SMTL ID : 8qzd.1

Soluble epoxide hydrolase in complex with Epoxykinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: R.319, G.320, H.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.319, A:H.321, A:H.321 EDO.2: 6 residues within 4Å: Chain A: I.108, E.109, R.270, N.271, R.274 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.271, A:R.274 EDO.3: 6 residues within 4Å: Chain A: R.270, N.271, M.272, E.273, R.274 Ligands: EDO.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.272, A:E.273, A:R.274 Water bridges: A:R.270 EDO.4: 6 residues within 4Å: Chain A: T.33, S.34, C.35, N.36, M.40, P.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.36, A:N.36 EDO.5: 4 residues within 4Å: Chain A: S.41, G.43, F.55, E.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.41, A:S.41, A:E.57 EDO.6: 6 residues within 4Å: Chain A: Q.131, P.152, V.155, R.156, I.289, P.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.156 EDO.7: 4 residues within 4Å: Chain A: Q.202, N.203, L.204, S.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.204, A:S.205 EDO.8: 7 residues within 4Å: Chain A: L.149, F.165, S.282, L.283, G.284, R.285, W.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.282, A:G.284 EDO.10: 5 residues within 4Å: Chain A: L.211, S.218, L.220, W.328 Ligands: XDZ.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.211, A:L.220 Water bridges: A:L.220 EDO.11: 3 residues within 4Å: Chain A: H.42, Y.44, E.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.44, A:E.101 EDO.13: 3 residues within 4Å: Chain A: P.105, E.107, E.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.107 EDO.14: 2 residues within 4Å: Chain A: R.285, K.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.286

1 x XDZ: 2-[5-bromanyl-3-[2,2,2-tris(fluoranyl)ethanoyl]indol-1-yl]-N-cycloheptyl-ethanamide(Non-covalent)

XDZ.9: 17 residues within 4Å: Chain A: F.70, D.138, W.139, M.142, Y.186, Q.187, F.190, L.211, M.222, L.231, Y.269, D.299, V.301, L.302, H.327 Ligands: EDO.10, BR.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.139, A:W.139, A:V.301, A:L.302, A:H.327 Hydrogen bonds: A:D.138, A:Y.269

1 x BR: BROMIDE ION(Non-covalent)

BR.12: 4 residues within 4Å: Chain A: K.298, D.299, F.300 Ligands: XDZ.9 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dotsch, L. et al., Discovery of the sEH Inhibitor Epoxykynin as a Potent Kynurenine Pathway Modulator. J.Med.Chem. (2024)

Release Date

2024-02-28

Peptides

Bifunctional epoxide hydrolase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional epoxide hydrolase 2

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