SMTL ID : 5aki.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.145, F.148, F.150, L.151 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:L.151, B:D.323 SO4.2: 7 residues within 4Å: Chain A: Y.344, I.364, A.366, N.473, W.474, A.477 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.344 Water bridges: A:W.474, A:W.474 SO4.11: 4 residues within 4Å: Chain B: K.145, F.148, F.150, L.151 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.151 SO4.12: 7 residues within 4Å: Chain B: Y.344, I.364, A.366, N.473, W.474, A.477 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.344, B:Y.344 Water bridges: B:W.474, B:W.474

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: W.337, Q.385, Y.467, M.470, N.473 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.385, A:Y.467, A:N.473 GOL.4: 4 residues within 4Å: Chain A: I.306, E.307, R.468, R.472 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.307, A:R.472, A:R.472 GOL.5: 1 residues within 4Å: Chain A: G.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.45, A:G.45 GOL.13: 6 residues within 4Å: Chain B: W.337, Q.385, Y.467, M.470, N.473 Ligands: SO4.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.385, B:Y.467, B:N.473 GOL.14: 4 residues within 4Å: Chain B: I.306, E.307, R.468, R.472 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.307, B:E.307, B:R.472, B:R.472 GOL.15: 1 residues within 4Å: Chain B: G.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.45, B:G.45

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

PEG.6: 2 residues within 4Å: Chain A: F.150, T.173 No protein-ligand interaction detected (PLIP) PEG.7: 5 residues within 4Å: Chain A: P.502, S.505, Q.506, R.517, H.519 No protein-ligand interaction detected (PLIP) PEG.8: 6 residues within 4Å: Chain A: Q.108, M.112, Q.221, T.225, P.226, P.228 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.108, A:Q.221 Water bridges: A:K.116, A:T.225 PEG.16: 2 residues within 4Å: Chain B: F.150, T.173 No protein-ligand interaction detected (PLIP) PEG.17: 5 residues within 4Å: Chain B: P.502, S.505, Q.506, R.517, H.519 No protein-ligand interaction detected (PLIP) PEG.18: 6 residues within 4Å: Chain B: Q.108, M.112, Q.221, T.225, P.226, P.228 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.108, B:Q.221 Water bridges: B:K.116

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

DMS.9: 2 residues within 4Å: Chain A: M.146, D.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.237 DMS.19: 2 residues within 4Å: Chain B: M.146, D.237 No protein-ligand interaction detected (PLIP)

2 x 6NF: N-(CYCLOHEXYLMETHYL)-3-(4-PYRIDYL)-1H-PYRAZOL-5-AMINE(Non-covalent)

6NF.10: 9 residues within 4Å: Chain A: F.268, D.336, W.337, Y.384, Q.385, L.409, M.420, Y.467, H.525 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.409 Hydrogen bonds: A:Y.384, A:Y.467, A:H.525 Water bridges: A:F.268 pi-Stacking: A:W.337, A:W.337, A:W.337 6NF.20: 9 residues within 4Å: Chain B: F.268, D.336, W.337, Y.384, Q.385, L.409, M.420, Y.467, H.525 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.409 Hydrogen bonds: B:H.525 Water bridges: B:F.268 pi-Stacking: B:W.337, B:W.337, B:W.337

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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