7RWG | pdb_00007rwg

"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 (Depositor), 0.136 (DCC) 
  • R-Value Work: 
    0.122 (Depositor), 0.124 (DCC) 
  • R-Value Observed: 
    0.123 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7RWG

Ligand Structure Quality Assessment 


This is version 1.3 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 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. 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).


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

Macromolecule Content 

  • Total Structure Weight: 45.13 kDa 
  • Atom Count: 3,908 
  • Modeled Residue Count: 384 
  • Deposited Residue Count: 396 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase isoform type-2396Homo 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 5 Unique
IDChains Name / 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
SAM

Query on SAM



Download:Ideal Coordinates CCD File
B [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
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
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
7UN BindingDB:  7RWG IC50: min: 14, max: 32 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free:  0.136 (Depositor), 0.136 (DCC) 
  • R-Value Work:  0.122 (Depositor), 0.124 (DCC) 
  • R-Value Observed: 0.123 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description