5EWL

CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH MK-22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists.

Stroebel, D.Buhl, D.L.Knafels, J.D.Chanda, P.K.Green, M.Sciabola, S.Mony, L.Paoletti, P.Pandit, J.

(2016) Mol.Pharmacol. 89: 541-551

  • DOI: 10.1124/mol.115.103036
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-methyl-d-aspartate receptors (NMDARs) are glutamate-gated ion channels that play key roles in brain physiology and pathology. Because numerous pathologic conditions involve NMDAR overactivation, subunit-selective antagonists hold strong therapeutic ...

    N-methyl-d-aspartate receptors (NMDARs) are glutamate-gated ion channels that play key roles in brain physiology and pathology. Because numerous pathologic conditions involve NMDAR overactivation, subunit-selective antagonists hold strong therapeutic potential, although clinical successes remain limited. Among the most promising NMDAR-targeting drugs are allosteric inhibitors of GluN2B-containing receptors. Since the discovery of ifenprodil, a range of GluN2B-selective compounds with strikingly different structural motifs have been identified. This molecular diversity raises the possibility of distinct binding sites, although supporting data are lacking. Using X-ray crystallography, we show that EVT-101, a GluN2B antagonist structurally unrelated to the classic phenylethanolamine pharmacophore, binds at the same GluN1/GluN2B dimer interface as ifenprodil but adopts a remarkably different binding mode involving a distinct subcavity and receptor interactions. Mutagenesis experiments demonstrate that this novel binding site is physiologically relevant. Moreover, in silico docking unveils that GluN2B-selective antagonists broadly divide into two distinct classes according to binding pose. These data widen the allosteric and pharmacological landscape of NMDARs and offer a renewed structural framework for designing next-generation GluN2B antagonists with therapeutic value for brain disorders.


    Organizational Affiliation

    Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.).,Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institut de Biologie de l'École Normale Supérieure (IBENS), Paris, France (D.S., L.M., P.P.); Pfizer Worldwide Research and Development, Cambridge, Massachusetts (D.L.B., M.G., S.S.); and Pfizer Worldwide Research and Development, Groton, Connecticut (J.D.K., P.K.C., J.P.) Derek.Buhl@pfizer.com Pierre.Paoletti@ens.fr Jayvardhan.Pandit@pfizer.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NMDA glutamate receptor subunit
A, C
390Xenopus laevisMutation(s): 2 
Gene Names: grin1
Find proteins for A0A1L8F5J9 (Xenopus laevis)
Go to UniProtKB:  A0A1L8F5J9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 2B
B, D
364Homo sapiensMutation(s): 1 
Gene Names: GRIN2B (NMDAR2B)
Find proteins for Q13224 (Homo sapiens)
Go to Gene View: GRIN2B
Go to UniProtKB:  Q13224
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
5SL
Query on 5SL

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Download CCD File 
A, C
~{N}-[(1~{S},3~{S})-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]cyclopentyl]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-amine
C20 H21 N7 O
JTKNIJDRSHYXLX-GJZGRUSLSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.162 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 268.880α = 90.00
b = 59.940β = 116.51
c = 144.450γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
BUSTERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-11-20 
  • Released Date: 2016-03-02 
  • Deposition Author(s): Pandit, J.

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2016-04-13
    Type: Database references