SMTL ID : 2qyn.1

Crystal structure of PDE4D2 in complex with inhibitor NPV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

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

NPV.1: 10 residues within 4Å: Chain A: Y.74, H.75, M.188, N.236, I.251, F.255, M.272, S.283, Q.284, F.287 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.74, A:I.251, A:F.255, A:F.255, A:F.287, A:F.287, A:F.287, A:F.287 Hydrogen bonds: A:Q.284 Water bridges: A:H.75, A:N.124, A:E.145, A:T.186, A:M.188 Salt bridges: A:H.75 NPV.4: 11 residues within 4Å: Chain B: Y.74, H.75, M.188, N.236, I.251, F.255, M.272, S.283, Q.284, F.287, I.291 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.74, B:N.236, B:I.251, B:F.255, B:F.255 Hydrogen bonds: B:Q.284 Water bridges: B:H.75, B:M.188 Salt bridges: B:H.75 pi-Stacking: B:F.287

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.79, H.115, D.116, D.233 Ligands: MG.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.79, A:H.115, A:D.116, A:D.233, H2O.1, H2O.1 ZN.5: 5 residues within 4Å: Chain B: H.79, H.115, D.116, D.233 Ligands: MG.6 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.79, B:H.115, B:D.116, B:D.233, H2O.9, H2O.9

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.116 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.116, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain B: D.116 Ligands: ZN.5 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.116, H2O.9, H2O.9, H2O.9, H2O.9, H2O.9

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

cAMP-specific 3',5'-cyclic phosphodiesterase 4D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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