SMTL ID : 3g4i.1 (3 other biounits)

Crystal structure of human phosphodiesterase 4d with d155871

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 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.7, H2O.7

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.125 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.5, H2O.7, H2O.7, H2O.8, H2O.10

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

SO4.3: 6 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, L.252, Q.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.31, A:R.32, A:Q.255 Salt bridges: A:H.29

1 x D71: 1-(3-nitrophenyl)-3-(pyridin-4-ylmethyl)pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione(Non-covalent)

D71.4: 13 residues within 4Å: Chain A: Y.83, H.84, L.243, N.245, Y.253, T.257, I.260, M.261, F.264, M.281, S.292, Q.293, F.296 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.245, A:Y.253, A:F.264, A:M.281, A:F.296 Hydrogen bonds: A:Q.293 Water bridges: A:Y.83 pi-Stacking: A:F.296

3 x EOH: ETHANOL(Non-functional Binders)

EOH.5: 3 residues within 4Å: Chain A: K.186, I.189, D.190 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.186 Hydrogen bonds: A:D.190 Water bridges: A:K.186, A:K.186, A:D.190 EOH.6: 3 residues within 4Å: Chain A: T.72, H.76, E.167 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.72, A:T.72 EOH.7: 4 residues within 4Å: Chain A: F.162, F.173, R.181, R.185 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.162 Water bridges: A:R.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgin, A.B. et al., Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety. Nat.Biotechnol. (2010)

Release Date

2010-01-19

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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