SMTL ID : 6fdc.1

Crystal structure of the PDE4D catalytic domain in complex with GEBR-32a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.6 ZN.7: 5 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 Ligands: MG.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.12, H2O.17

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.125 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.1, H2O.3, H2O.4, H2O.5, 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.2, H2O.4 MG.4: 1 residues within 4Å: Chain A: N.175 No protein-ligand interaction detected (PLIP) MG.8: 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.12, H2O.14, H2O.15, H2O.15, H2O.18 MG.9: 1 residues within 4Å: Chain B: H.302 No protein-ligand interaction detected (PLIP)

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

EDO.5: 6 residues within 4Å: Chain A: K.186, I.189, D.190 Chain B: N.148, D.149, S.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.186 Water bridges: A:D.190, A:D.190 EDO.10: 6 residues within 4Å: Chain A: N.148, D.149, S.150 Chain B: K.186, I.189, D.190 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.190 Water bridges: A:D.149, A:S.150

1 x DD5: (2~{R})-1-[3-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol(Non-covalent)

DD5.6: 20 residues within 4Å: Chain A: Y.83, H.84, S.132, M.197, N.245, P.246, 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.260, A:F.264, A:F.296, A:F.296, A:F.296 Hydrogen bonds: A:Q.293 Water bridges: A:H.84, A:H.128, A:Q.267

1 x D5N: (2~{S})-1-[5-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol(Non-covalent)

D5N.11: 17 residues within 4Å: Chain B: Y.83, H.84, M.197, L.243, N.245, P.246, Y.253, W.256, T.257, I.260, M.261, F.264, M.281, S.292, Q.293, F.296, I.300 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.260, B:I.260, B:F.264, B:F.296 Hydrogen bonds: B:Q.293 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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