SMTL ID : 3g4l.4 (3 other biounits)

Crystal structure of human phosphodiesterase 4d with roflumilast

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 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.2

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.124, D.125, E.154, T.195 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.1, H2O.1, H2O.2, H2O.2, H2O.3

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, L.252, Q.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.31, A:R.32, A:Q.255 Salt bridges: A:H.29

1 x ROF: 3-(CYCLOPROPYLMETHOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-(DIFLUOROMETHOXY)BENZAMIDE(Non-covalent)

ROF.4: 17 residues within 4Å: Chain A: Y.83, H.84, T.195, M.197, D.242, L.243, N.245, P.246, Y.253, W.256, T.257, I.260, M.261, M.281, S.292, Q.293, F.296 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.281 Hydrogen bonds: A:Q.293 Water bridges: A:D.242 pi-Stacking: A:F.296 Halogen bonds: A:D.242

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

EDO.5: 2 residues within 4Å: Chain A: K.186, D.190 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: T.72, H.76, E.167 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgin, A.B. et al., Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety. Nat.Biotechnol. (2010)

Release Date

2010-01-19

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

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

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