3WHW

MTH1 in complex with Ruthenium-based inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

An Organometallic Inhibitor for the Human Repair Enzyme 7,8-Dihydro-8-oxoguanosine Triphosphatase.

Streib, M., Kraeling, K., Richter, K., Xie, X., Steuber, H., Meggers, E.

(2014) Angew Chem Int Ed Engl 53: 305-309

  • DOI: https://doi.org/10.1002/anie.201307849
  • Primary Citation of Related Structures:  
    3WHW

  • PubMed Abstract: 

    The probe-based discovery of the first small-molecule inhibitor of the repair enzyme 8-oxo-dGTPase (MTH1) is presented, which is an unconventional cyclometalated ruthenium half-sandwich complex. The organometallic inhibitor with low-nanomolar activity displays astonishing specificity, as verified in tests with an extended panel of protein kinases and other ATP binding proteins. The binding of the organometallic inhibitor to MTH1 is investigated by protein crystallography.

    • Organizational Affiliation: 

    Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg (Germany).


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
7,8-dihydro-8-oxoguanine triphosphatase
A, B
156Homo sapiensMutation(s): 0 
Gene Names: NUDT1, MTH1
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RUX
Query on RUX
Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]		[4-amino-2-methyl-6-(pyridin-2-yl-kappaN)quinazolin-7-yl-kappaC~7~](carbonyl){1-[(2,6-dimethoxyphenoxy)carbonyl]cyclopenta-2,4-dien-1-yl}ruthenium
C29 H24 N4 O5 Ru
AOUPQUZYXKBCEC-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.76α = 90
b = 67.65β = 90
c = 79.54γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description