SMTL ID : 8zbl.1

Glycosidated glycyrrhetinic acid derivative as a soluble epoxide hydrolase inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x 01: 1-[[(2~{S},4~{a}~{S},6~{a}~{R},6~{a}~{S},6~{b}~{R},8~{a}~{R},10~{S},12~{a}~{S},14~{b}~{S})-10-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,4~{a},6~{a},6~{b},9,9,12~{a}-heptamethyl-13-oxidanylidene-3,4,5,6,6~{a},7,8,8~{a},10,11,12,14~{b}-dodecahydro-1~{H}-picen-2-yl]methyl]-3-(oxan-4-ylmethyl)urea

01.1: 20 residues within 4Å: Chain A: F.267, P.268, D.335, W.336, M.339, T.360, V.380, Y.383, Q.384, F.387, L.408, L.417, S.418, L.428, Y.466, F.497, V.498, L.499, H.524, W.525 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.267, A:V.380, A:Y.383, A:Y.383, A:Y.383, A:V.498, A:W.525 Hydrogen bonds: A:D.335, A:Y.383, A:Y.466, A:H.524 Water bridges: A:F.267

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.9, D.11, D.185 Ligands: PO4.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.9, A:D.11, A:D.185, A:D.185

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

PO4.3: 7 residues within 4Å: Chain A: D.9, L.10, D.11, T.123, N.124, K.160 Ligands: MG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.10, A:D.11, A:T.123, A:N.124, A:N.124 Salt bridges: A:K.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Q. et al., Discovery of glycosidated glycyrrhetinic acid derivatives: Natural product-based soluble epoxide hydrolase inhibitors. Eur.J.Med.Chem. (2024)

Release Date

2024-12-11

Peptides

Bifunctional epoxide hydrolase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional epoxide hydrolase 2

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