SMTL ID : 5tp9.1

Structure of the human GluN1/GluN2A LBD in complex with compound 2 (GNE9178)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 3 residues within 4Å: Chain A: R.39, Y.80, R.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.106 Water bridges: A:R.39 Salt bridges: A:R.39

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:G.171, A:Y.244 Salt bridges: A:H.87, A:R.120

1 x 7H0: 7-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-N-ethyl-2-methyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide(Non-covalent)

7H0.3: 17 residues within 4Å: Chain A: I.116, V.128, P.129, F.130, V.131, E.132, T.242, G.243, L.262, L.263, V.266, M.271 Chain B: K.140, P.141, Y.144, L.270, H.273 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:V.128, A:P.129, A:L.262, B:P.141, B:Y.144 Hydrogen bonds: A:P.129 Halogen bonds: A:T.242 Water bridges: B:G.250, B:G.250, B:G.250 pi-Stacking: B:Y.144, B:Y.144

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain B: W.261 No protein-ligand interaction detected (PLIP)

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:T.127, B:T.127, B:S.181, B:S.181, B:D.225 Water bridges: B:D.225 Salt bridges: B:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Villemure, E. et al., GluN2A-Selective Pyridopyrimidinone Series of NMDAR Positive Allosteric Modulators with an Improved in Vivo Profile. ACS Med Chem Lett (2017)

Release Date

2016-11-30

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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