SMTL ID : 2xx8.2 (1 other biounit)

Crystal structure of N,N-dimethyl-4-(3-(trifluoromethyl)-4,5,6,7- tetrahydro-1H-indazol-1-yl)benzamide in complex with the ligand binding domain of the Rat GluA2 receptor and glutamate at 2.2A resolution.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 11 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:P.89, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193, E.1 Water bridges: A:L.138, A:E.193, A:E.193 Salt bridges: A:R.96 GLU.7: 11 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:P.89, B:T.91, B:S.142, B:T.143, B:T.143, B:E.193, E.7 Water bridges: B:L.138, B:E.193, B:E.193 Salt bridges: B:R.96

2 x 1NE: N,N-DIMETHYL-4-[3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-INDAZOL-1-YL]BENZAMIDE(Non-covalent)

1NE.2: 19 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, S.217, K.218, L.239, S.242 Chain B: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, L.247 Ligands: 1NE.8 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.105, B:P.105 Water bridges: A:G.219, B:G.219 Halogen bonds: A:S.242, B:G.219 1NE.8: 19 residues within 4Å: Chain A: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, L.247 Chain B: K.104, P.105, F.106, M.107, S.108, S.217, K.218, L.239, S.242 Ligands: 1NE.2 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.105, B:P.105 Water bridges: A:G.219, B:G.219 Halogen bonds: A:G.219, B:S.242

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

SO4.3: 6 residues within 4Å: Chain A: R.163, A.165, E.166, S.168, F.170 Ligands: ZN.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.165 Water bridges: A:A.165, A:S.168, A:S.168, A:V.169 SO4.9: 6 residues within 4Å: Chain B: R.163, A.165, E.166, S.168, F.170 Ligands: ZN.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.165 Water bridges: B:A.165, B:S.168, B:S.168, B:V.169

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: E.166 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.166, A:E.166 ZN.5: 3 residues within 4Å: Chain A: K.20, H.23, E.30 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.23, A:E.30, A:E.30 ZN.6: 4 residues within 4Å: Chain A: E.42, K.45, H.46, L.241 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.42, A:H.46, H2O.7 ZN.10: 2 residues within 4Å: Chain B: E.166 Ligands: SO4.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.166, B:E.166 ZN.11: 3 residues within 4Å: Chain B: K.20, H.23, E.30 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.23, B:E.30, B:E.30 ZN.12: 4 residues within 4Å: Chain B: E.42, K.45, H.46, L.241 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:H.46, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ward, S.E. et al., Integration of Lead Optimization with Crystallography for a Membrane-Bound Ion Channel Target: Discovery of a New Class of Ampa Receptor Positive Allosteric Modulators. J.Med.Chem. (2011)

Release Date

2011-04-27

Peptides

GLUTAMATE RECEPTOR 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

GLUTAMATE RECEPTOR 2

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