SMTL ID : 5am4.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: Q.43, K.44, G.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.43, A:Q.43, A:G.45 Water bridges: A:G.45 SO4.2: 6 residues within 4Å: Chain A: D.336, W.337, M.340, T.361, Q.385, L.500 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.385 SO4.11: 3 residues within 4Å: Chain B: Q.43, K.44, G.45 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.43, B:Q.43, B:G.45 Water bridges: B:G.45 SO4.12: 6 residues within 4Å: Chain B: D.336, W.337, M.340, T.361, Q.385, L.500 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.385 Water bridges: B:Y.384

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

DMS.3: 6 residues within 4Å: Chain A: S.408, R.411, S.416, L.418, P.434, P.437 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: L.229, R.441, M.442, V.443, T.444 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.277 Salt bridges: A:E.447 DMS.5: 5 residues within 4Å: Chain A: C.142, L.256, A.283, Q.284 Chain B: G.326 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.284 DMS.6: 5 residues within 4Å: Chain A: K.145, F.148, D.149, F.150, L.151 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.145, A:K.145 DMS.7: 4 residues within 4Å: Chain A: P.34, R.35, G.36, L.37 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.40 DMS.9: 7 residues within 4Å: Chain A: R.354, P.488, D.546, A.547, R.548 Chain B: A.132, R.134 No protein-ligand interaction detected (PLIP) DMS.10: 6 residues within 4Å: Chain A: R.104, L.107, Q.108, L.111, H.147, T.231 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.108 DMS.13: 6 residues within 4Å: Chain B: S.408, R.411, S.416, L.418, P.434, P.437 No protein-ligand interaction detected (PLIP) DMS.14: 5 residues within 4Å: Chain B: L.229, R.441, M.442, V.443, T.444 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.277 Salt bridges: B:E.447 DMS.15: 5 residues within 4Å: Chain A: G.326 Chain B: C.142, L.256, A.283, Q.284 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.284 DMS.16: 5 residues within 4Å: Chain B: K.145, F.148, D.149, F.150, L.151 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:K.145, A:D.323 DMS.17: 4 residues within 4Å: Chain B: P.34, R.35, G.36, L.37 No protein-ligand interaction detected (PLIP) DMS.19: 7 residues within 4Å: Chain A: A.132, R.134 Chain B: R.354, P.488, D.546, A.547, R.548 No protein-ligand interaction detected (PLIP) DMS.20: 6 residues within 4Å: Chain B: R.104, L.107, Q.108, L.111, H.147, T.231 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.108

2 x MVJ: 5-cyclohexylspiro[1H-indole-3,4'-oxane]-2-one(Non-covalent)

MVJ.8: 13 residues within 4Å: Chain A: F.268, Y.384, F.388, L.409, V.417, L.418, M.420, L.429, D.497, F.498, V.499, H.525, W.526 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.268, A:Y.384, A:F.388, A:L.409, A:L.429, A:V.499, A:H.525, A:W.526 Hydrogen bonds: A:L.418, A:D.497, A:F.498, A:V.499 pi-Stacking: A:H.525 MVJ.18: 13 residues within 4Å: Chain B: F.268, Y.384, F.388, L.409, V.417, L.418, M.420, L.429, D.497, F.498, V.499, H.525, W.526 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.268, B:Y.384, B:F.388, B:L.409, B:L.429, B:V.499, B:H.525, B:W.526 Hydrogen bonds: B:L.418, B:D.497, B:D.497, B:F.498, B:V.499 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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