SMTL ID : 7cbj.1

Crystal structure of PDE4D catalytic domain in complex with compound 36

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 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.13: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.14 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

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.3, H2O.3, H2O.3, H2O.6 MG.14: 3 residues within 4Å: Chain B: D.137, E.166 Ligands: ZN.13 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.8, H2O.9, H2O.9, H2O.10, H2O.12

2 x FTX: (1S)-1-[(7-chloranyl-1H-indol-3-yl)methyl]-6,7-dimethoxy-3,4-dihydro-1H-isoquinoline-2-carbaldehyde(Non-covalent)

FTX.3: 11 residues within 4Å: Chain A: Y.95, H.96, M.209, N.257, T.269, I.272, F.276, M.293, Q.305, F.308, I.312 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.95, A:M.209, A:I.272, A:F.276, A:F.308, A:I.312 Hydrogen bonds: A:Q.305 pi-Stacking: A:F.308 FTX.15: 10 residues within 4Å: Chain B: Y.95, H.96, M.209, N.257, T.269, I.272, F.276, M.293, Q.305, F.308 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.95, B:M.209, B:I.272, B:F.308 Hydrogen bonds: B:Q.305 pi-Stacking: B:F.308

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

EDO.4: 4 residues within 4Å: Chain A: K.198, I.201, D.202 Chain B: N.160 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:D.161 Hydrogen bonds: A:K.198, A:D.202 EDO.5: 5 residues within 4Å: Chain A: D.202, L.205, A.206, K.211, Q.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.205, A:K.211, A:Q.247 EDO.6: 4 residues within 4Å: Chain A: F.174, F.185, R.193, R.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.193 Water bridges: A:R.197 EDO.7: 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.8: 4 residues within 4Å: Chain A: R.266, E.302, W.341, Y.342 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: N.51, A.91, N.97, N.98, I.99 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.51, A:N.98 Water bridges: A:N.98, A:N.98, A:R.271 EDO.10: 6 residues within 4Å: Chain A: T.70, F.71, K.72, N.187, L.188, Q.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.192, A:Q.192 EDO.11: 5 residues within 4Å: Chain A: T.122, L.124, E.125, S.195, M.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.122, A:S.195, A:S.195 Water bridges: A:R.242 EDO.12: 6 residues within 4Å: Chain A: S.144, F.276, Q.279, S.291, P.292, C.294 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.144, A:S.144, A:Q.279, A:P.292 Water bridges: A:S.291, A:S.291 EDO.16: 5 residues within 4Å: Chain A: N.160, S.162 Chain B: K.198, I.201, D.202 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:S.162 Hydrogen bonds: B:D.202 EDO.17: 5 residues within 4Å: Chain B: S.144, F.276, S.291, P.292, C.294 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.144, B:S.144, B:P.292 Water bridges: B:Q.279 EDO.18: 6 residues within 4Å: Chain B: N.51, E.86, D.87, Y.89, A.91, N.98 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.87, B:A.91, B:N.98 Water bridges: B:D.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, R. et al., Design, synthesis, and biological evaluation of tetrahydroisoquinolines derivatives as novel, selective PDE4 inhibitors for antipsoriasis treatment. Eur.J.Med.Chem. (2021)

Release Date

2021-06-16

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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