SMTL ID : 5wh6.1 (1 other biounit)

Crystal structure of PDE4D2 in complex with inhibitor (S_Zl-n-91)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

AKJ.1: 16 residues within 4Å: Chain A: Y.159, M.273, D.318, L.319, N.321, P.322, Y.329, W.332, T.333, I.336, M.337, F.340, M.357, S.368, Q.369, F.372 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.319, A:I.336, A:F.372 Hydrogen bonds: A:Q.369 Water bridges: A:Q.369 pi-Stacking: A:F.372

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.164, H.200, D.201, D.318 Ligands: MG.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.164, A:H.200, A:D.201, A:D.318, H2O.1, H2O.5

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.201 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.201, H2O.1, H2O.1, H2O.1, H2O.4, H2O.6 MG.4: 3 residues within 4Å: Chain A: D.151, Y.153, H.154 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.151, A:Y.153, H2O.6

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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