SMTL ID : 6njj.3 (3 other biounits)

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 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.2, H2O.3

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.2, H2O.2, H2O.2, H2O.4, H2O.5

1 x KR7: (4-{[2-(3-chlorophenyl)-6-(trifluoromethyl)pyridin-4-yl]methyl}phenyl)acetic acid(Non-covalent)

KR7.3: 18 residues within 4Å: Chain A: Y.83, H.84, M.197, N.245, P.246, Y.253, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296, F.357, I.358, T.361, F.362 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.260, A:F.264, A:F.264, A:F.296, A:F.296, A:F.357, A:F.362 Hydrogen bonds: A:Q.293 Water bridges: A:H.84, A:S.198 pi-Stacking: A:F.296 Halogen bonds: A:T.257

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 7 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, Q.251, L.252, Q.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.31, A:R.32, A:Q.251, A:Q.255 Salt bridges: A:H.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gurney, M.E. et al., Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors for the Treatment of Fragile X Syndrome and Other Brain Disorders. J.Med.Chem. (2019)

Release Date

2019-05-08

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

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

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