SMTL ID : 9kpi.1

Aromatic acetyl piperidine derivatives as soluble epoxide hydrolase inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x 01: 1-[1-[2-(3,5-dimethoxyphenyl)ethanoyl]piperidin-4-yl]-3-[[4-(trifluoromethyloxy)phenyl]methyl]urea

01.1: 20 residues within 4Å: Chain A: F.267, D.335, W.336, M.339, T.360, I.363, S.374, I.375, F.381, Y.383, Q.384, L.408, M.419, Y.466, M.469, V.498, L.499, M.503, H.524, W.525 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.336, A:F.381, A:L.408, A:V.498, A:L.499 Hydrogen bonds: A:D.335, A:D.335 Halogen bonds: A:L.408 01.4: 20 residues within 4Å: Chain B: F.267, D.335, W.336, M.339, T.360, I.363, S.374, I.375, F.381, Y.383, Q.384, L.408, M.419, Y.466, M.469, V.498, L.499, M.503, H.524, W.525 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.336, B:F.381, B:L.408, B:V.498, B:L.499 Hydrogen bonds: B:D.335, B:D.335, B:Y.383, B:Y.466 Halogen bonds: B:L.408

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.9, D.11, D.185 Ligands: PO4.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.9, A:D.11, A:D.185, H2O.3 MG.5: 4 residues within 4Å: Chain B: D.9, D.11, D.185 Ligands: PO4.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.9, B:D.11, B:D.185, H2O.13

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 7 residues within 4Å: Chain A: D.9, L.10, D.11, T.123, N.124, K.160 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.9, A:L.10, A:D.11, A:T.123, A:N.124 Water bridges: A:D.9, A:N.124, A:K.160, A:K.160, A:K.160 Salt bridges: A:K.160 PO4.6: 7 residues within 4Å: Chain B: D.9, L.10, D.11, T.123, N.124, K.160 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.9, B:L.10, B:D.11, B:N.124 Water bridges: B:D.9, B:N.124, B:K.160, B:K.160, B:K.160 Salt bridges: B:K.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Aromatic acetyl piperidine derivatives as soluble epoxide hydrolase inhibitor. To Be Published

Release Date

2025-04-16

Peptides

Bifunctional epoxide hydrolase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bifunctional epoxide hydrolase 2

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