SMTL ID : 9jfm.2 (1 other biounit)

Co-crystal Structure of sEH with tetrahydroberberine derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.13 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: D.9, D.11, G.12, 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: 7 residues within 4Å: Chain B: D.9, D.11, G.12, 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.9, B:L.10, B:D.11, B:D.11, B:N.124 Salt bridges: B:K.160

2 x 01: 1-[(13~{a}~{R})-2,3-dimethoxy-6,8,13,13~{a}-tetrahydro-5~{H}-isoquinolino[3,2-a]isoquinolin-10-yl]-3-[[4-(trifluoromethyloxy)phenyl]methyl]urea

01.3: 26 residues within 4Å: Chain A: F.267, P.268, D.335, W.336, M.339, I.363, P.364, A.365, N.366, P.371, S.374, I.375, F.381, Y.383, Q.384, L.408, L.417, M.419, L.428, Y.466, M.469, V.498, L.499, M.503, H.524, W.525 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.375, A:F.381, A:F.381, A:L.408, A:V.498, A:L.499 Hydrogen bonds: A:D.335, A:Y.383, A:Q.384, A:H.524 Halogen bonds: A:L.408 01.6: 26 residues within 4Å: Chain B: F.267, P.268, D.335, W.336, M.339, I.363, P.364, A.365, N.366, P.371, S.374, I.375, F.381, Y.383, Q.384, L.408, L.417, M.419, L.428, Y.466, M.469, V.498, L.499, M.503, H.524, W.525 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.375, B:F.381, B:F.381, B:L.408, B:V.498, B:L.499 Hydrogen bonds: B:D.335, B:Y.383, B:Q.384, B:H.524 Halogen bonds: B:L.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Co-crystal Structure of sEH with tetrahydroberberine derivative. To Be Published

Release Date

2025-09-10

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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