SMTL ID : 6fr2.1

Soluble epoxide hydrolase in complex with LK864

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

2 x E3N: 1-[(4~{S})-9-propan-2-ylsulfonyl-1-oxa-9-azaspiro[5.5]undecan-4-yl]-3-[[4-(trifluoromethyloxy)phenyl]methyl]urea(Non-covalent)

E3N.1: 15 residues within 4Å: Chain A: D.117, W.118, M.121, I.157, F.163, Y.165, Q.166, L.190, S.197, M.201, Y.248, M.251, V.280, H.306, W.307 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.118, A:I.157, A:F.163, A:F.163, A:L.190, A:V.280 Hydrogen bonds: A:D.117, A:Y.165, A:H.306 pi-Stacking: A:H.306, A:W.307 Halogen bonds: A:S.197 E3N.3: 15 residues within 4Å: Chain B: D.117, W.118, M.121, I.157, F.163, Y.165, Q.166, L.190, S.197, M.201, Y.248, M.251, V.280, H.306, W.307 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.118, B:I.157, B:F.163, B:F.163, B:L.190, B:V.280 Hydrogen bonds: B:D.117, B:Y.165, B:H.306 pi-Stacking: B:H.306, B:W.307 Halogen bonds: B:S.197

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: H.288, D.291 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.288, A:D.291, A:D.291, H2O.4 MG.4: 2 residues within 4Å: Chain B: H.288, D.291 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.288, B:D.291, B:D.291, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lukin, A. et al., Discovery of polar spirocyclic orally bioavailable urea inhibitors of soluble epoxide hydrolase. Bioorg. Chem. (2018)

Release Date

2018-09-12

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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