SMTL ID : 6aum.1

Crystal structure of human soluble epoxide hydrolase complexed with trans-4-[4-(3-trifluoromethoxyphenyl-l-ureido)-cyclohexyloxy]-benzoic acid.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: D.9, L.10, D.11, F.20, T.123, N.124, K.160, D.185 Ligands: MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.10, A:D.11, A:T.123, A:N.124 Water bridges: A:D.9, A:D.11 Salt bridges: A:K.160 PO4.7: 9 residues within 4Å: Chain B: D.9, L.10, D.11, F.20, T.123, N.124, K.160, D.185 Ligands: MG.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:L.10, B:D.11, B:N.124 Water bridges: B:D.9, B:D.11, B:D.11, B:D.11 Salt bridges: B:K.160

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.9, D.11, D.184, D.185 Ligands: PO4.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.9, A:D.11, A:D.185, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain B: D.9, D.11, D.184, D.185 Ligands: PO4.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.9, B:D.11, B:D.185, H2O.1, H2O.2

2 x BXV: 4-{[trans-4-({[4-(trifluoromethoxy)phenyl]carbamoyl}amino)cyclohexyl]oxy}benzoic acid(Non-covalent)

BXV.3: 19 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, F.387, L.408, L.417, M.419, L.428, Y.466, V.498, M.503 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.267, A:T.360, A:I.363, A:I.375, A:F.381, A:Y.383 Hydrogen bonds: A:D.335, A:D.335 BXV.9: 19 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, F.387, L.408, L.417, M.419, L.428, Y.466, V.498, M.503 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.267, B:T.360, B:I.363, B:I.375, B:F.381, B:Y.383 Hydrogen bonds: B:D.335, B:D.335, B:Y.383, B:Y.466

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

CL.4: 1 residues within 4Å: Chain A: M.419 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.144, F.147 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: Y.276, T.443 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: M.419 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: K.144, F.147 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: Y.276, T.443 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kodani, S.D. et al., Identification and optimization of soluble epoxide hydrolase inhibitors with dual potency towards fatty acid amide hydrolase. Bioorg. Med. Chem. Lett. (2018)

Release Date

2018-02-07

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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