9MUL | pdb_00009mul

Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 1, Glycine and Glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.252 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design, Synthesis, and Characterization of GluN2A Negative Allosteric Modulators Suitable for In Vivo Exploration.

Bischoff, F.P.Van Brandt, S.Viellevoye, M.De Cleyn, M.Surkyn, M.Carbajo, R.J.Dominguez Blanco, M.Wroblowski, B.Karpowich, N.K.Steele, R.A.Schalk-Hihi, C.Miller, R.Duda, D.Shaffer, P.Ballentine, S.Simavorian, S.Lord, B.Neff, R.A.Bonaventure, P.Gijsen, H.J.M.

(2025) J Med Chem 68: 4672-4693

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02751
  • Primary Citation of Related Structures:  
    9MUL, 9MUM

  • PubMed Abstract: 

    N -Methyl-d-aspartate receptors are ionotropic glutamate receptors that mediate fast excitatory neurotransmission in the central nervous system. These receptors play essential roles in synaptic plasticity, learning, and memory and are implicated in various neuropathological and psychiatric disorders. Selective modulation of NMDAR subtypes, particularly GluN2A, has proven challenging. The TCN-201 derivatives MPX-004 and MPX-007 are potent and selective for GluN2A receptors, yet their physical properties limit their in vivo utility. In this study, we optimized the MPX-004 / MPX-007 scaffold by modifying the linker region between the distal halogenated aromatic ring and the central pyrazine nucleus, resulting in the identification of potent and selective compounds with improved drug-like properties. Notably, compound 1 was used to develop the first GluN2A NAM-based radioligand, and compound 11 showed improved pharmacokinetics and dose-dependent receptor occupancy in vivo. Thus, we provide an array of powerful new tools for the study of GluN2A receptors.


  • Organizational Affiliation

    Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1306Homo sapiensMutation(s): 0 
Gene Names: GRIN1NMDAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q05586 (Homo sapiens)
Explore Q05586 
Go to UniProtKB:  Q05586
PHAROS:  Q05586
GTEx:  ENSG00000176884 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05586
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2A297Homo sapiensMutation(s): 0 
Gene Names: GRIN2ANMDAR2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q12879 (Homo sapiens)
Explore Q12879 
Go to UniProtKB:  Q12879
PHAROS:  Q12879
GTEx:  ENSG00000183454 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12879
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.252 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.928α = 90
b = 90.013β = 90
c = 124.006γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
PHENIXphasing
xia2data scaling

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: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Database references