SMTL ID : 4myq.1

Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 19T: (4-{[2-(5-chlorothiophen-2-yl)-5-ethyl-6-methylpyrimidin-4-yl]amino}phenyl)acetic acid(Non-covalent)

19T.1: 14 residues within 4Å: Chain A: Y.86, H.87, S.135, M.200, N.248, T.260, I.263, F.267, M.284, Q.296, F.299, L.355, K.358, F.359 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.299, A:F.299, A:F.359 Hydrogen bonds: A:Q.296 Water bridges: A:Y.86, A:S.135, A:K.358 Salt bridges: A:K.358 pi-Stacking: 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.2, H2O.2, H2O.6, H2O.7

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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.91, A:H.127, A:D.128, A:D.245, H2O.7

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: E.77, D.78, Y.80, S.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.80, A:S.82

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

EDO.5: 5 residues within 4Å: Chain A: L.23, E.24, L.26, N.27, E.55 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.24, A:N.27 EDO.6: 4 residues within 4Å: Chain A: F.62, R.63, N.178, Q.183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.63, A:Q.183, A:Q.183 Water bridges: A:R.63 EDO.7: 5 residues within 4Å: Chain A: A.110, V.111, F.112, T.113, R.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fox, D. et al., Structural basis for the design of selective phosphodiesterase 4B inhibitors. Cell Signal (2014)

Release Date

2014-01-01

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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