8P1W

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with allosteric compound STL232591


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.112 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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-2A [auth AAA]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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WK5 (Subject of Investigation/LOI)
Query on WK5

Download Ideal Coordinates CCD File 
D [auth AAA]8-methoxy-1-(4-methoxyphenyl)-3-methyl-2-oxidanyl-[1]benzofuro[3,2-c]pyridine
C20 H18 N O4
KFTZMBXBOCZEMA-UHFFFAOYSA-N
MTA
Query on MTA

Download Ideal Coordinates CCD File 
B [auth AAA]5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
ABA
Query on ABA

Download Ideal Coordinates CCD File 
C [auth AAA]ALPHA-AMINOBUTYRIC ACID
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth AAA],
F [auth AAA],
G [auth AAA]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.112 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.132α = 90
b = 93.785β = 90
c = 116.706γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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