SMTL ID : 5alp.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.145, F.148, F.150, L.151 Ligands: GOL.12 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:D.323, A:L.151 Hydrogen bonds: A:F.150 Salt bridges: A:K.145 SO4.2: 6 residues within 4Å: Chain A: L.418, M.420, V.499, H.525, W.526 Ligands: QYD.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.418 Water bridges: A:V.499, A:H.525, A:H.525 SO4.3: 8 residues within 4Å: Chain A: L.229, Y.277, R.441, M.442, V.443, T.444, E.447 Ligands: PEG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.277, A:Y.277, A:R.441 SO4.4: 5 residues within 4Å: Chain A: Y.344, I.364, A.366, W.474, A.477 No protein-ligand interaction detected (PLIP) SO4.8: 5 residues within 4Å: Chain B: K.145, F.148, F.150, L.151 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.150 Water bridges: B:L.151 Salt bridges: B:K.145 SO4.9: 6 residues within 4Å: Chain B: L.418, M.420, V.499, H.525, W.526 Ligands: QYD.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.418 Water bridges: B:V.499, B:H.525, B:H.525 SO4.10: 8 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, V.443, T.444, E.447 Ligands: PEG.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.277, B:Y.277, B:R.441 SO4.11: 5 residues within 4Å: Chain B: Y.344, I.364, A.366, W.474, A.477 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.344, B:Y.344

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: D.323 Chain B: C.142, K.145, M.146 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.142, B:M.146 GOL.12: 5 residues within 4Å: Chain A: C.142, K.145, M.146 Chain B: D.323 Ligands: SO4.1 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:D.323 Hydrogen bonds: A:C.142, A:M.146

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

PEG.6: 8 residues within 4Å: Chain A: L.229, Y.277, R.441, M.442, M.529, D.530, K.531 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.277, A:R.441, A:M.442, A:D.530 Water bridges: A:R.276 PEG.13: 8 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, M.529, D.530, K.531 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.441, B:M.442, B:D.530 Water bridges: B:R.276

2 x QYD: N-(4-NITROPHENYL)-2-PHENYL-THIOMORPHOLINE-4-CARBOXAMIDE(Non-covalent)

QYD.7: 14 residues within 4Å: Chain A: F.268, P.269, D.336, W.337, T.361, F.382, Y.384, Q.385, L.409, M.420, Y.467, H.525, W.526 Ligands: SO4.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.268, A:W.337, A:Y.384, A:W.526 Hydrogen bonds: A:D.336, A:Y.384, A:Y.467 pi-Stacking: A:F.382 QYD.14: 14 residues within 4Å: Chain B: F.268, P.269, D.336, W.337, T.361, F.382, Y.384, Q.385, L.409, M.420, Y.467, H.525, W.526 Ligands: SO4.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.268, B:W.337, B:Y.384, B:W.526 Hydrogen bonds: B:D.336 pi-Stacking: B:F.382

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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