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 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report



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:  
    5I2N, 5I2K, 5KDT

  • 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2AA285Homo sapiensMutation(s): 0 
Gene Names: GRIN2ANMDAR2A
Find proteins for Q12879 (Homo sapiens)
Explore Q12879 
Go to UniProtKB:  Q12879
NIH Common Fund Data Resources
PHAROS  Q12879
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1B293Homo sapiensMutation(s): 0 
Gene Names: GRIN1NMDAR1
Find proteins for Q05586 (Homo sapiens)
Explore Q05586 
Go to UniProtKB:  Q05586
NIH Common Fund Data Resources
PHAROS  Q05586
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6RV
Query on 6RV

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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
GLU
Query on GLU

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A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
GLY
Query on GLY

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B
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6RVEC50:  6200   nM  BindingDB
6RVEC50:  7400   nM  BindingDB
6RVEC50:  21   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.325α = 90
b = 90.127β = 90
c = 123.185γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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