SMTL ID : 8s76.1 (1 other biounit)

Soluble epoxide hydrolase in complex with PROTAC JSF67

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x 01: ~{N}-[[4-[3-[1-[2-[2-[2-[[2-[2,6-bis(oxidanylidene)piperidin-3-yl]-1,3-bis(oxidanylidene)isoindol-5-yl]amino]-2-oxidanylidene-ethoxy]ethoxy]ethyl]-1,2,3-triazol-4-yl]propylsulfonylamino]-2-(trifluoromethyl)phenyl]methyl]-1-[(3-fluorophenyl)methyl]indole-5-carboxamide

01.1: 18 residues within 4Å: Chain A: F.70, P.71, D.138, W.139, M.142, T.163, P.164, F.184, Y.186, Q.187, L.211, M.222, Y.269, V.301, L.302, M.306, H.327, W.328 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.163, A:F.184, A:Y.269, A:V.301, A:L.302, A:H.327 Hydrogen bonds: A:Y.269 Water bridges: A:D.299, A:V.301 pi-Stacking: A:W.139, A:W.139, A:W.139, A:H.327, A:W.328 Halogen bonds: A:F.70

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

EDO.2: 6 residues within 4Å: Chain A: L.53, M.96, K.97, L.116, E.119, M.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.97, A:E.119, A:E.119 EDO.3: 5 residues within 4Å: Chain A: S.41, H.42, 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.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: 3 residues within 4Å: Chain A: K.318, R.319, W.344 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.319 Water bridges: A:K.318, A:R.319, A:W.344, A:S.347 EDO.6: 4 residues within 4Å: Chain A: P.37, Y.75, E.248, F.252 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: K.118, V.121, T.122, Y.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.122 EDO.8: 8 residues within 4Å: Chain A: L.149, F.165, P.167, S.282, L.283, G.284, R.285, W.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.282, A:S.282

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 4 residues within 4Å: Chain A: G.61, P.62, R.156 Ligands: PEG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.61, A:R.156 PEG.10: 8 residues within 4Å: Chain A: G.61, P.62, A.63, R.90, L.129, Q.131, R.156 Ligands: PEG.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.63, A:R.90, A:S.130, A:Q.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Soluble epoxide hydrolase in complex with PROTAC JSF67. To Be Published

Release Date

2025-03-12

Peptides

Bifunctional epoxide hydrolase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional epoxide hydrolase 2

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