SMTL ID : 6inm.1

Crystal structure of PDE4D complexed with a novel inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.100, H.136, D.137, D.254 Ligands: MG.2 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.4 ZN.4: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.5 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.7, H2O.9

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.137 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.137, H2O.1, H2O.2, H2O.3, H2O.4, H2O.5 MG.5: 3 residues within 4Å: Chain B: D.137, E.166 Ligands: ZN.4 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.7, H2O.7, H2O.7, H2O.7, H2O.9

2 x AKU: (1S)-1-[2-(1H-indol-3-yl)ethyl]-6,7-dimethoxy-3,4-dihydroisoquinoline-2(1H)-carbaldehyde(Non-covalent)

AKU.3: 10 residues within 4Å: Chain A: Y.95, H.96, M.209, N.257, I.272, F.276, M.293, Q.305, F.308, I.312 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.272, A:F.276, A:F.308, A:F.308, A:I.312 Hydrogen bonds: A:Q.305 pi-Stacking: A:F.308 AKU.6: 10 residues within 4Å: Chain B: Y.95, H.96, M.209, N.257, I.272, F.276, M.293, Q.305, F.308, I.312 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.95, B:I.272, B:F.308, B:F.308, B:I.312 Hydrogen bonds: B:Q.305 pi-Stacking: B:F.308

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

EDO.7: 4 residues within 4Å: Chain B: S.144, F.276, P.292, C.294 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.144, B:P.292 Water bridges: B:Q.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Structure-Aided Identification and Optimization of Tetrahydro-isoquinolines as Novel PDE4 Inhibitors Leading to Discovery of an Effective Antipsoriasis Agent. J.Med.Chem. (2019)

Release Date

2019-10-23

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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