SMTL ID : 5m2v.1

Structure of GluK1 ligand-binding domain (S1S2) in complex with (2S,4R)-4-(2-carboxyphenoxy)pyrrolidine-2-carboxylic acid at 3.18 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.18 Å

Oligo State

homo-dimer

Ligands

2 x 7E5: (2~{S},4~{R})-4-(2-carboxyphenoxy)pyrrolidine-2-carboxylic acid(Non-covalent)

7E5.1: 12 residues within 4Å: Chain A: Y.61, P.88, L.89, T.90, R.95, G.140, S.141, T.142, S.173, M.189, E.190, S.193 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.61, A:M.189 Hydrogen bonds: A:P.88, A:P.88, A:T.90, A:T.90, A:S.141, A:S.141, A:T.142, A:T.142, A:E.190 Salt bridges: A:R.95 7E5.6: 12 residues within 4Å: Chain B: E.13, Y.61, P.88, L.89, T.90, R.95, S.141, T.142, S.173, M.189, E.190, S.193 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.61 Hydrogen bonds: B:P.88, B:T.90, B:S.141, B:S.141, B:T.142, B:E.190 Salt bridges: B:R.95

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: E.195, H.244, K.247 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.244, A:K.247 SO4.3: 2 residues within 4Å: Chain A: R.31, K.54 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.31, A:K.54 SO4.4: 2 residues within 4Å: Chain A: R.20, S.22 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.20, A:K.24 SO4.7: 2 residues within 4Å: Chain B: H.244, K.247 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.244, B:K.247 SO4.8: 1 residues within 4Å: Chain B: R.31 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.31 SO4.9: 2 residues within 4Å: Chain A: R.227 Chain B: R.227 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.227 Salt bridges: B:R.227

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: M.106, T.107, Q.238 Chain B: S.213 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: P.104, F.105, M.106, T.107, Q.238 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krogsgaard-Larsen, N. et al., Design and Synthesis of a Series of l-trans-4-Substituted Prolines as Selective Antagonists for the Ionotropic Glutamate Receptors Including Functional and X-ray Crystallographic Studies of New Subtype Selective Kainic Acid Receptor Subtype 1 (GluK1) Antagonist (2S,4R)-4-(2-Carboxyphenoxy)pyrrolidine-2-carboxylic Acid. J. Med. Chem. (2017)

Release Date

2017-01-11

Peptides

Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1

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