SMTL ID : 6imi.1

Crystal structure of PDE4D complexed with a novel inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 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.3 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.8 MG.2: 3 residues within 4Å: Chain A: D.87, Y.89, H.90 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:Y.89 MG.11: 2 residues within 4Å: Chain B: D.137 Ligands: ZN.12 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.11, H2O.11, H2O.11, H2O.12, H2O.14

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.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.1, H2O.4 ZN.12: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.11 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 AH6: 6-ethoxy-7-methoxy-3,4-dihydroisoquinoline-2(1H)-carbaldehyde(Non-covalent)

AH6.4: 9 residues within 4Å: Chain A: N.257, Y.265, W.268, T.269, I.272, F.276, M.293, Q.305, F.308 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.257, A:Y.265, A:W.268, A:I.272, A:F.276 Hydrogen bonds: A:Q.305 pi-Stacking: A:F.308 AH6.13: 9 residues within 4Å: Chain B: N.257, Y.265, W.268, T.269, I.272, F.276, M.293, Q.305, F.308 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.257, B:Y.265, B:W.268, B:I.272, B:I.272, B:F.276 Hydrogen bonds: B:Q.305 pi-Stacking: B:F.308

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

EDO.5: 4 residues within 4Å: Chain A: K.198, I.201, D.202 Chain B: N.160 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:D.161, A:D.202 Hydrogen bonds: A:K.198, A:D.202 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: 5 residues within 4Å: Chain A: S.144, F.276, S.291, P.292, C.294 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.144, A:S.144, A:P.292 Water bridges: A:Q.279 EDO.8: 5 residues within 4Å: Chain A: F.174, F.185, R.193, L.196, R.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.193 Water bridges: A:R.193, A:R.197 EDO.9: 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.10: 8 residues within 4Å: Chain A: V.110, L.111, T.114, W.320, V.324, D.327, A.328, I.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.110, A:T.114, A:W.320 EDO.14: 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.15: 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.16: 1 residues within 4Å: Chain B: P.347 No protein-ligand interaction detected (PLIP) EDO.17: 3 residues within 4Å: Chain B: L.262, D.337, W.341 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.337 Water bridges: B:W.341 EDO.18: 5 residues within 4Å: Chain B: E.86, D.87, Y.89, A.91, N.98 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.87, B:D.87, B:Y.89, B:N.98

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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