SMTL ID : 5i2n.1

Structure of the human GluN1/GluN2A LBD in complex with N-ethyl-7-{[2-fluoro-3-(trifluoromethyl)phenyl]methyl}-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide (compound 29)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: D.259 Chain B: F.138 No protein-ligand interaction detected (PLIP)

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 10 residues within 4Å: Chain A: H.87, S.113, L.114, T.115, R.120, G.171, S.172, T.173, Y.213, D.214 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.213 Hydrogen bonds: A:S.113, A:T.115, A:T.115, A:T.115, A:S.172, A:T.173, A:T.173, A:D.214, E.2 Water bridges: A:E.174, A:Y.244 Salt bridges: A:H.87, A:R.120

1 x 67J: N-ethyl-7-{[2-fluoro-3-(trifluoromethyl)phenyl]methyl}-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide(Non-covalent)

67J.3: 16 residues within 4Å: Chain A: V.128, P.129, F.130, V.131, E.132, T.241, T.242, G.243, L.262, L.263, V.266 Chain B: K.140, P.141, Y.144, L.270, H.273 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Water bridges: B:G.250, B:G.250 pi-Stacking: B:Y.144 Hydrophobic interactions: A:V.128, A:P.129, A:T.241, A:L.263 Hydrogen bonds: A:P.129 Halogen bonds: A:T.242

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 8 residues within 4Å: Chain B: S.4, T.5, R.6, L.7, K.8, D.120, P.260, W.261 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.256, B:R.256 Salt bridges: B:D.120, B:D.120

1 x GLY: GLYCINE(Non-covalent)

GLY.5: 10 residues within 4Å: Chain B: F.93, P.125, L.126, T.127, R.132, S.180, S.181, W.224, D.225, F.251 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:P.125, B:T.127, B:T.127, B:S.181, B:S.181 Water bridges: B:D.225 Salt bridges: B:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volgraf, M. et al., Discovery of GluN2A-Selective NMDA Receptor Positive Allosteric Modulators (PAMs): Tuning Deactivation Kinetics via Structure-Based Design. J.Med.Chem. (2016)

Release Date

2016-03-16

Peptides

Glutamate receptor ionotropic, NMDA 2A: A
Glutamate receptor ionotropic, NMDA 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, NMDA 2A

Glutamate receptor ionotropic, NMDA 1

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