5NGT

Crystal structure of human MTH1 in complex with inhibitor 7-(furan-2-yl)-5-methyl-1,3-benzoxazol-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space.

Rudling, A.Gustafsson, R.Almlof, I.Homan, E.Scobie, M.Warpman Berglund, U.Helleday, T.Stenmark, P.Carlsson, J.

(2017) J. Med. Chem. 60: 8160-8169

  • DOI: 10.1021/acs.jmedchem.7b01006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fragment-based lead discovery has emerged as a leading drug development strategy for novel therapeutic targets. Although fragment-based drug discovery benefits immensely from access to atomic-resolution information, structure-based virtual screening ...

    Fragment-based lead discovery has emerged as a leading drug development strategy for novel therapeutic targets. Although fragment-based drug discovery benefits immensely from access to atomic-resolution information, structure-based virtual screening has rarely been used to drive fragment discovery and optimization. Here, molecular docking of 0.3 million fragments to a crystal structure of cancer target MTH1 was performed. Twenty-two predicted fragment ligands, for which analogs could be acquired commercially, were experimentally evaluated. Five fragments inhibited MTH1 with IC50 values ranging from 6 to 79 μM. Structure-based optimization guided by predicted binding modes and analogs from commercial chemical libraries yielded nanomolar inhibitors. Subsequently solved crystal structures confirmed binding modes predicted by docking for three scaffolds. Structure-guided exploration of commercial chemical space using molecular docking gives access to fragment libraries that are several orders of magnitude larger than those screened experimentally and can enable efficient optimization of hits to potent leads.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7,8-dihydro-8-oxoguanine triphosphatase
A
159Homo sapiensMutation(s): 0 
Gene Names: NUDT1 (MTH1)
EC: 3.6.1.55
Find proteins for P36639 (Homo sapiens)
Go to Gene View: NUDT1
Go to UniProtKB:  P36639
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
8WZ
Query on 8WZ

Download SDF File 
Download CCD File 
A
7-(furan-2-yl)-5-methyl-1,3-benzoxazol-2-amine
C12 H10 N2 O2
PCWTZLKSTFUZKW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.326α = 90.00
b = 60.617β = 90.00
c = 66.672γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish e-Science Research CenterSweden--
Science for Life LaboratorySweden--
Knut and Alice Wallenberg FoundationSweden--
Wenner-Gren FoundationSweden--
Clas Groschinskys FoundationSweden--
Ake Wiberg FoundationSweden--
Goran Gustafsson FoundationSweden--
Swedish Children's Cancer FoundationSweden--
Swedish Pain Relief FoundationSweden--
Torsten and Ragnar Soderberg FoundationSweden--
Swedish Cancer SocietySweden--
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references