SMTL ID : 6f8v.1

Crystal structure of the PDE4D catalytic domain in complex with GEBR-18b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 Ligands: MG.2, D0B.5 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.88, A:H.124, A:D.125, A:D.242, H2O.2, H2O.5 ZN.6: 6 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 Ligands: MG.7, D0B.8 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.88, B:H.124, B:D.125, B:D.242, H2O.11, H2O.13

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.125 Ligands: ZN.1, D0B.5 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.2, H2O.2, H2O.4, H2O.5, H2O.8 MG.3: 1 residues within 4Å: Chain A: D.22 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: D.225, D.229 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.225, A:D.229, H2O.4, H2O.5, H2O.5 MG.7: 3 residues within 4Å: Chain B: D.125 Ligands: ZN.6, D0B.8 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.125, H2O.11, H2O.12, H2O.14, H2O.14, H2O.15

2 x D0B: 3-[3-(3-cyclopentyloxy-4-methoxy-phenyl)pyrazol-1-yl]-1-[(2~{R},6~{R})-2,6-dimethylmorpholin-4-yl]propan-1-one(Non-covalent)

D0B.5: 20 residues within 4Å: Chain A: Y.83, H.84, S.132, T.195, M.197, D.242, L.243, N.245, Y.253, W.256, T.257, I.260, M.261, F.264, M.281, S.292, Q.293, F.296 Ligands: ZN.1, MG.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.243, A:I.260, A:F.264, A:F.264, A:F.296, A:F.296 Hydrogen bonds: A:M.197, A:Q.293 Water bridges: A:D.196 pi-Stacking: A:F.296 D0B.8: 20 residues within 4Å: Chain B: Y.83, H.84, S.132, T.195, M.197, D.242, L.243, N.245, Y.253, W.256, T.257, I.260, M.261, F.264, M.281, S.292, Q.293, F.296 Ligands: ZN.6, MG.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.260, B:I.260, B:F.264, B:F.296 Hydrogen bonds: B:M.197, B:Q.293 Water bridges: B:E.154 pi-Stacking: B:F.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prosdocimi, T. et al., Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds. Biochemistry (2018)

Release Date

2018-05-16

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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