5FSI

MTH1 substrate recognition: Complex with 8-oxo-dGTP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mth1 Substrate Recognition--an Example of Specific Promiscuity.

Nissink, J.W.M.Bista, M.Breed, J.Carter, N.Embrey, K.Read, J.Winter-Holt, J.J.

(2016) PLoS One 11: 51154

  • DOI: https://doi.org/10.1371/journal.pone.0151154
  • Primary Citation of Related Structures:  
    5FSI, 5FSK, 5FSL, 5FSM, 5FSN, 5FSO

  • PubMed Abstract: 

    MTH1 (NUDT1) is an oncologic target involved in the prevention of DNA damage. We investigate the way MTH1 recognises its substrates and present substrate-bound structures of MTH1 for 8-oxo-dGTP and 8-oxo-rATP as examples of novel strong and weak binding substrate motifs. Investigation of a small set of purine-like fragments using 2D NMR resulted in identification of a fragment with weak potency. The protein-ligand X-Ray structure of this fragment provides insight into the role of water molecules in substrate selectivity. Wider fragment screening by NMR resulted in three new protein structures exhibiting alternative binding configurations to the key Asp-Asp recognition element of the protein. These inhibitor binding modes demonstrate that MTH1 employs an intricate yet promiscuous mechanism of substrate anchoring through its Asp-Asp pharmacophore. The structures suggest that water-mediated interactions convey selectivity towards oxidized substrates over their non-oxidised counterparts, in particular by stabilization of a water molecule in a hydrophobic environment through hydrogen bonding. These findings may be useful in the design of inhibitors of MTH1.


  • Organizational Affiliation

    Chemistry, Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Unit 310 (Darwin Building), Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom, and Alderley Park, Cheshire, SK10 4TG, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE156Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8DG
Query on 8DG

Download Ideal Coordinates CCD File 
B [auth A]8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
BUZOGVVQWCXXDP-VPENINKCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.469α = 90
b = 66.149β = 90
c = 36.083γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references, Refinement description
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other