SMTL ID : 5ale.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: D.336, W.337, M.340, Q.385, L.500 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.337, A:Q.385 SO4.2: 5 residues within 4Å: Chain A: K.145, F.148, F.150, L.151 Ligands: GOL.6 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.145, A:K.145, A:K.145, A:L.151, A:L.151 Salt bridges: A:K.145 SO4.3: 6 residues within 4Å: Chain A: L.229, Y.277, R.441, M.442, V.443, T.444 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.277, A:R.441 Water bridges: A:Y.277 SO4.8: 5 residues within 4Å: Chain B: D.336, W.337, M.340, Q.385, L.500 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.337 Water bridges: B:Y.384, B:Y.384, B:Q.385, B:Q.385 SO4.9: 5 residues within 4Å: Chain B: K.145, F.148, F.150, L.151 Ligands: GOL.13 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Water bridges: A:D.323, B:K.145, B:K.145, B:L.151, B:L.151 Salt bridges: B:K.145 SO4.10: 6 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, V.443, T.444 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.441 Water bridges: B:Y.277, B:Y.277, B:Y.277, B:Y.277

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: Q.43, K.44, G.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.43, A:G.45 Water bridges: A:G.45 GOL.5: 5 residues within 4Å: Chain A: L.256, A.283, Q.284 Chain B: G.326, S.328 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.283 Water bridges: A:S.258, A:Q.284, A:Q.284, A:Q.284, B:S.328 GOL.6: 5 residues within 4Å: Chain A: C.142, K.145, M.146 Chain B: D.323 Ligands: SO4.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.146 Water bridges: B:D.323 GOL.11: 3 residues within 4Å: Chain B: Q.43, K.44, G.45 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.43, B:G.45 Water bridges: B:G.45 GOL.12: 5 residues within 4Å: Chain A: G.326, S.328 Chain B: L.256, A.283, Q.284 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.283 Water bridges: B:S.258, B:Q.284, B:Q.284, B:Q.284, A:S.328 GOL.13: 5 residues within 4Å: Chain A: D.323 Chain B: C.142, K.145, M.146 Ligands: SO4.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:D.323, A:D.323 Hydrogen bonds: B:M.146

2 x ONR: 4-chloro-2-isoxazol-5-yl-phenol(Non-covalent)

ONR.7: 9 residues within 4Å: Chain A: F.268, Y.384, F.388, L.409, M.420, Y.467, V.499, H.525, W.526 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.384, A:L.409, A:V.499, A:H.525, A:W.526 Water bridges: A:D.336, A:Y.384 pi-Stacking: A:W.526 ONR.14: 9 residues within 4Å: Chain B: F.268, Y.384, F.388, L.409, M.420, Y.467, V.499, H.525, W.526 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.384, B:L.409, B:V.499, B:H.525, B:W.526 Water bridges: B:D.336, B:Y.384 pi-Stacking: B:W.526

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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