5H8Q

Structure of the human GluN1/GluN2A LBD in complex with GNE8324


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Positive Allosteric Modulators of GluN2A-Containing NMDARs with Distinct Modes of Action and Impacts on Circuit Function.

Hackos, D.H.Lupardus, P.J.Grand, T.Chen, Y.Wang, T.M.Reynen, P.Gustafson, A.Wallweber, H.J.Volgraf, M.Sellers, B.D.Schwarz, J.B.Paoletti, P.Sheng, M.Zhou, Q.Hanson, J.E.

(2016) Neuron 89: 983-999

  • DOI: 10.1016/j.neuron.2016.01.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To enhance physiological function of NMDA receptors (NMDARs), we identified positive allosteric modulators (PAMs) of NMDARs with selectivity for GluN2A subunit-containing receptors. X-ray crystallography revealed a binding site at the GluN1-GluN2A di ...

    To enhance physiological function of NMDA receptors (NMDARs), we identified positive allosteric modulators (PAMs) of NMDARs with selectivity for GluN2A subunit-containing receptors. X-ray crystallography revealed a binding site at the GluN1-GluN2A dimer interface of the extracellular ligand-binding domains (LBDs). Despite the similarity between the LBDs of NMDARs and AMPA receptors (AMPARs), GluN2A PAMs with good selectivity against AMPARs were identified. Potentiation was observed with recombinant triheteromeric GluN1/GluN2A/GluN2B NMDARs and with synaptically activated NMDARs in brain slices from wild-type (WT), but not GluN2A knockout (KO), mice. Individual GluN2A PAMs exhibited variable degrees of glutamate (Glu) dependence, impact on NMDAR Glu EC50, and slowing of channel deactivation. These distinct PAMs also exhibited differential impacts during synaptic plasticity induction. The identification of a new NMDAR modulatory site and characterization of GluN2A-selective PAMs provide powerful molecular tools to dissect NMDAR function and demonstrate the feasibility of a therapeutically desirable type of NMDAR enhancement.


    Organizational Affiliation

    Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
A
285Homo sapiensMutation(s): 0 
Gene Names: GRIN2A (NMDAR2A)
Find proteins for Q12879 (Homo sapiens)
Go to Gene View: GRIN2A
Go to UniProtKB:  Q12879
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1
B
293Homo sapiensMutation(s): 0 
Gene Names: GRIN1 (NMDAR1)
Find proteins for Q05586 (Homo sapiens)
Go to Gene View: GRIN1
Go to UniProtKB:  Q05586
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download SDF File 
Download CCD File 
B
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GLU
Query on GLU

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Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
5YE
Query on 5YE

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Download CCD File 
B
6-[[ethyl-(4-fluorophenyl)amino]methyl]-2,3-dihydro-1~{H}-cyclopenta[3,4][1,3]thiazolo[1,4-~{a}]pyrimidin-8-one
C18 H18 F N3 O S
MKBFOAQLSFHEGN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.729α = 90.00
b = 90.048β = 90.00
c = 125.198γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references, Derived calculations