SMTL ID : 6f6u.1

Crystal structure of the PDE4D catalytic domain in complex with GEBR-7b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.125 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.4, H2O.4, H2O.5, H2O.7, H2O.8 MG.3: 1 residues within 4Å: Chain A: D.22 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: D.125 Ligands: ZN.7 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.125, H2O.15, H2O.15, H2O.17, H2O.17, H2O.18

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 Ligands: MG.1 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.4, H2O.7 ZN.7: 5 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 Ligands: MG.6 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.15, H2O.18

2 x CV8: 2-[(~{E})-(3-cyclopentyloxy-4-methoxy-phenyl)methylideneamino]oxy-1-[(2~{R},6~{S})-2,6-dimethylmorpholin-4-yl]ethanone(Non-covalent)

CV8.4: 17 residues within 4Å: Chain A: Y.83, S.132, M.197, N.245, Y.253, W.256, T.257, I.260, M.261, F.264, Q.267, P.280, M.281, C.282, S.292, Q.293, F.296 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.260, A:F.264, A:F.264, A:F.296 Hydrogen bonds: A:Q.293 Water bridges: A:Q.267 pi-Stacking: A:F.296 CV8.8: 16 residues within 4Å: Chain B: Y.83, S.132, M.197, N.245, Y.253, W.256, T.257, I.260, M.261, F.264, S.279, M.281, C.282, S.292, Q.293, F.296 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.260, B:F.264, B:F.296, B:F.296, B:F.296 Hydrogen bonds: B:Q.293

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: D.127, H.156, A.159, V.160, K.163 Chain B: M.146 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.156 GOL.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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