SMTL ID : 5ali.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: V.417, M.420, V.499, H.525, W.526 Ligands: Q3B.6 4 PLIP interactions: 4 interactions with chain A Water bridges: A:V.499, A:H.525, A:H.525 Salt bridges: A:H.525 SO4.2: 7 residues within 4Å: Chain A: L.229, Y.277, R.441, M.442, V.443, T.444, E.447 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.277, A:R.441 Water bridges: A:Y.277, A:Y.277, A:E.447 SO4.3: 4 residues within 4Å: Chain A: Q.43, K.44, G.45, G.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.43, A:G.45 SO4.4: 5 residues within 4Å: Chain A: K.145, M.146, F.148, F.150, L.151 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:D.323, A:L.151, A:L.151 Salt bridges: A:K.145 SO4.8: 6 residues within 4Å: Chain B: V.417, M.420, V.499, H.525, W.526 Ligands: Q3B.13 4 PLIP interactions: 4 interactions with chain B Water bridges: B:V.499, B:H.525, B:H.525 Salt bridges: B:H.525 SO4.9: 7 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, V.443, T.444, E.447 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.441 Water bridges: B:Y.277, B:Y.277, B:Y.277, B:E.447 SO4.10: 4 residues within 4Å: Chain B: Q.43, K.44, G.45, G.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.43, B:G.45 SO4.11: 5 residues within 4Å: Chain B: K.145, M.146, F.148, F.150, L.151 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.145, B:L.151, B:L.151 Salt bridges: B:K.145

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

PEG.5: 5 residues within 4Å: Chain A: L.486, H.514 Chain B: S.62, Q.63 Ligands: PEG.14 No protein-ligand interaction detected (PLIP) PEG.7: 2 residues within 4Å: Chain A: P.66 Ligands: PEG.12 No protein-ligand interaction detected (PLIP) PEG.12: 5 residues within 4Å: Chain A: S.62, Q.63 Chain B: L.486, H.514 Ligands: PEG.7 No protein-ligand interaction detected (PLIP) PEG.14: 2 residues within 4Å: Chain B: P.66 Ligands: PEG.5 No protein-ligand interaction detected (PLIP)

2 x Q3B: 1-[3-[5-(7-aminothiazolo[5,4-d]pyrimidin-2-yl)-1-[[(2S)-tetrahydrofuran-2-yl]methyl]imidazol-4-yl]phenyl]-3-(4-methoxyphenyl)urea(Non-covalent)

Q3B.6: 16 residues within 4Å: Chain A: F.268, D.336, W.337, M.340, Y.344, I.364, F.382, Y.384, Q.385, L.409, M.420, Y.467, L.500, M.504, H.525 Ligands: SO4.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.268, A:W.337, A:W.337, A:Y.384, A:L.500 Hydrogen bonds: A:D.336, A:I.364, A:Y.384, A:Q.385, A:Y.467, A:H.525 pi-Stacking: A:F.382 Q3B.13: 16 residues within 4Å: Chain B: F.268, D.336, W.337, M.340, Y.344, I.364, F.382, Y.384, Q.385, L.409, M.420, Y.467, L.500, M.504, H.525 Ligands: SO4.8 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.268, B:W.337, B:W.337, B:Y.384, B:L.500 Hydrogen bonds: B:D.336, B:Y.344, B:I.364, B:Q.385, B:H.525 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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