SMTL ID : 5wh5.1 (1 other biounit)

Crystal structure of the PDE4D2 catalytic domain in complex with inhibitor (R)-Zl-n-91

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x R91: 1-[4-(difluoromethoxy)-3-{[(3R)-oxolan-3-yl]oxy}phenyl]-3-methylbutan-1-one(Non-covalent)

R91.1: 16 residues within 4Å: Chain A: Y.74, M.188, D.233, L.234, N.236, P.237, Y.244, W.247, T.248, I.251, M.252, F.255, M.272, S.283, Q.284, F.287 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.234, A:I.251, A:F.255, A:F.287 Hydrogen bonds: A:Q.284

1 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.5

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.2, H2O.4, H2O.5 MG.4: 3 residues within 4Å: Chain A: D.66, Y.68, H.69 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.66, A:Y.68, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, X. et al., Identification of a PDE4-Specific Pocket for the Design of Selective Inhibitors. Biochemistry (2018)

Release Date

2018-07-18

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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