› 5i2k

X-ray diffraction
2.86Å resolution

Structure of the human GluN1/GluN2A LBD in complex with 7-{[ethyl(4-fluorophenyl)amino]methyl}-N,2-dimethyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide (compound 19)

Released:
DOI: 10.2210/pdb5i2k/pdb
PDB entry 5i2k coloured by chain, front view.
PDB entry 5i2k coloured by chain, side view.
PDB entry 5i2k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of GluN2A-Selective NMDA Receptor Positive Allosteric Modulators (PAMs): Tuning Deactivation Kinetics via Structure-Based Design.
Volgraf M, Sellers BD, Jiang Y, Wu G, Ly CQ, Villemure E, Pastor RM, Yuen PW, Lu A, Luo X, Liu M, Zhang S, Sun L, Fu Y, Lupardus PJ, Wallweber HJ, Liederer BM, Deshmukh G, Plise E, Tay S, Reynen P, Herrington J, Gustafson A, Liu Y, Dirksen A, Dietz MG, Liu Y, Wang TM, Hanson JE, Hackos D, Scearce-Levie K, Schwarz JB
J Med Chem 59 2760-79 (2016)
PMID: 26919761

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170222 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glutamate receptor ionotropic, NMDA 2A Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 31.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12879 (Residues: 401-539, 661-802; Coverage: 20%)
Gene names: GRIN2A, NMDAR2A
Sequence domains:
Structure domains: Periplasmic binding protein-like II
Glutamate receptor ionotropic, NMDA 1 Chain: B
Molecule details ›
Chain: B
Length: 293 amino acids
Theoretical weight: 33.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q05586 (Residues: 394-544, 663-800; Coverage: 31%)
Gene names: GRIN1, NMDAR1
Sequence domains:
Structure domains: Periplasmic binding protein-like II

Ligands and Environments

3 bound ligands:
Ligand GLU 1 x GLU
Ligand GLY 1 x GLY
Ligand 67H 1 x 67H
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P212121
Unit cell:
a: 55.655Å b: 89.329Å c: 119.447Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.173 0.256
Expression system: Escherichia coli

Quick links

Citations

13 review citations

Structure, function, and allosteric modulation of NMDA receptors.
Hansen et al. (2018)
12 more