SMTL ID : 3wk4.1

Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.9, D.11, D.184, D.185 Ligands: PO4.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.9, A:D.11, A:D.185, H2O.2 MG.4: 5 residues within 4Å: Chain B: D.9, D.11, D.184, D.185 Ligands: PO4.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.9, B:D.11, B:D.185, H2O.6

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

PO4.2: 7 residues within 4Å: Chain A: D.9, L.10, D.11, T.123, N.124, K.160 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.9, A:D.9, A:L.10, A:D.11, A:N.124 Water bridges: A:D.11, A:D.11, A:K.160, A:K.160 Salt bridges: A:K.160 PO4.5: 7 residues within 4Å: Chain B: D.9, L.10, D.11, T.123, N.124, K.160 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.9, B:D.9, B:L.10, B:D.11, B:T.123, B:N.124 Water bridges: B:K.160, B:K.160 Salt bridges: B:K.160

2 x S0A: 1-[(1R)-1-cyclopropylethyl]-3-phenylurea(Non-covalent)

S0A.3: 12 residues within 4Å: Chain A: F.267, D.335, W.336, M.339, T.360, Y.383, Q.384, M.419, Y.466, L.499, H.524, W.525 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.267, A:W.336, A:T.360, A:Y.383, A:L.499, A:W.525 Hydrogen bonds: A:D.335, A:D.335, A:Y.383, A:Y.466 S0A.6: 12 residues within 4Å: Chain B: F.267, D.335, W.336, M.339, T.360, Y.383, Q.384, M.419, Y.466, L.499, H.524, W.525 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.267, B:W.336, B:T.360, B:Y.383, B:L.499, B:W.525 Hydrogen bonds: B:D.335, B:D.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amano, Y. et al., Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography. Bioorg.Med.Chem. (2014)

Release Date

2014-04-16

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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