SMTL ID : 3i8v.1

Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.108, H.144, D.145, D.262 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.108, A:H.144, A:D.145, A:D.262, H2O.3, H2O.5 ZN.6: 5 residues within 4Å: Chain B: H.108, H.144, D.145, D.262 Ligands: MG.7 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.108, B:H.144, B:D.145, B:D.262, H2O.8, H2O.12

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.145, E.174, T.215 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.145, H2O.1, H2O.2, H2O.3, H2O.3, H2O.3 MG.7: 2 residues within 4Å: Chain B: D.145 Ligands: ZN.6 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.145, H2O.8, H2O.8, H2O.8, H2O.8, H2O.10

2 x 0MO: (4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one(Non-covalent)

0MO.3: 13 residues within 4Å: Chain A: Y.103, T.215, M.217, N.265, W.276, T.277, I.280, M.281, F.284, M.301, S.312, Q.313, F.316 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.284, A:M.301, A:F.316, A:F.316 Hydrogen bonds: A:Q.313 Water bridges: A:D.262 pi-Cation interactions: A:H.104 0MO.8: 14 residues within 4Å: Chain B: Y.103, T.215, M.217, D.262, N.265, W.276, T.277, I.280, M.281, F.284, M.301, S.312, Q.313, F.316 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.284, B:M.301, B:F.316, B:F.316, B:F.316 Hydrogen bonds: B:Q.313 Water bridges: B:D.262

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: H.98, D.147, P.149 Chain B: H.98 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.98 GOL.9: 3 residues within 4Å: Chain B: D.318, H.322, R.347 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.318, B:H.322 Water bridges: B:D.318, B:H.322 GOL.10: 4 residues within 4Å: Chain B: T.122, P.123, D.335, I.339 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.122 Water bridges: B:A.121, B:T.122

1 x CO: COBALT (II) ION(Non-covalent)

CO.5: 2 residues within 4Å: Chain A: H.98, D.100 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, H2O.7, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, R.K.Y. et al., Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone. To be Published

Release Date

2009-07-21

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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