SMTL ID : 5alt.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: L.229, Y.277, R.441, M.442, V.443, T.444 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.277, A:R.441 SO4.8: 6 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, V.443, T.444 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.277, B:R.441

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

DMS.2: 5 residues within 4Å: Chain A: K.145, M.146, F.148, F.150, L.151 No protein-ligand interaction detected (PLIP) DMS.3: 4 residues within 4Å: Chain A: P.502, Q.503, Q.506, R.517 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: F.268, D.336, Y.384, M.420, Y.467 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.336 DMS.5: 7 residues within 4Å: Chain A: Y.344, I.364, P.365, A.366, W.474, A.477 Ligands: 9XZ.7 No protein-ligand interaction detected (PLIP) DMS.9: 5 residues within 4Å: Chain B: K.145, M.146, F.148, F.150, L.151 No protein-ligand interaction detected (PLIP) DMS.10: 4 residues within 4Å: Chain B: P.502, Q.503, Q.506, R.517 No protein-ligand interaction detected (PLIP) DMS.11: 5 residues within 4Å: Chain B: F.268, D.336, Y.384, M.420, Y.467 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.384, B:Y.467 Salt bridges: B:D.336 DMS.12: 7 residues within 4Å: Chain B: Y.344, I.364, P.365, A.366, W.474, A.477 Ligands: 9XZ.14 No protein-ligand interaction detected (PLIP)

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

PEG.6: 6 residues within 4Å: Chain A: S.258, G.259, P.260, G.286, R.548, N.549 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.258 Water bridges: A:N.549 PEG.13: 6 residues within 4Å: Chain B: S.258, G.259, P.260, G.286, R.548, N.549 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.258 Water bridges: B:N.549

2 x 9XZ: 3-(2-methyltetrazol-5-yl)-5-(3-thienyl)pyridin-2-amine(Non-covalent)

9XZ.7: 11 residues within 4Å: Chain A: D.336, W.337, M.340, I.364, S.375, I.376, F.382, Q.385, M.470, L.500 Ligands: DMS.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.364, A:I.376, A:L.500 pi-Stacking: A:W.337, A:W.337, A:F.382 9XZ.14: 11 residues within 4Å: Chain B: D.336, W.337, M.340, I.364, S.375, I.376, F.382, Q.385, M.470, L.500 Ligands: DMS.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.364, B:I.376, B:L.500 pi-Stacking: B:W.337, B:W.337, 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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