SMTL ID : 3o0j.1

PDE4B In complex with ligand an2898

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.77, H.113, D.114, D.231 Ligands: MG.2, 3OJ.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.77, A:H.113, A:D.114, A:D.231, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.114 Ligands: ZN.1, 3OJ.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.114, H2O.3, H2O.3, H2O.5, H2O.5

1 x 3OJ: 4-[(1-hydroxy-1,3-dihydro-2,1-benzoxaborol-5-yl)oxy]benzene-1,2-dicarbonitrile(Non-covalent)

3OJ.3: 11 residues within 4Å: Chain A: H.73, H.77, D.114, H.117, M.186, D.231, L.232, M.270, F.285 Ligands: ZN.1, MG.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.232, A:F.285, A:F.285 Hydrogen bonds: A:Q.282 Water bridges: A:E.143, A:E.143

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

EDO.4: 7 residues within 4Å: Chain A: T.47, F.48, N.164, L.165, T.166, Q.169 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.164, A:T.166, A:Q.169 EDO.5: 10 residues within 4Å: Chain A: R.49, I.50, S.51, T.54, D.160, I.161, F.162, M.163, N.164 Ligands: EDO.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.51, A:S.51, A:T.54, A:M.163 Water bridges: A:R.49, A:N.164 EDO.6: 4 residues within 4Å: Chain A: S.90, P.92, D.95 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.90 Water bridges: A:R.42 EDO.7: 7 residues within 4Å: Chain A: L.88, T.91, W.297, V.301, D.304, A.305, I.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.91, A:W.297 EDO.8: 4 residues within 4Å: Chain A: D.179, A.183, K.188, R.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.179, A:R.224 EDO.9: 5 residues within 4Å: Chain A: L.132, M.135, Y.136, H.145, A.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.136, A:Y.136 EDO.10: 8 residues within 4Å: Chain A: H.73, H.117, G.119, V.120, S.121, E.252, F.253, Q.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.73, A:Q.256 EDO.11: 5 residues within 4Å: Chain A: S.51, D.53, T.54, H.158 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.51, A:D.53, A:T.54 EDO.12: 3 residues within 4Å: Chain A: F.162, R.170, R.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.170, A:R.174 Water bridges: A:R.170 EDO.13: 6 residues within 4Å: Chain A: N.13, E.41, R.42, H.86, S.90 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.41, A:S.90 EDO.14: 6 residues within 4Å: Chain A: L.89, L.94, D.95, A.96, V.97, F.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.95, A:A.96, A:V.97, A:F.98 EDO.15: 6 residues within 4Å: Chain A: R.42, D.43, L.44, T.47, D.100, I.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.47, A:T.47 EDO.16: 5 residues within 4Å: Chain A: T.47, F.48, D.100, Q.169 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.100, A:D.100 Water bridges: A:D.100 EDO.17: 5 residues within 4Å: Chain A: E.139, S.140, D.185, S.187, K.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.188, A:K.188 Water bridges: A:S.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freund, Y.R. et al., Boron-based phosphodiesterase inhibitors show novel binding of boron to PDE4 bimetal center. Febs Lett. (2012)

Release Date

2011-08-10

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

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