SMTL ID : 6ind.1

Crystal structure of PDE4D complexed with a novel inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

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

AKO.1: 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.272, A:F.276, A:I.312 Hydrogen bonds: A:Q.305 pi-Stacking: A:F.308 AKO.8: 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

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.137 Ligands: ZN.3 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.9: 1 residues within 4Å: Chain B: D.237 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.237, H2O.8, H2O.9 MG.10: 3 residues within 4Å: Chain B: D.137, E.166 Ligands: ZN.11 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.8, H2O.8, H2O.8, H2O.9, H2O.11

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.5 ZN.11: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.10 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.8, H2O.10

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

EDO.4: 5 residues within 4Å: Chain A: S.144, F.276, S.291, P.292, C.294 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.144, A:S.144, A:P.292 Water bridges: A:Q.279, A:Q.279 EDO.5: 3 residues within 4Å: Chain A: H.314, P.315, E.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.314 Water bridges: A:D.310 EDO.6: 4 residues within 4Å: Chain A: K.198, I.201, D.202 Chain B: N.160 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.202 EDO.7: 5 residues within 4Å: Chain A: N.160, S.162 Chain B: K.198, I.201, D.202 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:S.162 Hydrogen bonds: B:K.198, B:D.202 EDO.12: 5 residues within 4Å: Chain B: S.144, F.276, S.291, P.292, C.294 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.144, B:P.292 Water bridges: B:S.291

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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