8G18 | pdb_00008g18

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.246 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.174 (Depositor) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8G18

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Novel GluN2B-Selective NMDA Receptor Negative Allosteric Modulator Possesses Intrinsic Analgesic Properties and Enhances Analgesia of Morphine in a Rodent Tail Flick Pain Model.

Harris, L.D.Regan, M.C.Myers, S.J.Nocilla, K.A.Akins, N.S.Tahirovic, Y.A.Wilson, L.J.Dingledine, R.Furukawa, H.Traynelis, S.F.Liotta, D.C.

(2023) ACS Chem Neurosci 14: 917-935

  • DOI: https://doi.org/10.1021/acschemneuro.2c00779
  • Primary Citation Related Structures: 
    8G18

  • PubMed Abstract: 

    Many cases of accidental death associated with drug overdose are due to chronic opioid use, tolerance, and addiction. Analgesic tolerance is characterized by a decreased response to the analgesic effects of opioids, requiring increasingly higher doses to maintain the desired level of pain relief. Overactivation of GluN2B-containing N -methyl-d-Aspartate receptors is thought to play a key role in mechanisms underlying cellular adaptation that takes place in the development of analgesic tolerance. Herein, we describe a novel GluN2B-selective negative allosteric modulator, EU93-108 , that shows high potency and brain penetrance. We describe the structural basis for binding at atomic resolution. This compound possesses intrinsic analgesic properties in the rodent tail immersion test. EU93-108 has an acute and significant anodyne effect, whereby morphine when combined with EU93-108 produces a higher tail flick latency compared to that of morphine alone. These data suggest that engagement of GluN2B as a target has utility in the treatment of pain, and EU93-108 could serve as an appropriate tool compound to interrogate this hypothesis. Future structure-activity relationship work around this scaffold could give rise to compounds that can be co-administered with opioids to diminish the onset of tolerance due to chronic opioid use, thereby modifying their utility.


  • Organizational Affiliation
    • Department of Chemistry, Emory University, Atlanta, Georgia30322, United States.

Macromolecule Content 

  • Total Structure Weight: 170.55 kDa 
  • Atom Count: 11,400 
  • Modeled Residue Count: 1,443 
  • Deposited Residue Count: 1,496 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1
A, C
385Xenopus laevisMutation(s): 0 
Gene Names: grin1
Membrane Entity: Yes 
UniProt
Find proteins for A0A8J0TPH2 (Xenopus laevis)
Explore A0A8J0TPH2 
Go to UniProtKB:  A0A8J0TPH2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8J0TPH2
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2B
B, D
363Rattus norvegicusMutation(s): 0 
Gene Names: Grin2b
Membrane Entity: Yes 
UniProt
Find proteins for Q00960 (Rattus norvegicus)
Explore Q00960 
Go to UniProtKB:  Q00960
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00960
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q00960-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
5N/A
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YGW
(Subject of Investigation/LOI)

Query on YGW



Download:Ideal Coordinates CCD File
J [auth B],
P [auth D]
N-(4-{3-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-oxopropoxy}phenyl)methanesulfonamide
C20 H23 F2 N3 O4 S
DOZAIKQGJALOLT-UHFFFAOYSA-N
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A]
H [auth B]
I [auth B]
K [auth C]
L [auth C]
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
N [auth D],
O [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA
(Subject of Investigation/LOI)

Query on NA



Download:Ideal Coordinates CCD File
G [auth A],
M [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.246 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.174 (Depositor) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 269.172α = 90
b = 60.076β = 117.02
c = 145.572γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH085926
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS113632

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary