SMTL ID : 6imt.1

Crystal structure of PDE4D complexed with a novel inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 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.5 ZN.9: 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.11, H2O.13

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.137, E.166 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.4, H2O.7 MG.10: 2 residues within 4Å: Chain B: D.137 Ligands: ZN.9 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.11, H2O.11, H2O.12, H2O.13, H2O.15

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

EDO.3: 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.4: 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:H.90, A:N.98, A:R.271 EDO.5: 4 residues within 4Å: Chain A: R.266, E.302, W.341, Y.342 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.342 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.7: 4 residues within 4Å: Chain A: K.198, I.201, D.202 Chain B: N.160 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.202, A:D.202 EDO.11: 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.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.13: 7 residues within 4Å: Chain B: 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:T.114, B:W.320 EDO.14: 2 residues within 4Å: Chain B: D.337, W.341 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.337, B:D.337, B:N.338 EDO.15: 5 residues within 4Å: Chain B: N.51, A.91, N.97, N.98, I.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.51, B:N.98 Water bridges: B:N.98

2 x AK0: (1S)-1-[2-(6-fluoro-1H-indol-3-yl)ethyl]-6,7-dimethoxy-3,4-dihydroisoquinoline-2(1H)-carbaldehyde(Non-covalent)

AK0.8: 10 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.272, A:F.276, A:F.308, A:F.308 Hydrogen bonds: A:Q.305 pi-Stacking: A:F.308 AK0.16: 11 residues within 4Å: Chain B: Y.95, H.96, M.209, N.257, W.268, 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:I.272, B:F.308, B:F.308 Hydrogen bonds: B:Q.305 pi-Stacking: B:F.308

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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