SMTL ID : 5alu.1

ligand complex structure of soluble epoxide hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

6 x HD2: 4-cyclopentyl-N-[(1S,3R)-5-oxidanyl-2-adamantyl]-2-[[(3S)-oxolan-3-yl]amino]pyrimidine-5-carboxamide(Non-covalent)

HD2.1: 20 residues within 4Å: Chain A: D.12, A.19, V.20, F.21, G.22, F.42, Q.43, G.46, P.47, T.51, T.52, M.55, R.100, N.125, W.127, V.160, K.161, P.162, D.186, I.187 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.12, A:F.21, A:F.42, A:Q.43, A:T.51, A:W.127 Hydrogen bonds: A:T.52, A:N.125 Water bridges: A:D.12, A:D.12, A:Q.43, A:T.52 HD2.4: 16 residues within 4Å: Chain A: F.363, I.364, P.365, N.367, M.370, P.372, S.375, I.376, N.379, F.382, Q.385, M.470, M.504, H.507 Ligands: DMS.3, HD2.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.364, A:I.376, A:F.382, A:F.382 Hydrogen bonds: A:Q.385, A:Q.385 Water bridges: A:N.367 HD2.7: 22 residues within 4Å: Chain A: F.268, P.269, D.336, W.337, M.340, T.361, I.364, F.382, Y.384, Q.385, F.388, L.409, M.420, L.429, Y.467, D.497, F.498, V.499, L.500, H.525, W.526 Ligands: HD2.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.337, A:I.364, A:Y.384, A:L.409, A:Y.467, A:L.500 Hydrogen bonds: A:D.336, A:D.497 Water bridges: A:H.525 pi-Stacking: A:H.525 HD2.8: 20 residues within 4Å: Chain B: D.12, A.19, V.20, F.21, G.22, F.42, Q.43, G.46, P.47, T.51, T.52, M.55, R.100, N.125, W.127, V.160, K.161, P.162, D.186, I.187 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:D.12, B:F.21, B:F.42, B:Q.43, B:T.51, B:W.127 Hydrogen bonds: B:T.52, B:N.125 Water bridges: B:D.12, B:D.12, B:D.12, B:Q.43 HD2.11: 16 residues within 4Å: Chain B: F.363, I.364, P.365, N.367, M.370, P.372, S.375, I.376, N.379, F.382, Q.385, M.470, M.504, H.507 Ligands: DMS.10, HD2.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.364, B:I.376, B:F.382, B:F.382 Hydrogen bonds: B:Q.385, B:Q.385 Water bridges: B:N.367 HD2.14: 22 residues within 4Å: Chain B: F.268, P.269, D.336, W.337, M.340, T.361, I.364, F.382, Y.384, Q.385, F.388, L.409, M.420, L.429, Y.467, D.497, F.498, V.499, L.500, H.525, W.526 Ligands: HD2.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.337, B:I.364, B:Y.384, B:L.409, B:Y.467, B:L.500 Hydrogen bonds: B:D.336, B:Y.384, B:Y.467, B:D.497 Water bridges: B:H.525 pi-Stacking: B:H.525

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

DMS.2: 5 residues within 4Å: Chain A: K.145, M.146, F.148, F.150, L.151 No protein-ligand interaction detected (PLIP) DMS.3: 9 residues within 4Å: Chain A: M.311, M.340, I.364, P.365, A.366, N.473, W.474, A.477 Ligands: HD2.4 No protein-ligand interaction detected (PLIP) DMS.5: 6 residues within 4Å: Chain A: L.229, Y.277, 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.6: 4 residues within 4Å: Chain A: L.191, T.201, I.202, L.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.201, A:L.203 DMS.9: 5 residues within 4Å: Chain B: K.145, M.146, F.148, F.150, L.151 No protein-ligand interaction detected (PLIP) DMS.10: 9 residues within 4Å: Chain B: M.311, M.340, I.364, P.365, A.366, N.473, W.474, A.477 Ligands: HD2.11 No protein-ligand interaction detected (PLIP) DMS.12: 6 residues within 4Å: Chain B: L.229, Y.277, R.441, M.442, V.443, T.444 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.447 DMS.13: 4 residues within 4Å: Chain B: L.191, T.201, I.202, L.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.203

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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