SMTL ID : 5ak6.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: L.229, Y.277, R.441, M.442, V.443, T.444, E.447 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.277, A:Y.277, A:R.441 SO4.2: 6 residues within 4Å: Chain A: K.145, M.146, F.148, D.149, F.150, L.151 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:D.323, A:K.145, A:L.151 Salt bridges: A:K.145 SO4.9: 7 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, V.443, T.444, E.447 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.277, B:Y.277, B:R.441 SO4.10: 6 residues within 4Å: Chain B: K.145, M.146, F.148, D.149, F.150, L.151 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.145, B:L.151 Salt bridges: B:K.145

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

PEG.3: 5 residues within 4Å: Chain A: T.533, N.536, Q.537, I.540, K.541 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.533, A:K.541 PEG.4: 6 residues within 4Å: Chain A: P.372, S.375, I.376, N.379, F.382 Ligands: YPN.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.372, A:N.379 Water bridges: A:S.375 PEG.11: 5 residues within 4Å: Chain B: T.533, N.536, Q.537, I.540, K.541 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.533, B:K.541 PEG.12: 6 residues within 4Å: Chain B: P.372, S.375, I.376, N.379, F.382 Ligands: YPN.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.372, B:N.379 Water bridges: B:S.375

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: C.142, A.283, Q.284 Chain B: G.326, S.328 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:S.258, A:S.258, A:A.283, B:G.326, B:S.328 GOL.13: 5 residues within 4Å: Chain A: G.326, S.328 Chain B: C.142, A.283, Q.284 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:S.258, B:S.258, B:A.283, A:G.326, A:S.328

6 x YPN: 2-[(5-CHLORO-2-PYRIDYL)SULFANYL]ETHANOL(Non-covalent)

YPN.6: 9 residues within 4Å: Chain A: D.336, W.337, M.340, Y.384, Q.385, Y.467, M.470 Ligands: YPN.7, YPN.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.384, A:Q.385, A:Y.467, A:Y.467 pi-Stacking: A:W.337, A:W.337 YPN.7: 12 residues within 4Å: Chain A: D.336, Y.384, L.409, R.411, S.416, M.420, D.497, V.499, L.500, H.525, W.526 Ligands: YPN.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.526 Hydrogen bonds: A:R.411, A:R.411 Water bridges: A:V.499 pi-Stacking: A:H.525 YPN.8: 10 residues within 4Å: Chain A: M.340, Y.344, P.362, I.364, A.366, W.474, L.500, M.504 Ligands: PEG.4, YPN.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.364 Water bridges: A:N.367 YPN.14: 9 residues within 4Å: Chain B: D.336, W.337, M.340, Y.384, Q.385, Y.467, M.470 Ligands: YPN.15, YPN.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.385, B:Y.467 pi-Stacking: B:W.337, B:W.337 YPN.15: 12 residues within 4Å: Chain B: D.336, Y.384, L.409, R.411, S.416, M.420, D.497, V.499, L.500, H.525, W.526 Ligands: YPN.14 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.526 Hydrogen bonds: B:R.411, B:R.411 Water bridges: B:V.499 pi-Stacking: B:H.525 YPN.16: 10 residues within 4Å: Chain B: M.340, Y.344, P.362, I.364, A.366, W.474, L.500, M.504 Ligands: PEG.12, YPN.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.364 Water bridges: B:N.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oster, L. et al., Successful Generation of Structural Information for Fragment-Based Drug Discovery. Drug Discov Today (2015)

Release Date

2015-05-13

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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