SMTL ID : 3wka.1

Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.9, D.11, D.184, D.185, I.186 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.9, A:D.11, A:D.185 MG.4: 6 residues within 4Å: Chain B: D.9, D.11, D.184, D.185, I.186 Ligands: PO4.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.9, B:D.11, B:D.185

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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.9, A:D.9, A:L.10, A:D.11, A:N.124 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 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.9, B:D.9, B:L.10, B:D.11, B:T.123, B:N.124 Salt bridges: B:K.160

2 x S0G: 6-amino-1-methyl-5-(piperidin-1-yl)pyrimidine-2,4(1H,3H)-dione(Non-covalent)

S0G.3: 8 residues within 4Å: Chain A: F.267, Y.383, M.419, D.496, F.497, V.498, H.524, W.525 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.267, A:Y.383, A:W.525 Hydrogen bonds: A:D.496, A:F.497, A:V.498 S0G.6: 8 residues within 4Å: Chain B: F.267, Y.383, M.419, D.496, F.497, V.498, H.524, W.525 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.267, B:Y.383, B:W.525 Hydrogen bonds: B:D.496, B:F.497, B:V.498 Water bridges: B:Y.383

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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