7BHV

Crystal structure of MAT2a bound to allosteric inhibitor and in vivo tool compound 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 
    0.157 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.149 (Depositor) 

Starting Model: other
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TQBClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Fragment-Based Design of a Potent MAT2a Inhibitor and in Vivo Evaluation in an MTAP Null Xenograft Model.

De Fusco, C.Schimpl, M.Borjesson, U.Cheung, T.Collie, I.Evans, L.Narasimhan, P.Stubbs, C.Vazquez-Chantada, M.Wagner, D.J.Grondine, M.Sanders, M.G.Tentarelli, S.Underwood, E.Argyrou, A.Smith, J.M.Lynch, J.T.Chiarparin, E.Robb, G.Bagal, S.K.Scott, J.S.

(2021) J Med Chem 64: 6814-6826

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00067
  • Primary Citation of Related Structures:  
    7BHR, 7BHS, 7BHT, 7BHU, 7BHV, 7BHW, 7BHX

  • PubMed Abstract: 

    MAT2a is a methionine adenosyltransferase that synthesizes the essential metabolite S -adenosylmethionine (SAM) from methionine and ATP. Tumors bearing the co-deletion of p16 and MTAP genes have been shown to be sensitive to MAT2a inhibition, making it an attractive target for treatment of MTAP-deleted cancers. A fragment-based lead generation campaign identified weak but efficient hits binding in a known allosteric site. By use of structure-guided design and systematic SAR exploration, the hits were elaborated through a merging and growing strategy into an arylquinazolinone series of potent MAT2a inhibitors. The selected in vivo tool compound 28 reduced SAM-dependent methylation events in cells and inhibited proliferation of MTAP-null cells in vitro . In vivo studies showed that 28 was able to induce antitumor response in an MTAP knockout HCT116 xenograft model.


  • Organizational Affiliation

    Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase isoform type-2397Homo sapiensMutation(s): 0 
Gene Names: MAT2AAMS2MATA2
EC: 2.5.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P31153 (Homo sapiens)
Explore P31153 
Go to UniProtKB:  P31153
PHAROS:  P31153
GTEx:  ENSG00000168906 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31153
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
TQB BindingDB:  7BHV IC50: min: 22, max: 200 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free:  0.157 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.149 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.176α = 90
b = 93.853β = 90
c = 117.069γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
STARANISOdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TQBClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2021-06-09
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description