SMTL ID : 7cbq.1

Crystal structure of PDE4D catalytic domain in complex with Apremilast

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

3 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.2, H2O.2, H2O.3, H2O.3, H2O.7 MG.3: 3 residues within 4Å: Chain A: D.87, Y.89, H.90 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, A:Y.89, H2O.5 MG.13: 2 residues within 4Å: Chain B: D.137 Ligands: ZN.14 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.10, H2O.10, H2O.11, H2O.12, H2O.14

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.2, H2O.2 ZN.14: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.13 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.10, H2O.12

11 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.198, A:D.202 Water bridges: A:D.202, B:D.161 EDO.5: 5 residues within 4Å: Chain A: T.122, L.124, E.125, S.195, M.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.122, A:S.195, A:S.195 EDO.6: 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.7: 4 residues within 4Å: Chain A: H.90, D.92, V.93, P.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.92 EDO.8: 4 residues within 4Å: Chain A: L.205, A.206, K.211, Q.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.247 EDO.9: 4 residues within 4Å: Chain A: V.110, S.113, T.114, D.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.113, A:T.114 EDO.10: 3 residues within 4Å: Chain A: L.262, D.337, N.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.338 EDO.12: 5 residues within 4Å: Chain A: N.160, S.162 Chain B: K.198, I.201, D.202 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:D.161, A:S.162 Hydrogen bonds: B:D.202 EDO.15: 5 residues within 4Å: Chain B: A.91, D.92, V.93, A.94, E.274 No protein-ligand interaction detected (PLIP) EDO.16: 8 residues within 4Å: Chain B: V.110, L.111, T.114, W.320, V.324, D.327, A.328, I.331 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.110, B:W.320 EDO.17: 4 residues within 4Å: Chain B: E.154, L.155, M.158, H.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.154 Water bridges: B:H.168

2 x A9L: N-{2-[(1S)-1-(3-ethoxy-4-methoxyphenyl)-2-(methylsulfonyl)ethyl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}acetamide(Non-covalent)

A9L.11: 16 residues within 4Å: Chain A: Y.95, H.96, S.144, M.209, D.254, L.255, N.257, W.268, T.269, I.272, F.276, Q.279, M.293, S.304, Q.305, F.308 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.272, A:I.272, A:F.276, A:F.308 Hydrogen bonds: A:Q.305 Water bridges: A:S.291 pi-Stacking: A:F.308 A9L.18: 17 residues within 4Å: Chain B: Y.95, H.96, S.144, M.209, D.254, L.255, N.257, W.268, T.269, I.272, F.276, Q.279, P.292, M.293, S.304, Q.305, F.308 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.276, B:F.276, B:F.308, B:F.308 Hydrogen bonds: B:Q.305 Water bridges: B:S.291

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

2021-01-27

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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