SMTL ID : 4kp6.1

Crystal structure of human phosphodiesterase 4B (PDE4B) in complex with a [1,3,5]triazine derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x 1S1: 2-ethyl-2-{[4-(methylamino)-6-(1H-1,2,4-triazol-1-yl)-1,3,5-triazin-2-yl]amino}butanenitrile(Non-covalent)

1S1.1: 13 residues within 4Å: Chain A: Y.86, H.87, M.200, L.246, N.248, Y.256, T.260, I.263, F.267, M.284, S.295, Q.296, F.299 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.263 Hydrogen bonds: A:N.248, A:Q.296 Water bridges: A:Y.86, A:D.245 pi-Stacking: A:F.267, A:F.299, A:F.299

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.128 Ligands: ZN.3 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.128, H2O.1, H2O.1, H2O.5, H2O.5, H2O.5

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.91, H.127, D.128, D.245 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.91, A:H.127, A:D.128, A:D.245, H2O.5, H2O.5

19 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: T.61, F.62, N.178, L.179, T.180, Q.183 Ligands: EDO.21 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: R.63, I.64, S.65, T.68, D.174, I.175, M.177, N.178 Ligands: EDO.14 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: N.136, I.140, D.152, E.153, S.154, V.155, D.199, S.201 Ligands: EDO.22 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: G.30, L.31, I.33, D.94, K.251, L.255, W.259 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: S.104, T.105, P.106, D.109 Ligands: EDO.19 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: L.102, T.105, W.311, V.315, D.318, I.322 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: D.193, L.196, A.197, K.202, R.238 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: L.146, M.149, Y.150, H.159, A.162 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain A: H.87, H.131, G.133, V.134, S.135, E.266, F.267, Q.270 Ligands: EDO.18 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: S.65, D.67 Ligands: EDO.14 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: S.65, D.67, T.68, H.172 Ligands: EDO.5, EDO.13 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: F.176, R.184, R.188 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: L.168, D.174, R.184, R.188 Ligands: EDO.15 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: N.27, E.55, R.56, H.100, S.104 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: S.135, F.267, S.282, P.283, M.284, C.285 Ligands: EDO.12 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: L.103, L.108, D.109, A.110, V.111, F.112, I.117 Ligands: EDO.8 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: R.56, D.57, L.58, T.61, D.114, I.117 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: T.61, F.62, D.114, Q.183 Ligands: EDO.4 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: E.153, S.154, D.199, K.202 Ligands: EDO.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gewald, R. et al., Discovery of triazines as potent, selective and orally active PDE4 inhibitors. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-07-10

Peptides

cAMP-specific 3',5'-cyclic phosphodiesterase 4B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cAMP-specific 3',5'-cyclic phosphodiesterase 4B