SMTL ID : 5akj.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.277, A:R.441 SO4.2: 5 residues within 4Å: Chain A: M.420, V.499, H.525, W.526 Ligands: 6N4.8 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.418, A:L.418, A:V.499 Salt bridges: A:H.525 SO4.9: 7 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, V.443, T.444, E.447 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.277, B:R.441 SO4.10: 5 residues within 4Å: Chain B: M.420, V.499, H.525, W.526 Ligands: 6N4.16 4 PLIP interactions: 4 interactions with chain B Water bridges: B:L.418, B:L.418, B:D.497 Salt bridges: B:H.525

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

DMS.3: 5 residues within 4Å: Chain A: P.34, R.35, G.36, L.37, D.40 No protein-ligand interaction detected (PLIP) DMS.4: 2 residues within 4Å: Chain A: K.145, F.148 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.151 DMS.5: 4 residues within 4Å: Chain A: R.411, E.415, S.438, L.439 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.438 Salt bridges: A:E.415 DMS.6: 3 residues within 4Å: Chain A: Q.43, K.44, G.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.43, A:G.45 DMS.7: 4 residues within 4Å: Chain A: N.86, S.88, E.91, I.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.88 Salt bridges: A:E.91 DMS.11: 5 residues within 4Å: Chain B: P.34, R.35, G.36, L.37, D.40 No protein-ligand interaction detected (PLIP) DMS.12: 2 residues within 4Å: Chain B: K.145, F.148 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.151 DMS.13: 4 residues within 4Å: Chain B: R.411, E.415, S.438, L.439 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.438 Salt bridges: B:E.415 DMS.14: 3 residues within 4Å: Chain B: Q.43, K.44, G.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.43, B:G.45 DMS.15: 4 residues within 4Å: Chain B: N.86, S.88, E.91, I.92 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.88 Salt bridges: B:E.91

2 x 6N4: 2-(1H-BENZIMIDAZOL-2-YLSULFANYL)ETHANOL(Non-covalent)

6N4.8: 11 residues within 4Å: Chain A: F.268, D.336, W.337, Y.384, Q.385, L.409, Y.467, L.500, H.525, W.526 Ligands: SO4.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.384, A:L.409, A:W.526 Hydrogen bonds: A:Y.384 Water bridges: A:Q.385 pi-Stacking: A:F.268 6N4.16: 11 residues within 4Å: Chain B: F.268, D.336, W.337, Y.384, Q.385, L.409, Y.467, L.500, H.525, W.526 Ligands: SO4.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.384, B:L.409, B:W.526 Hydrogen bonds: B:Y.384, B:Y.384, B:Y.467 Water bridges: B:Q.385 pi-Stacking: B:F.268

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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