SMTL ID : 5am2.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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:V.443 SO4.2: 7 residues within 4Å: Chain A: W.337, M.340, F.382, Q.385, Y.467, L.500 Ligands: KUF.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.385, A:Q.385 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:V.443 SO4.10: 7 residues within 4Å: Chain B: W.337, M.340, F.382, Q.385, Y.467, L.500 Ligands: KUF.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.385, B:Q.385 Water bridges: B:Y.384, B:Y.467

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

DMS.3: 4 residues within 4Å: Chain A: K.145, F.148, F.150, L.151 No protein-ligand interaction detected (PLIP) DMS.11: 4 residues within 4Å: Chain B: K.145, F.148, F.150, L.151 No protein-ligand interaction detected (PLIP)

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

PEG.4: 4 residues within 4Å: Chain A: I.306, Q.389, P.391, R.468 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.389 PEG.12: 4 residues within 4Å: Chain B: I.306, Q.389, P.391, R.468 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.389

8 x KUF: 7-METHYL-2H-ISOQUINOLIN-1-ONE(Non-covalent)

KUF.5: 7 residues within 4Å: Chain A: F.268, Y.384, F.388, L.409, L.429, V.499 Ligands: KUF.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.384, A:Y.384, A:F.388, A:L.409, A:L.429, A:L.429, A:V.499 Water bridges: A:Y.467 pi-Stacking: A:Y.384 KUF.6: 8 residues within 4Å: Chain A: L.409, K.496, D.497, F.498, V.499, H.525, W.526 Ligands: KUF.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.498, A:V.499, A:H.525 pi-Stacking: A:W.526 KUF.7: 8 residues within 4Å: Chain A: W.337, M.340, Y.344, I.364, M.470, N.473 Ligands: SO4.2, KUF.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.344, A:N.473 Hydrogen bonds: A:N.473 Water bridges: A:Q.385, A:Q.385, A:Y.467, A:N.469 pi-Stacking: A:W.337 KUF.8: 5 residues within 4Å: Chain A: I.364, P.372, S.375, F.382 Ligands: KUF.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.364, A:F.382 Hydrogen bonds: A:S.375, A:S.375 KUF.13: 7 residues within 4Å: Chain B: F.268, Y.384, F.388, L.409, L.429, V.499 Ligands: KUF.14 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.384, B:Y.384, B:F.388, B:L.409, B:L.429, B:L.429, B:V.499 Water bridges: B:Y.467 pi-Stacking: B:Y.384 KUF.14: 8 residues within 4Å: Chain B: L.409, K.496, D.497, F.498, V.499, H.525, W.526 Ligands: KUF.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.498, B:V.499, B:H.525 pi-Stacking: B:W.526 KUF.15: 8 residues within 4Å: Chain B: W.337, M.340, Y.344, I.364, M.470, N.473 Ligands: SO4.10, KUF.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.344, B:N.473 Hydrogen bonds: B:N.473 Water bridges: B:Q.385, B:Q.385, B:Y.467, B:N.469 pi-Stacking: B:W.337 KUF.16: 5 residues within 4Å: Chain B: I.364, P.372, S.375, F.382 Ligands: KUF.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.364, B:F.382 Hydrogen bonds: B:S.375, B:S.375

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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