SMTL ID : 7xaa.1

Crystal structure of PDE4D catalytic domain complexed with compound 21d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.164, H.200, D.201, D.318 Ligands: MG.2 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.3, H2O.6 ZN.4: 6 residues within 4Å: Chain B: H.160, H.164, H.200, D.201, D.318 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.164, B:H.200, B:D.201, B:D.318, H2O.12, H2O.12

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.201 Ligands: ZN.1, AQL.3 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.201, H2O.2, H2O.3, H2O.3, H2O.6, H2O.8 MG.5: 4 residues within 4Å: Chain B: D.201, E.230 Ligands: ZN.4, AQL.6 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.201, H2O.12, H2O.12, H2O.13, H2O.13, H2O.15

2 x AQL: 8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-9-oxidanyl-5-(pyridin-4-ylmethoxy)pyrano[3,2-b]xanthen-6-one(Non-covalent)

AQL.3: 14 residues within 4Å: Chain A: Y.159, T.271, M.273, D.318, N.321, P.322, W.332, T.333, I.336, M.357, Q.369, F.372, I.376 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.159, A:M.273, A:P.322, A:I.336, A:I.336, A:I.376 Hydrogen bonds: A:Q.369 Water bridges: A:M.273 pi-Stacking: A:F.340, A:F.372, A:F.372 AQL.6: 13 residues within 4Å: Chain B: Y.159, T.271, M.273, D.318, N.321, P.322, W.332, T.333, I.336, M.357, Q.369, F.372 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:M.273, B:P.322, B:I.336, B:I.336, B:F.372 Hydrogen bonds: B:Q.369 Water bridges: B:M.273 pi-Stacking: B:F.372, B:F.372 pi-Cation interactions: B:H.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., Discovery of novel PDE4 inhibitors targeting the M-pocket from natural mangostanin with improved safety for the treatment of Inflammatory Bowel Diseases. Eur.J.Med.Chem. (2022)

Release Date

2023-02-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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