5KCJ

Structure of the human GluN1/GluN2A LBD in complex with GNE6901

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 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 Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: hanson.jesse@gene.com.,Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR8197, INSERM U1024, 75005 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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
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
6RM
Query on 6RM
Download SDF File 
Download CCD File 
B
7-[(4-fluoranylphenoxy)methyl]-3-[(1~{R},2~{R})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one
C18 H17 F N2 O3 S
CJDCZVBFZVDWJU-XHDPSFHLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6RMEC50: 382 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.410α = 90.00
b = 89.730β = 90.00
c = 124.700γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release