7RWG

"Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AGI-43192

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

Leveraging Structure-Based Drug Design to Identify Next-Generation MAT2A Inhibitors, Including Brain-Penetrant and Peripherally Efficacious Leads.

Li, M., Konteatis, Z., Nagaraja, N., Chen, Y., Zhou, S., Ma, G., Gross, S., Marjon, K., Hyer, M.L., Mandley, E., Lein, M., Padyana, A.K., Jin, L., Tong, S., Peters, R., Murtie, J., Travins, J., Medeiros, M., Liu, P., Frank, V., Judd, E.T., Biller, S.A., Marks, K.M., Sui, Z., Reznik, S.K.

(2022) J Med Chem 65: 4600-4615

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01595
  • Primary Citation of Related Structures:  
    7RW5, 7RW7, 7RWG, 7RWH

  • PubMed Abstract: 

    • Inhibition of the S -adenosyl methionine (SAM)-producing metabolic enzyme, methionine adenosyltransferase 2A (MAT2A), has received significant interest in the field of medicinal chemistry due to its implication as a synthetic lethal target in cancers with the deletion of the methylthioadenosine phosphorylase (MTAP) gene ...

    Inhibition of the S -adenosyl methionine (SAM)-producing metabolic enzyme, methionine adenosyltransferase 2A (MAT2A), has received significant interest in the field of medicinal chemistry due to its implication as a synthetic lethal target in cancers with the deletion of the methylthioadenosine phosphorylase (MTAP) gene. Here, we report the identification of novel MAT2A inhibitors with distinct in vivo properties that may enhance their utility in treating patients. Following a high-throughput screening, we successfully applied the structure-based design lessons from our first-in-class MAT2A inhibitor, AG-270 , to rapidly redesign and optimize our initial hit into two new lead compounds: a brain-penetrant compound, AGI-41998 , and a potent, but limited brain-penetrant compound, AGI-43192 . We hope that the identification and first disclosure of brain-penetrant MAT2A inhibitors will create new opportunities to explore the potential therapeutic effects of SAM modulation in the central nervous system (CNS).

    Related Citations: 
    • DISCOVERY OF AG-270, A FIRST-IN-CLASS ORAL MAT2A INHIBITOR DISCOVERY OF AG-270, A FIRST-IN-CLASS ORAL MAT2A INHIBITOR
      Konteatis, Z., Travins, J.
      (2021) J Med Chem 64: 4430
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S-adenosylmethionine synthase isoform type-2A396Homo sapiensMutation(s): 0 
Gene Names: MAT2A, AMS2, MATA2
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31153
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7UN (Subject of Investigation/LOI)
Query on 7UN
Download Ideal Coordinates CCD File 
I [auth A](8R)-8-(4-chlorophenyl)-6-(2-methyl-2H-indazol-5-yl)-2-[(2,2,2-trifluoroethyl)amino]-5,8-dihydropyrido[4,3-d]pyrimidin-7(6H)-one
C23 H16 Cl F3 N6 O
XXCYDSDPIJJBSI-UHFFFAOYSA-N		 Ligand Interaction
SAM
Query on SAM
Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.99α = 90
b = 93.72β = 90
c = 116.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Database references
  • Version 1.2: 2022-04-06
    Changes: Database references