SMTL ID : 5ewj.2 (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 NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: Y.106, H.112, L.113, F.115, D.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.342 Water bridges: A:K.109

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

NAG.2: 5 residues within 4Å: Chain A: N.272, N.275, S.277, A.278, V.333 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.278, A:V.333 Hydrogen bonds: A:S.277 NAG.3: 1 residues within 4Å: Chain B: N.44 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain B: N.311, T.313 No protein-ligand interaction detected (PLIP)

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

QEL.5: 17 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, T.144, Y.145, F.146, P.147, E.206 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.48, B:P.48, B:A.77, B:Q.80, B:I.81, B:F.84, B:F.84, A:Y.87, A:L.113, A:L.113, A:L.113 Hydrogen bonds: B:Q.80, B:Q.80, B:T.144, B:Y.145, B:E.206 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
C

B
D

NMDA glutamate receptor subunit

Glutamate receptor ionotropic, NMDA 2B

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