5KDT

Structure of the human GluN1/GluN2A LBD in complex with GNE0723


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of GluN2A-Selective NMDA Receptor Positive Allosteric Modulators (PAMs): Tuning Deactivation Kinetics via Structure-Based Design.

Volgraf, M.Sellers, B.D.Jiang, Y.Wu, G.Ly, C.Q.Villemure, E.Pastor, R.M.Yuen, P.W.Lu, A.Luo, X.Liu, M.Zhang, S.Sun, L.Fu, Y.Lupardus, P.J.Wallweber, H.J.Liederer, B.M.Deshmukh, G.Plise, E.Tay, S.Reynen, P.Herrington, J.Gustafson, A.Liu, Y.Dirksen, A.Dietz, M.G.Liu, Y.Wang, T.M.Hanson, J.E.Hackos, D.Scearce-Levie, K.Schwarz, J.B.

(2016) J. Med. Chem. 59: 2760-2779

  • DOI: 10.1021/acs.jmedchem.5b02010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The N-methyl-D-aspartate receptor (NMDAR) is a Na(+) and Ca(2+) permeable ionotropic glutamate receptor that is activated by the coagonists glycine and glutamate. NMDARs are critical to synaptic signaling and plasticity, and their dysfunction has bee ...

    The N-methyl-D-aspartate receptor (NMDAR) is a Na(+) and Ca(2+) permeable ionotropic glutamate receptor that is activated by the coagonists glycine and glutamate. NMDARs are critical to synaptic signaling and plasticity, and their dysfunction has been implicated in a number of neurological disorders, including schizophrenia, depression, and Alzheimer's disease. Herein we describe the discovery of potent GluN2A-selective NMDAR positive allosteric modulators (PAMs) starting from a high-throughput screening hit. Using structure-based design, we sought to increase potency at the GluN2A subtype, while improving selectivity against related α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs). The structure-activity relationship of channel deactivation kinetics was studied using a combination of electrophysiology and protein crystallography. Effective incorporation of these strategies resulted in the discovery of GNE-0723 (46), a highly potent and brain penetrant GluN2A-selective NMDAR PAM suitable for in vivo characterization.


    Organizational Affiliation

    Ion Channels Group, Evotec AG ; Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany.,Pharmaron-Beijing Co. Ltd. , 6 Taihe Road, BDA, Beijing 100176, PR China.




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

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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
6RV
Query on 6RV

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Download CCD File 
A
(1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl)pyrazol-1-yl]methyl]-5-oxidanylidene-2-(trifluoromethyl)-[1,3]thiazolo[3,2-a]pyrimidin-3-yl]cyclopropane-1-carbonitrile
C16 H8 Cl F6 N5 O S
FTIBNGABJNFFAI-POYBYMJQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.325α = 90.00
b = 90.127β = 90.00
c = 123.185γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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