SMTL ID : 3iad.2 (3 other biounits)

Crystal structure of human phosphodiesterase 4D with bound allosteric modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 x 15X: 1-{4-[(2-fluoro-6-methoxy-3'-nitrobiphenyl-3-yl)methyl]phenyl}urea(Non-covalent)

15X.1: 16 residues within 4Å: Chain A: H.84, S.132, M.197, L.243, N.245, T.257, I.260, M.261, F.264, S.292, Q.293, F.296, F.357, I.358, T.361, F.362 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.243, A:I.260, A:F.264, A:F.264, A:F.296, A:F.357, A:T.361 Hydrogen bonds: A:S.292, A:Q.293 Water bridges: A:V.131 pi-Stacking: A:F.296

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.125, E.154 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.125, H2O.1, H2O.2, H2O.2, H2O.2

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 5 residues within 4Å: Chain A: P.62, D.64, T.65, N.169, Q.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.64 EPE.5: 8 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, E.35, Q.251, L.252, Q.255 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.31, A:R.32, A:Q.251 Salt bridges: A:H.29, A:E.35, A:E.35

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

2010-01-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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