SMTL ID : 6njh.1 (3 other biounits)

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-48

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.88, A:H.124, A:D.125, A:D.242, H2O.2

2 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.1, H2O.3, H2O.3, H2O.5 MG.4: 1 residues within 4Å: Chain A: E.142 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.142, A:E.142, H2O.6

1 x KRD: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)acetamide(Non-covalent)

KRD.3: 16 residues within 4Å: Chain A: H.84, S.132, M.197, 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.245, A:Y.253, A:I.260, A:F.296, A:F.296, A:F.357, A:F.357, A:T.361 Hydrogen bonds: A:Q.293 Water bridges: A:Y.83, A:H.84, A:N.133 pi-Stacking: A:F.296

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
A

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

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