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 
  • R-Value Observed: 0.164 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1124/mol.115.103036
  • Primary Citation of Related Structures:  
    5EWJ, 5EWL, 5EWM

  • 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 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.).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NMDA glutamate receptor subunit
A, C
390Xenopus laevisMutation(s): 2 
Gene Names: grin1NR1
UniProt
Find proteins for A0A1L8F5J9 (Xenopus laevis)
Explore A0A1L8F5J9 
Go to UniProtKB:  A0A1L8F5J9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L8F5J9
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2B
B, D
364Homo sapiensMutation(s): 1 
Gene Names: GRIN2BNMDAR2B
UniProt & NIH Common Fund Data Resources
Find proteins for Q13224 (Homo sapiens)
Explore Q13224 
Go to UniProtKB:  Q13224
PHAROS:  Q13224
GTEx:  ENSG00000273079 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13224
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q13224-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5SL
Query on 5SL

Download Ideal Coordinates CCD File 
H [auth A],
Q [auth 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
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]
K [auth B]
L [auth B]
P [auth C]
R [auth D]
G [auth A],
K [auth B],
L [auth B],
P [auth C],
R [auth D],
S [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]
I [auth A]
J [auth A]
M [auth B]
N [auth B]
F [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 268.88α = 90
b = 59.94β = 116.51
c = 144.45γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2016-04-13
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary