SMTL ID : 8w4q.1

Crystal structure of PDE4D complexed with CX-4945

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.137 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.137, H2O.1, H2O.1, H2O.1, H2O.1, H2O.2 MG.7: 2 residues within 4Å: Chain B: D.137 Ligands: ZN.8 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.3, H2O.3, H2O.4, H2O.4, H2O.4

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.100, H.136, D.137, D.254 Ligands: MG.1 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.100, A:H.136, A:D.137, A:D.254, H2O.1, H2O.1 ZN.8: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.7 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.100, B:H.136, B:D.137, B:D.254, H2O.3, H2O.3

2 x 3NG: 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid(Non-covalent)

3NG.3: 8 residues within 4Å: Chain A: H.96, M.209, I.272, F.276, M.293, Q.305, F.308 Ligands: EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.272, A:F.276, A:F.308 Hydrogen bonds: A:Q.305 Salt bridges: A:H.96 pi-Stacking: A:F.308, A:F.308 3NG.9: 8 residues within 4Å: Chain B: H.96, M.209, I.272, F.276, M.293, Q.305, F.308 Ligands: EDO.11 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.272, B:F.276, B:F.308 Hydrogen bonds: B:Q.305 Water bridges: B:H.96 Salt bridges: B:H.96 pi-Stacking: B:F.308, B:F.308

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: Y.95, N.257, Y.265, T.269, I.272, Q.305 Ligands: 3NG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.95, A:T.269, A:Q.305 EDO.5: 5 residues within 4Å: Chain A: S.144, F.276, S.291, P.292, C.294 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.144, A:S.144, A:P.292 Water bridges: A:S.291 EDO.6: 3 residues within 4Å: Chain A: D.337, N.338, W.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.338 EDO.10: 7 residues within 4Å: Chain B: S.144, F.276, Q.279, S.291, P.292, M.293, C.294 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.144, B:Q.279 Water bridges: B:S.291 EDO.11: 9 residues within 4Å: Chain B: Y.95, N.257, Y.265, W.268, T.269, I.272, Q.305, F.308 Ligands: 3NG.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.95, B:T.269 EDO.12: 3 residues within 4Å: Chain B: K.198, I.201, D.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Drug repurposing and structure-based discovery of new PDE4 and PDE5 inhibitors. Eur.J.Med.Chem. (2023)

Release Date

2023-11-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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