8XB0 | pdb_00008xb0

Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with SAM and Compound 292


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 
    0.139 (Depositor), 0.139 (DCC) 
  • R-Value Work: 
    0.124 (Depositor), 0.124 (DCC) 
  • R-Value Observed: 
    0.124 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8XB0

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with High Selectivity, Brain Penetration, and In Vivo Efficacy.

Zheng, J.Zhang, T.Tong, S.Liu, T.Cui, J.Xu, H.Hu, D.Shen, Y.Yin, Y.Zhao, D.Tan, C.Dong, X.Chen, J.Ji, F.Tong, C.Li, J.J.Li, J.Zhang, G.

(2024) J Med Chem 67: 9431-9446

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00552
  • Primary Citation Related Structures: 
    8XAR, 8XB0

  • PubMed Abstract: 

    Synthetic lethality has recently emerged as a new approach for the treatment of mutated genes that were previously considered undruggable. Targeting methionine adenosyltransferase 2A (MAT2A) in cancers with deletion of the methylthioadenosine phosphorylase (MTAP) gene leads to synthetic lethality and thus has attracted significant interest in the field of precise anticancer drug development. Herein, we report the discovery of a series of novel MAT2A inhibitors featuring a pyrazolo[3,4- c ]quinolin-4-one skeleton based on structure-based drug design. Further optimization led to compound 39 , which has a high potency for inhibiting MAT2A and a remarkable selectivity for MTAP-deleted cancer cell lines. Compound 39 has a favorable pharmacokinetic profile with high plasma exposure and oral bioavailability, and it exhibits significant efficacy in xenograft MTAP-depleted models. Moreover, 39 demonstrates excellent brain exposure with a K puu of 0.64 in rats.


  • Organizational Affiliation
    • Center for Drug Design and Development, Suzhou Genhouse Bio Co., Ltd., No. 1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, China.

Macromolecule Content 

  • Total Structure Weight: 46.72 kDa 
  • Atom Count: 3,835 
  • Modeled Residue Count: 380 
  • Deposited Residue Count: 409 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase isoform type-2409Homo sapiensMutation(s): 0 
Gene Names: MAT2A
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
SAM

Query on SAM



Download:Ideal Coordinates CCD File
F [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
YN8
(Subject of Investigation/LOI)

Query on YN8



Download:Ideal Coordinates CCD File
E [auth A]7-chloranyl-5-(2-cyclopropylpyridin-3-yl)-8-fluoranyl-2-methyl-pyrazolo[3,4-c]quinolin-4-one
C19 H14 Cl F N4 O
LJPOSFHRBZRBMV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
L [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
YN8 BindingDB:  8XB0 IC50: min: 11, max: 74 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free:  0.139 (Depositor), 0.139 (DCC) 
  • R-Value Work:  0.124 (Depositor), 0.124 (DCC) 
  • R-Value Observed: 0.124 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.276α = 90
b = 94.105β = 90
c = 117.011γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release