SMTL ID : 4wcu.1

PDE4 complexed with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x 3KQ: N-benzyl-2-{6-[(3,5-dichloropyridin-4-yl)acetyl]-2,3-dimethoxyphenoxy}acetamide(Non-covalent)

3KQ.1: 19 residues within 4Å: Chain A: Y.81, H.82, T.193, M.195, D.240, L.241, N.243, W.254, T.255, I.258, M.259, F.262, M.279, Q.291, F.294, I.298, F.354, Q.355, L.358 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.195, A:L.358 Hydrogen bonds: A:Q.291 Water bridges: A:Q.291 pi-Stacking: A:F.294, A:F.354 3KQ.4: 17 residues within 4Å: Chain B: Y.81, H.82, T.193, M.195, D.240, L.241, N.243, Y.251, T.255, I.258, F.262, M.279, Q.291, F.294, I.298, F.354, Q.355 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:M.195, B:I.258 Hydrogen bonds: B:Q.291, B:Q.355 pi-Stacking: B:F.294, B:F.354 3KQ.7: 15 residues within 4Å: Chain C: Y.81, T.193, M.195, D.240, L.241, N.243, T.255, I.258, F.262, M.279, Q.291, F.294, I.298, F.354, Q.355 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:M.195, C:I.258 Hydrogen bonds: C:Q.291, C:Q.355 pi-Stacking: C:F.294, C:F.354 3KQ.10: 17 residues within 4Å: Chain D: Y.81, T.193, M.195, D.240, L.241, N.243, Y.251, T.255, I.258, F.262, M.279, Q.291, F.294, I.298, F.354, Q.355, L.358 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:M.195, D:F.354, D:F.354, D:L.358 Hydrogen bonds: D:Q.291 Water bridges: D:M.195 pi-Stacking: D:F.294

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.86, A:H.122, A:D.123, A:D.240 ZN.5: 6 residues within 4Å: Chain B: H.82, H.86, H.122, D.123, D.240 Ligands: MG.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.86, B:H.122, B:D.123, B:D.240 ZN.8: 6 residues within 4Å: Chain C: H.82, H.86, H.122, D.123, D.240 Ligands: MG.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.86, C:H.122, C:D.123, C:D.240 ZN.11: 5 residues within 4Å: Chain D: H.86, H.122, D.123, D.240 Ligands: MG.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.86, D:H.122, D:D.123, D:D.240

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: D.123 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.123, H2O.4 MG.6: 2 residues within 4Å: Chain B: D.123 Ligands: ZN.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.123 MG.9: 2 residues within 4Å: Chain C: D.123 Ligands: ZN.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.123 MG.12: 2 residues within 4Å: Chain D: D.123 Ligands: ZN.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.123

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

2014-10-08

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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