SMTL ID : 5akz.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: K.145, M.146, F.148, D.149, F.150, L.151 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.145 SO4.2: 5 residues within 4Å: Chain A: L.409, S.416, M.420, H.525, W.526 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.416, A:W.526 Water bridges: A:H.525, A:H.525 SO4.3: 7 residues within 4Å: Chain A: L.229, Y.277, R.441, M.442, V.443, T.444, E.447 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.277, A:Y.277, A:R.441 SO4.4: 6 residues within 4Å: Chain A: Y.344, A.366, N.473, W.474, A.477 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.367, A:W.474, A:W.474 SO4.8: 6 residues within 4Å: Chain B: K.145, M.146, F.148, D.149, F.150, L.151 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.145 SO4.9: 5 residues within 4Å: Chain B: L.409, S.416, M.420, H.525, W.526 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.416, B:W.526 Water bridges: B:H.525, B:H.525 SO4.10: 7 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, V.443, T.444, E.447 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.277, B:Y.277, B:R.441 SO4.11: 6 residues within 4Å: Chain B: Y.344, A.366, N.473, W.474, A.477 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.367, B:W.474, B:W.474

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: W.337, I.376, Q.385, Y.467, M.470, N.473 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.385, A:Q.389, A:Y.467, A:N.473 Water bridges: A:M.470 GOL.6: 6 residues within 4Å: Chain A: L.481, G.482, R.483, K.484, D.510, W.511 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.482, A:W.511 GOL.12: 7 residues within 4Å: Chain B: W.337, I.376, Q.385, Y.467, M.470, N.473 Ligands: SO4.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.385, B:Q.389, B:Y.467, B:N.473 Water bridges: B:M.470 GOL.13: 6 residues within 4Å: Chain B: L.481, G.482, R.483, K.484, D.510, W.511 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.482, B:W.511

2 x 6NX: 1-CYCLOHEXYL-3-METHYL-UREA(Non-covalent)

6NX.7: 7 residues within 4Å: Chain A: D.336, W.337, Y.384, Q.385, Y.467, L.500, H.525 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.337, A:L.500 Hydrogen bonds: A:D.336, A:Y.384, A:Y.467, A:H.525 6NX.14: 7 residues within 4Å: Chain B: D.336, W.337, Y.384, Q.385, Y.467, L.500, H.525 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.337, B:L.500 Hydrogen bonds: B:D.336, B:H.525

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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