7BHR | pdb_00007bhr

Crystal structure of MAT2a with triazinone fragment 1 bound in the allosteric site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 
    0.183 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 7BHR

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 44.52 kDa 
  • Atom Count: 3,305 
  • Modeled Residue Count: 380 
  • Deposited Residue Count: 397 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM

Query on SAM



Download:Ideal Coordinates CCD File
C [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
TQE
(Subject of Investigation/LOI)

Query on TQE



Download:Ideal Coordinates CCD File
B [auth A]4-(dimethylamino)-6-ethoxy-1~{H}-1,3,5-triazin-2-one
C7 H12 N4 O2
GWBDQYGLNMYNTP-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TQE BindingDB:  7BHR Kd: 2.50e+5 (nM) from 1 assay(s)
IC50: 2.06e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free:  0.183 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.454α = 90
b = 94.211β = 90
c = 117.297γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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