SMTL ID : 8w4r.1

Crystal structure of PDE4D complexed with CVT-313

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

2 x AJR: 2,2'-{[6-{[(4-methoxyphenyl)methyl]amino}-9-(propan-2-yl)-9H-purin-2-yl]azanediyl}di(ethan-1-ol)(Non-covalent)

AJR.1: 14 residues within 4Å: Chain A: H.96, M.209, L.255, I.272, M.273, F.276, F.277, M.293, V.301, S.304, Q.305, F.308 Ligands: EDO.4, EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.255, A:I.272, A:M.293 pi-Stacking: A:F.276, A:F.276, A:F.308 AJR.9: 14 residues within 4Å: Chain B: H.96, M.209, L.255, I.272, M.273, F.276, F.277, M.293, V.301, S.304, Q.305, F.308 Ligands: EDO.12, EDO.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.255, B:I.272, B:M.293 pi-Stacking: B:F.276, B:F.276, B:F.308

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.1, H2O.2, H2O.3, H2O.4 MG.10: 2 residues within 4Å: Chain B: D.137 Ligands: ZN.11 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.5, H2O.6, H2O.6, H2O.7, H2O.8

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.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.3 ZN.11: 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.5, H2O.7

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

EDO.4: 5 residues within 4Å: Chain A: N.257, Y.265, T.269, Q.305 Ligands: AJR.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.95, A:Y.95, A:Q.305 EDO.5: 5 residues within 4Å: Chain A: S.144, F.276, P.292, C.294 Ligands: AJR.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.292 Water bridges: A:S.144, A:Q.279 EDO.6: 4 residues within 4Å: Chain A: K.198, I.201, D.202 Chain B: N.160 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:D.161 Hydrogen bonds: A:D.202 EDO.7: 5 residues within 4Å: Chain A: N.51, A.91, N.97, N.98, I.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.51, A:N.98 Water bridges: A:H.90, A:N.98 EDO.8: 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.12: 5 residues within 4Å: Chain B: N.257, Y.265, T.269, Q.305 Ligands: AJR.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.95, B:Q.305 EDO.13: 5 residues within 4Å: Chain B: S.144, F.276, P.292, C.294 Ligands: AJR.9 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.14: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Drug repurposing and structure-based discovery of new PDE4 and PDE5 inhibitors. Eur.J.Med.Chem. (2023)

Release Date

2023-11-22

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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