5KDT | pdb_00005kdt

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 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1021/acs.jmedchem.5b02010
  • Primary Citation Related Structures: 
    5I2K, 5I2N, 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 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
    • Pharmaron-Beijing Co. Ltd. , 6 Taihe Road, BDA, Beijing 100176, PR China.

Macromolecule Content 

  • Total Structure Weight: 66.04 kDa 
  • Atom Count: 4,607 
  • Modeled Residue Count: 562 
  • Deposited Residue Count: 578 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2A285Homo sapiensMutation(s): 0 
Gene Names: GRIN2ANMDAR2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q12879 (Homo sapiens)
Explore Q12879 
Go to UniProtKB:  Q12879
PHAROS:  Q12879
GTEx:  ENSG00000183454 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12879
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1293Homo sapiensMutation(s): 0 
Gene Names: GRIN1NMDAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q05586 (Homo sapiens)
Explore Q05586 
Go to UniProtKB:  Q05586
PHAROS:  Q05586
GTEx:  ENSG00000176884 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05586
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6RV

Query on 6RV



Download:Ideal Coordinates CCD File
E [auth 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
GLU

Query on GLU



Download:Ideal Coordinates CCD File
D [auth A]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
GLY

Query on GLY



Download:Ideal Coordinates CCD File
F [auth B]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
6RV BindingDB:  5KDT EC50: min: 21, max: 7400 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free:  0.240 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary