8P4H

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric compound IDEAYA cmpd A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of novel methionine adenosyltransferase 2A (MAT2A) allosteric inhibitors by structure-based virtual screening.

Kalliokoski, T.Kettunen, H.Kumpulainen, E.Kettunen, E.Thieulin-Pardo, G.Neumann, L.Thomsen, M.Paul, R.Malyutina, A.Georgiadou, M.

(2023) Bioorg Med Chem Lett 94: 129450-129450

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129450
  • Primary Citation of Related Structures:  
    8P1T, 8P1V, 8P1W, 8P4H

  • PubMed Abstract: 

    Methionine adenosyltransferase 2A (MAT2A) has been indicated as a drug target for oncology indications. Clinical trials with MAT2A inhibitors are currently on-going. Here, a structure-based virtual screening campaign was performed on the commercially available chemical space which yielded two novel MAT2A-inhibitor chemical series. The binding modes of the compounds were confirmed with X-ray crystallography. Both series have acceptable physicochemical properties and show nanomolar activity in the biochemical MAT2A inhibition assay and single-digit micromolar activity in the proliferation assay (MTAP -/- cell line). The identified compounds and the relating structural data could be helpful in related drug discovery projects.


  • Organizational Affiliation

    Orion Pharma, Orionintie 1A, 02101 Espoo, Finland. Electronic address: tuomo.kalliokoski@orionpharma.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase isoform type-2
A, B, C, D
412Homo 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
SAM
Query on SAM

Download Ideal Coordinates CCD File 
K [auth B],
Q [auth D]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
UM6 (Subject of Investigation/LOI)
Query on UM6

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
O [auth C],
S [auth D]
7-chloranyl-4-[(3R)-3-fluoranylpyrrolidin-1-yl]-1-phenyl-quinazolin-2-one
C18 H15 Cl F N3 O
GPTUSHRRTGGGTD-CYBMUJFWSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
N [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
P [auth C],
T [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth B],
U [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth B],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.898α = 90
b = 106.742β = 93.18
c = 114.996γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-10-23
    Changes: Structure summary