SMTL ID : 5all.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

6 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.442, A:T.444 Water bridges: A:Y.277, A:Y.277 SO4.2: 7 residues within 4Å: Chain A: K.145, M.146, F.148, D.149, F.150, L.151 Ligands: DMS.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.148 Water bridges: A:L.151 Salt bridges: A:K.145 SO4.3: 6 residues within 4Å: Chain A: D.336, W.337, Y.384, Y.467, L.500 Ligands: II6.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.336 SO4.7: 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:M.442, B:T.444 SO4.8: 7 residues within 4Å: Chain B: K.145, M.146, F.148, D.149, F.150, L.151 Ligands: DMS.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.148 Water bridges: B:L.151 Salt bridges: B:K.145 SO4.9: 6 residues within 4Å: Chain B: D.336, W.337, Y.384, Y.467, L.500 Ligands: II6.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.336, B:Y.384, B:Y.467

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain A: C.142, K.145, M.146 Chain B: D.323 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.323 DMS.6: 3 residues within 4Å: Chain B: Y.242, R.250 Ligands: DMS.12 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:Y.242 DMS.10: 5 residues within 4Å: Chain A: D.323 Chain B: C.142, K.145, M.146 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.323 DMS.12: 3 residues within 4Å: Chain A: Y.242, R.250 Ligands: DMS.6 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.242

2 x II6: [(1R,3S,5R)-3-(aminomethyl)-5-methyl-cyclohexyl]methanol(Non-covalent)

II6.5: 8 residues within 4Å: Chain A: F.268, D.336, Y.384, L.409, Y.467, H.525, W.526 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.384, A:Y.384, A:L.409, A:W.526 Hydrogen bonds: A:Y.384 II6.11: 8 residues within 4Å: Chain B: F.268, D.336, Y.384, L.409, Y.467, H.525, W.526 Ligands: SO4.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.384, B:Y.384, B:L.409, B:W.526 Hydrogen bonds: B:Y.384, B:Y.384, B:Y.467

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

SOLUBLE EPOXIDE HYDROLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

SOLUBLE EPOXIDE HYDROLASE

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