SMTL ID : 6im6.1

Crystal structure of PDE4D complexed with a novel inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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.2, H2O.6 ZN.16: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.17 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.9, H2O.11

4 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.2, H2O.3, H2O.3, H2O.4, H2O.7 MG.3: 2 residues within 4Å: Chain A: H.90, D.139 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.90, A:D.139, H2O.2, H2O.4, H2O.5 MG.4: 4 residues within 4Å: Chain A: D.87, Y.89, H.90, A.91 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, A:Y.89, H2O.5 MG.17: 2 residues within 4Å: Chain B: D.137 Ligands: ZN.16 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.9, H2O.9, H2O.10, H2O.11, H2O.12

2 x AH3: 7-ethoxy-6-methoxy-3,4-dihydroisoquinoline-2(1H)-carbaldehyde(Non-covalent)

AH3.5: 10 residues within 4Å: Chain A: H.96, N.257, Y.265, W.268, T.269, I.272, F.276, M.293, Q.305, F.308 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.257, A:Y.265, A:I.272, A:F.276 Hydrogen bonds: A:Q.305 pi-Stacking: A:F.308 AH3.18: 10 residues within 4Å: Chain B: H.96, 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

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

EDO.6: 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.7: 5 residues within 4Å: Chain A: R.266, E.302, W.341, Y.342, T.345 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.266, A:Y.342 EDO.8: 4 residues within 4Å: Chain A: D.327, D.330, I.331 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.330, A:D.330 Water bridges: A:D.327, A:I.331 EDO.9: 8 residues within 4Å: Chain A: V.110, L.111, T.114, W.320, V.324, D.327, A.328 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.110, A:T.114 EDO.10: 3 residues within 4Å: Chain A: K.198, I.201, D.202 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.198, A:D.202 Water bridges: B:D.161 EDO.11: 5 residues within 4Å: Chain A: D.202, L.205, A.206, K.211, Q.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.247 EDO.12: 6 residues within 4Å: Chain A: N.51, A.91, N.97, N.98, I.99, R.271 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.51, A:N.51, A:N.98, A:R.271, A:R.271 Water bridges: A:A.91, A:V.93, A:N.98 EDO.13: 5 residues within 4Å: Chain A: F.43, A.46, E.47, N.51, I.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.47, A:E.47, A:N.51 Water bridges: A:R.271 EDO.14: 3 residues within 4Å: Chain A: H.41, P.261, Q.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.263 EDO.15: 7 residues within 4Å: Chain A: T.70, F.71, K.72, N.187, L.188, T.189, Q.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.189, A:Q.192, A:Q.192 EDO.19: 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 B, 1 interactions with chain A Hydrogen bonds: B:D.202 Water bridges: A:D.161 EDO.20: 5 residues within 4Å: Chain B: S.144, F.276, S.291, P.292, C.294 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.144, B:S.144, B:P.292 Water bridges: B:Q.279, B:S.291 EDO.21: 5 residues within 4Å: Chain B: L.235, L.236, D.237, N.238, D.241 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.235, B:D.237, B:N.238, B:D.241

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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