5TPA

Structure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500)

• PDB DOI:  https://doi.org/10.2210/pdb5TPA/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-10-20 Released: 2016-11-30 
• Deposition Author(s): Wallweber, H.J.A., Lupardus, P.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.241 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

GluN2A-Selective Pyridopyrimidinone Series of NMDAR Positive Allosteric Modulators with an Improved in Vivo Profile.

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

(2017) ACS Med Chem Lett 8: 84-89

• PubMed: 28105280 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00388
• Primary Citation of Related Structures:  
  5TP9, 5TPA


• PubMed Abstract: 
  

The N -methyl-d-aspartate receptor (NMDAR) is an ionotropic glutamate receptor, gated by the endogenous coagonists glutamate and glycine, permeable to Ca ²⁺ and Na ⁺ . NMDAR dysfunction is associated with numerous neurological and psychiatric disorders, including schizophrenia, depression, and Alzheimer's disease. Recently, we have disclosed GNE-0723 ( 1 ), a GluN2A subunit-selective and brain-penetrant positive allosteric modulator (PAM) of NMDARs. This work highlights the discovery of a related pyridopyrimidinone core with distinct structure-activity relationships, despite the structural similarity to GNE-0723. GNE-5729 ( 13 ), a pyridopyrimidinone-based NMDAR PAM, was identified with both an improved pharmacokinetic profile and increased selectivity against AMPARs. We also include X-ray structure analysis and modeling to propose hypotheses for the activity and selectivity differences.

---

Organizational Affiliation: 

Department of Discovery Chemistry, Department of Neurosciences, Department of Biochemical and Cellular Pharmacology, Department of Drug Metabolism and Pharmacokinetics, and Department of Structural Biology, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.92 kDa 
• Atom Count: 4,539 
• Modelled Residue Count: 554 
• Deposited Residue Count: 578 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A	A	285	Homo sapiens	Mutation(s): 0  Gene Names: GRIN2A, NMDAR2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q12879 (Homo sapiens) Explore Q12879  Go to UniProtKB:  Q12879
PHAROS:  Q12879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	B	293	Homo sapiens	Mutation(s): 0  Gene Names: GRIN1, NMDAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q05586 (Homo sapiens) Explore Q05586  Go to UniProtKB:  Q05586
PHAROS:  Q05586

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7H2	D [auth A]	(1R,2R)-2-(2-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-6-yl)cyclopropane-1-carbonitrile C18 H13 Cl F3 N5 O PXLJMGCNGCDJTO-CMPLNLGQSA-N
GLU	C [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
GLY	E [auth B]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7H2	BindingDB:  5TPA	EC50: min: 41, max: 77 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.241 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.757	α = 90
b = 90.239	β = 90
c = 122.658	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-30 
Deposition Author(s): Wallweber, H.J.A., Lupardus, P.J.

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2016-12-28
  Changes: Database references
• Version 1.2: 2017-02-01
  Changes: Database references