SMTL ID : 6njj.1 (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

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 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.1 ZN.5: 2 residues within 4Å: Chain A: H.76 Ligands: BTB.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76

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.1, H2O.3, H2O.4, H2O.5

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

KR7.3: 16 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, S.292, Q.293, F.296, F.357, I.358, T.361 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.260, A:F.264, A:F.296, A:F.296, A:F.357 Hydrogen bonds: A:Q.293 Water bridges: A:S.132, A:N.133, A:M.197, A:M.197 pi-Stacking: A:F.296 Halogen bonds: A:T.257

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.4: 3 residues within 4Å: Chain A: H.76, E.167 Ligands: ZN.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.167 Salt bridges: A:E.167

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

SO4.6: 6 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, L.252, Q.255 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.30, A:F.31, A:R.32, A:Q.255 Water bridges: A:E.35 Salt bridges: A:H.29

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

EDO.7: 7 residues within 4Å: Chain A: L.99, T.102, W.308, V.312, D.315, A.316, I.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.102, A:W.308

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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