SMTL ID : 4w1o.1 (1 other biounit)

PDE4D complexed with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 3GJ: N-(3,5-dichloropyridin-4-yl)-3-[(3-ethyl-1,2-oxazol-5-yl)methoxy]-4-methoxybenzamide(Non-covalent)

3GJ.1: 15 residues within 4Å: Chain A: Y.81, H.82, T.193, M.195, D.240, L.241, N.243, Y.251, T.255, I.258, F.262, M.279, S.290, Q.291, F.294 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.81, A:F.294, A:F.294 Hydrogen bonds: A:Q.291 Water bridges: A:Y.81 Halogen bonds: A:D.240 3GJ.4: 17 residues within 4Å: Chain B: Y.81, H.82, T.193, M.195, D.240, L.241, N.243, Y.251, W.254, T.255, I.258, F.262, M.279, S.290, Q.291, F.294, I.298 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.294, B:I.298 Hydrogen bonds: B:Q.291 Water bridges: B:M.195 pi-Stacking: B:F.294 Halogen bonds: B:D.240

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.86, A:H.122, A:D.123, A:D.240 ZN.3: 2 residues within 4Å: Chain A: D.123 Ligands: ZN.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.123, H2O.1, H2O.1, H2O.2, H2O.2 ZN.5: 4 residues within 4Å: Chain B: H.86, H.122, D.123, D.240 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.86, B:H.122, B:D.123, B:D.240 ZN.6: 2 residues within 4Å: Chain B: H.122, D.123 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.123, H2O.4, H2O.6, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Felding, J. et al., Discovery and Early Clinical Development of 2-{6-[2-(3,5-Dichloro-4-pyridyl)acetyl]-2,3-dimethoxyphenoxy}-N-propylacetamide (LEO 29102), a Soft-Drug Inhibitor of Phosphodiesterase 4 for Topical Treatment of Atopic Dermatitis. J.Med.Chem (2014)

Release Date

2014-11-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

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

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