SMTL ID : 6f8r.1

Crystal structure of the PDE4D catalytic domain in complex with GEBR-54

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x CZK: (2~{S})-1-[3-(3-cyclopentyloxy-4-methoxy-phenyl)pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol(Non-covalent)

CZK.1: 19 residues within 4Å: Chain A: Y.83, H.84, S.132, M.197, N.245, Y.253, W.256, T.257, I.260, M.261, F.264, Q.267, S.279, 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.296, A:F.296 Hydrogen bonds: A:Q.293 Water bridges: A:H.84, A:S.279 CZK.6: 15 residues within 4Å: Chain B: Y.83, M.197, N.245, Y.253, W.256, T.257, I.260, M.261, F.264, M.281, S.292, Q.293, G.295, F.296, I.300 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.83, B:F.264, B:M.281, B:F.296, B:F.296 Hydrogen bonds: B:Q.293

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.125 Ligands: ZN.5 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.1, H2O.4, H2O.6, H2O.6, H2O.8 MG.3: 2 residues within 4Å: Chain A: D.225, D.229 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.225, A:D.229, H2O.3, H2O.5 MG.4: 1 residues within 4Å: Chain A: N.175 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: D.125 Ligands: ZN.8 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.125, H2O.13, H2O.15, H2O.17, H2O.18, H2O.18

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 Ligands: MG.2 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.1, H2O.7 ZN.8: 5 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 Ligands: MG.7 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.13, H2O.19

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

EDO.9: 5 residues within 4Å: Chain A: N.148, D.149 Chain B: K.186, I.189, D.190 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:D.149, A:D.149 Hydrogen bonds: B:D.190

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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