SMTL ID : 5ai4.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 5 residues within 4Å: Chain A: L.229, Y.277, R.441, M.442, T.444 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.277 Salt bridges: A:E.447 DMS.2: 5 residues within 4Å: Chain A: K.145, F.148, D.149, F.150, L.151 No protein-ligand interaction detected (PLIP) DMS.3: 3 residues within 4Å: Chain A: R.250, S.301, K.457 No protein-ligand interaction detected (PLIP) DMS.4: 2 residues within 4Å: Chain A: E.399, S.458 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.399 DMS.5: 6 residues within 4Å: Chain A: P.362, I.364, F.382, L.500, M.504 Ligands: 4VY.8 No protein-ligand interaction detected (PLIP) DMS.6: 5 residues within 4Å: Chain A: L.4, R.5, K.116, G.117, F.118 No protein-ligand interaction detected (PLIP) DMS.10: 5 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, T.444 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.277 Salt bridges: B:E.447 DMS.11: 5 residues within 4Å: Chain B: K.145, F.148, D.149, F.150, L.151 No protein-ligand interaction detected (PLIP) DMS.12: 3 residues within 4Å: Chain B: R.250, S.301, K.457 No protein-ligand interaction detected (PLIP) DMS.13: 2 residues within 4Å: Chain B: E.399, S.458 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.399 DMS.14: 6 residues within 4Å: Chain B: P.362, I.364, F.382, L.500, M.504 Ligands: 4VY.17 No protein-ligand interaction detected (PLIP) DMS.15: 5 residues within 4Å: Chain B: L.4, R.5, K.116, G.117, F.118 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: M.311, W.337, Y.344, M.470, N.473, A.477 Ligands: 4VY.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.473, A:N.473 Water bridges: A:Y.344 GOL.16: 7 residues within 4Å: Chain B: M.311, W.337, Y.344, M.470, N.473, A.477 Ligands: 4VY.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.473, B:N.473

4 x 4VY: 2-[(5-BROMO-2-PYRIDYL)-METHYL-AMINO]ETHANOL(Non-covalent)

4VY.8: 13 residues within 4Å: Chain A: D.336, W.337, M.340, T.361, F.382, Y.384, Q.385, Y.467, M.470, L.500 Ligands: DMS.5, GOL.7, 4VY.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.384, A:Q.385 pi-Stacking: A:W.337 4VY.9: 10 residues within 4Å: Chain A: F.268, D.336, Y.384, L.409, M.420, Y.467, V.499, H.525, W.526 Ligands: 4VY.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.526, A:W.526 pi-Stacking: A:H.525 4VY.17: 13 residues within 4Å: Chain B: D.336, W.337, M.340, T.361, F.382, Y.384, Q.385, Y.467, M.470, L.500 Ligands: DMS.14, GOL.16, 4VY.18 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.384, B:Y.384, B:Q.385, B:Y.467 Water bridges: B:D.336 pi-Stacking: B:W.337 4VY.18: 10 residues within 4Å: Chain B: F.268, D.336, Y.384, L.409, M.420, Y.467, V.499, H.525, W.526 Ligands: 4VY.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.526, B:W.526 pi-Stacking: 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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