SMTL ID : 2qyl.1

Crystal structure of PDE4B2B in complex with inhibitor NPV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.88, A:H.124, A:D.125, A:D.242, H2O.1, H2O.1

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.125 Ligands: ZN.1, NPV.4 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.3: 2 residues within 4Å: Chain A: H.78, D.127 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.78, A:D.127, H2O.1, H2O.1, H2O.1, H2O.1

1 x NPV: 4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid(Non-covalent)

NPV.4: 12 residues within 4Å: Chain A: Y.83, H.84, M.197, N.245, T.257, I.260, F.264, M.281, S.292, Q.293, F.296 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.83, A:I.260, A:I.260, A:F.264, A:F.264 Hydrogen bonds: A:Q.293 Water bridges: A:M.197 pi-Stacking: A:F.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors. Biochem.J. (2007)

Release Date

2008-04-08

Peptides

Phosphodiesterase 4B, cAMP-specific: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphodiesterase 4B, cAMP-specific