SMTL ID : 5ake.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 5 residues within 4Å: Chain A: K.145, F.148, D.149, F.150, L.151 No protein-ligand interaction detected (PLIP) DMS.2: 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 Water bridges: A:Y.277 Salt bridges: A:E.447 DMS.7: 5 residues within 4Å: Chain B: K.145, F.148, D.149, F.150, L.151 No protein-ligand interaction detected (PLIP) DMS.8: 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 Salt bridges: B:E.447

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: T.27, L.31, P.84, N.86, F.87, S.88, E.91, I.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.86, A:N.86, A:S.88 GOL.4: 3 residues within 4Å: Chain A: A.285, I.540, D.544 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.537 GOL.9: 8 residues within 4Å: Chain B: T.27, L.31, P.84, N.86, F.87, S.88, E.91, I.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.86, B:N.86, B:S.88 GOL.10: 3 residues within 4Å: Chain B: A.285, I.540, D.544 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.537

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

SO4.5: 5 residues within 4Å: Chain A: L.409, V.499, H.525, W.526 Ligands: 6N0.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.499 SO4.11: 5 residues within 4Å: Chain B: L.409, V.499, H.525, W.526 Ligands: 6N0.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.499

2 x 6N0: N-(5,5-dioxodibenzothiophen-2-yl)-4,4-difluoro-piperidine-1-carboxamide(Non-covalent)

6N0.6: 17 residues within 4Å: Chain A: F.268, D.336, W.337, M.340, T.361, Y.384, Q.385, L.409, L.418, M.420, L.429, Y.467, V.499, L.500, H.525, W.526 Ligands: SO4.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.268, A:W.337, A:Y.384, A:Y.384, A:L.418, A:L.429, A:V.499, A:W.526 Hydrogen bonds: A:D.336 6N0.12: 17 residues within 4Å: Chain B: F.268, D.336, W.337, M.340, T.361, Y.384, Q.385, L.409, L.418, M.420, L.429, Y.467, V.499, L.500, H.525, W.526 Ligands: SO4.11 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.268, B:W.337, B:Y.384, B:Y.384, B:L.418, B:L.429, B:V.499, B:W.526 Hydrogen bonds: B:D.336, B:Y.384, B:Y.467

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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