacokinetic properties in rat. Elucidation of the DNA damage response, cell viability, and intracellular concentrations of oxo-NTPs (oxidized nucleoside triphosphates) as a function of MTH1 knockdown and/or small molecule inhibition was studied. Based on our findings, we were unable to provide evidence to further pursue MTH1 as an oncology target.


  • Organizational Affiliation

    Gilead Sciences, Inc. 333 Lakeside Drive, Foster City, California 94404, United States.


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), 3.6.1 (UniProt)
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S3O (Subject of Investigation/LOI)
Query on S3O

Download Ideal Coordinates CCD File 
B [auth A]N-[5-(2,3-dimethylphenyl)-1,2,3,4-tetrahydro-1,6-naphthyridin-7-yl]acetamide
C18 H21 N3 O
HKZLJFYLGVHCCO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.182 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.315α = 90
b = 59.953β = 90
c = 66.672γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description