9GID | pdb_00009gid

NMDA bound to compound 338

• PDB DOI: https://doi.org/10.2210/pdb9GID/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-19 Released: 2024-11-27 
• Deposition Author(s): Carr, K.H., Ascic, E., Leonard, P.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 

Starting Model: experimental

Literature

Advancements in NMDA Receptor-Targeted Antidepressants: From d-Cycloserine Discovery to Preclinical Efficacy of Lu AF90103.

Ascic, E., Marigo, M., David, L., Frisch Herrik, K., Grupe, M., Hougaard, C., Mork, A., Jones, C.R., Badolo, L., Frederiksen, K., Boonen, H.C.M., Jensen, H.S., Kilburn, J.P.

(2024) J Med Chem 67: 20135-20155

• PubMed: 39560374 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c01477
• Primary Citation Related Structures: 
  9GIB, 9GIC, 9GID, 9GIE, 9GIF, 9GIG, 9GJ1


• PubMed Abstract: 
  

  The discovery of d-cycloserine ( DCS ), a partial agonist of the NMDA receptor that exhibits antidepressant effects without the psychotomimetic effects of ketamine, has fueled interest in new NMDA-targeting antidepressants. Our objective was to identify potent partial agonists mirroring DCS , particularly tailored for the GluN2B subtype of the NMDA receptor. Through a structure-based drug design approach, we discovered compound 42d . This compound acts as a partial agonist of the GluN1/GluN2B complex, exhibiting 24% efficacy, and has an EC ₅₀ value of 78 nM. Subsequent investigations led us to 42e (Lu AF90103), a methyl ester prodrug of 42d capable of penetrating the blood-brain barrier, as confirmed by rat microdialysis studies. In different rat in vivo models relevant to neuropsychiatric diseases, administering 42e led to 42d demonstrating both acute effects, observed in a seizure model and EEG, and lasting effects in the stress-sensitive hippocampal pathway and an antidepressant-sensitive model.

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Organizational Affiliation: 
• Neuroscience Drug Discovery Denmark, H. Lundbeck A/S, 9 Ottiliavej, Valby, DK-2500 Copenhagen, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.98 kDa 
• Atom Count: 2,414 
• Modeled Residue Count: 288 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	A	292	Homo sapiens	Mutation(s): 0  Gene Names: GRIN1, NMDAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q05586 (Homo sapiens) Explore Q05586  Go to UniProtKB:  Q05586
PHAROS:  Q05586 GTEx:  ENSG00000176884

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ILT (Subject of Investigation/LOI)	B [auth A]	(2~{R})-2-azanyl-3-[(7-bromanyl-4-fluoranyl-3~{H}-1-benzothiophen-2-yl)carbonylamino]propanoic acid C12 H12 Br F N2 O3 S JJQWSFTXAIAWHD-MRVPVSSYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.56	α = 90
b = 72.5	β = 90
c = 95.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Carr, K.H., Ascic, E., Leonard, P.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release
  
• Version 1.1: 2024-12-11
  Changes: Database references