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

Crystal structure of PDE4D catalytic domain complexed with Selaginpulvilins K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x J20: 1-[2-(4-hydroxyphenyl)ethynyl]-9,9-bis(4-methoxyphenyl)-7-oxidanyl-fluorene-2-carbaldehyde(Non-covalent)

J20.1: 13 residues within 4Å: Chain A: H.82, S.130, M.195, H.198, I.258, F.262, Q.265, P.278, M.279, C.280, Q.291, F.294, I.298 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:M.195, A:I.258, A:F.262, A:P.278, A:M.279, A:F.294, A:F.294, A:F.294, A:I.298 Hydrogen bonds: A:S.130, A:Q.291 Water bridges: A:H.82, A:H.126, A:H.126, A:Q.265 pi-Stacking: A:F.294

1 x ZN: ZINC ION(Non-covalent)

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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.123, E.152 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.123, H2O.2, H2O.2, H2O.2, H2O.2, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Y. et al., The discovery, complex crystal structure, and recognition mechanism of a novel natural PDE4 inhibitor from Selaginella pulvinata. Biochem. Pharmacol. (2017)

Release Date

2017-02-22

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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