8XAM

Co-crystal structure of compound 7 in complex with MAT2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.121 

Starting Model: experimental
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Literature

Discovery of novel MAT2A inhibitors by an allosteric site-compatible fragment growing approach.

Gao, F.Ding, X.Cao, Z.Zhu, W.Fan, Y.Steurer, B.Wang, H.Cai, X.Zhang, M.Aliper, A.Ren, F.Ding, X.Zhavoronkov, A.

(2024) Bioorg Med Chem 100: 117633-117633

  • DOI: https://doi.org/10.1016/j.bmc.2024.117633
  • Primary Citation of Related Structures:  
    8XAM

  • PubMed Abstract: 

    The methionine adenosyltransferase MAT2A catalyzes the synthesis ofthe methyl donor S-adenosylmethionine (SAM) and thereby regulates critical aspects of metabolism and transcription. Aberrant MAT2A function can lead to metabolic and transcriptional reprogramming of cancer cells, and MAT2A has been shown to promote survival of MTAP-deficient tumors, a genetic alteration that occurs in ∼ 13 % of all tumors. Thus, MAT2A holds great promise as a novel anticancer target. Here, we report a novel series of MAT2A inhibitors generated by a fragment growing approach from AZ-28, a low-molecular weight MAT2A inhibitor with promising pre-clinical properties. X-ray co-crystal structure revealed that compound 7 fully occupies the allosteric pocket of MAT2A as a single molecule mimicking MAT2B. By introducing additional backbone interactions and rigidifying the requisite linker extensions, we generated compound 8, which exhibited single digit nanomolar enzymatic and sub-micromolar cellular inhibitory potency for MAT2A.


  • Organizational Affiliation

    Insilico Medicine Shanghai Ltd., Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase isoform type-2
A, B
380Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XRH (Subject of Investigation/LOI)
Query on XRH

Download Ideal Coordinates CCD File 
D [auth B]2-[3-[7-chloranyl-4-(dimethylamino)-2-oxidanylidene-quinazolin-1-yl]phenoxy]-~{N}-[3-[7-chloranyl-4-(dimethylamino)-2-oxidanylidene-quinazolin-1-yl]phenyl]ethanamide
C34 H29 Cl2 N7 O4
GOGVJELCHJYKRJ-UHFFFAOYSA-N
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.121 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.968α = 90
b = 94.043β = 90
c = 116.892γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata 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: 2024-02-28
    Type: Initial release