SMTL ID : 5ewj.1 (1 other biounit)

CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 4 residues within 4Å: Chain A: Q.349, N.367, S.369, Y.370 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: Y.106, F.115, D.342 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.109, A:F.115

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 4 residues within 4Å: Chain A: N.275, S.277, A.278, V.333 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.275 NAG.4: 1 residues within 4Å: Chain B: N.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.44 NAG.5: 1 residues within 4Å: Chain B: N.311 No protein-ligand interaction detected (PLIP)

1 x QEL: 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol(Non-covalent)

QEL.6: 16 residues within 4Å: Chain A: Y.87, T.88, F.91, R.93, S.110, I.111, L.113 Chain B: P.48, A.77, Q.80, I.81, F.84, Y.145, F.146, P.147, E.206 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:Y.87, A:L.113, A:L.113, B:P.48, B:P.48, B:A.77, B:I.81, B:F.84, B:F.84 Hydrogen bonds: B:Q.80, B:T.144, B:E.206 Water bridges: B:Y.145 pi-Stacking: B:F.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroebel, D. et al., A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists. Mol.Pharmacol. (2016)

Release Date

2016-03-02

Peptides

NMDA glutamate receptor subunit: A
Glutamate receptor ionotropic, NMDA 2B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NMDA glutamate receptor subunit

Glutamate receptor ionotropic, NMDA 2B

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