7KCC

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AG-270


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of AG-270, a First-in-Class Oral MAT2A Inhibitor for the Treatment of Tumors with Homozygous MTAP Deletion.

Konteatis, Z.Travins, J.Gross, S.Marjon, K.Barnett, A.Mandley, E.Nicolay, B.Nagaraja, R.Chen, Y.Sun, Y.Liu, Z.Yu, J.Ye, Z.Jiang, F.Wei, W.Fang, C.Gao, Y.Kalev, P.Hyer, M.L.DeLaBarre, B.Jin, L.Padyana, A.K.Dang, L.Murtie, J.Biller, S.A.Sui, Z.Marks, K.M.

(2021) J Med Chem 64: 4430-4449

  • DOI: 10.1021/acs.jmedchem.0c01895
  • Primary Citation of Related Structures:  
    7KCE, 7KCF, 7KCC, 7KDB, 7KDA

  • PubMed Abstract: 
  • The metabolic enzyme methionine adenosyltransferase 2A (MAT2A) was recently implicated as a synthetic lethal target in cancers with deletion of the methylthioadenosine phosphorylase ( MTAP ) gene, which is adjacent to the CDKN2A tumor suppressor and codeleted with CDKN2A in approximately 15% of all cancers ...

    The metabolic enzyme methionine adenosyltransferase 2A (MAT2A) was recently implicated as a synthetic lethal target in cancers with deletion of the methylthioadenosine phosphorylase ( MTAP ) gene, which is adjacent to the CDKN2A tumor suppressor and codeleted with CDKN2A in approximately 15% of all cancers. Previous attempts to target MAT2A with small-molecule inhibitors identified cellular adaptations that blunted their efficacy. Here, we report the discovery of highly potent, selective, orally bioavailable MAT2A inhibitors that overcome these challenges. Fragment screening followed by iterative structure-guided design enabled >10 000-fold improvement in potency of a family of allosteric MAT2A inhibitors that are substrate noncompetitive and inhibit release of the product, S -adenosyl methionine (SAM), from the enzyme's active site. We demonstrate that potent MAT2A inhibitors substantially reduce SAM levels in cancer cells and selectively block proliferation of MTAP -null cells both in tissue culture and xenograft tumors. These data supported progressing AG-270 into current clinical studies (ClinicalTrials.gov NCT03435250).


    Organizational Affiliation

    Agios Pharmaceuticals, Inc., 88 Sidney Street, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S-adenosylmethionine synthase isoform type-2A396Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WBG (Subject of Investigation/LOI)
Query on WBG

Download Ideal Coordinates CCD File 
I [auth A]3-(cyclohex-1-en-1-yl)-6-(4-methoxyphenyl)-2-phenyl-5-[(pyridin-2-yl)amino]pyrazolo[1,5-a]pyrimidin-7(4H)-one
C30 H27 N5 O2
HSVRUECLQUGTDS-UHFFFAOYSA-N
 Ligand Interaction
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
H [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A], F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.148α = 90
b = 94.055β = 90
c = 116.898γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2020-10-05 
  • Released Date: 2021-04-21 
  • Deposition Author(s): Padyana, A., Jin, L.

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