SMTL ID : 6boj.1 (4 other biounits)

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

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.7 ZN.4: 1 residues within 4Å: Chain A: H.76 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.76, H2O.1, H2O.10, H2O.11

1 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.4, H2O.4, H2O.6, H2O.9

1 x E31: 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide(Non-covalent)

E31.3: 17 residues within 4Å: Chain A: H.84, S.132, M.197, L.243, N.245, Y.253, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296, F.357, I.358, T.361 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.243, A:N.245, A:Y.253, A:I.260, A:I.260, A:F.296, A:F.296, A:F.296, A:F.357, A:F.357, A:T.361 Hydrogen bonds: A:Q.293 Water bridges: A:H.84, A:V.131, A:S.132, A:S.132 pi-Stacking: A:F.296

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, L.252 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., Memory enhancing effects of BPN14770, an allosteric inhibitor of phosphodiesterase-4D, in wild-type and humanized mice. Neuropsychopharmacology (2018)

Release Date

2018-08-22

Peptides

cAMP-specific 3',5'-cyclic phosphodiesterase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cAMP-specific 3',5'-cyclic phosphodiesterase 4D

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