SMTL ID : 1xon.2 (1 other biounit)

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Piclamilast

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.100, H.136, D.137, D.254 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.100, A:H.136, A:D.137, A:D.254, H2O.1, H2O.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.137, E.166 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.137, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1

1 x PIL: 3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE(Non-covalent)

PIL.3: 16 residues within 4Å: Chain A: Y.95, H.96, T.207, M.209, D.254, L.255, N.257, W.268, T.269, I.272, M.273, F.276, M.293, S.304, Q.305, F.308 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.276, A:F.308, A:F.308, A:F.308 Hydrogen bonds: A:Q.305 Water bridges: A:H.96, A:M.209, A:D.254 Halogen bonds: A:D.254

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

EDO.4: 4 residues within 4Å: Chain A: E.302, W.341, Y.342, T.345 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.266 EDO.5: 4 residues within 4Å: Chain A: D.34, K.37, G.39, H.41 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.41 EDO.6: 5 residues within 4Å: Chain A: S.144, F.276, S.291, P.292, C.294 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.144, A:S.144, A:P.292 Water bridges: A:Q.279, A:Q.279 EDO.7: 3 residues within 4Å: Chain A: N.238, Y.239 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.239 Water bridges: A:N.238, A:S.240 EDO.8: 1 residues within 4Å: Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.125 EDO.9: 5 residues within 4Å: Chain A: F.174, F.185, R.193, R.197 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.193 Water bridges: A:R.197 EDO.10: 4 residues within 4Å: Chain A: R.193, Q.194, R.197 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.193 EDO.11: 3 residues within 4Å: Chain A: K.198, I.201, D.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.202 Water bridges: A:K.198, A:D.202 EDO.12: 6 residues within 4Å: Chain A: N.51, E.86, D.87, Y.89, A.91, N.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.87, A:A.91, A:N.98 EDO.13: 3 residues within 4Å: Chain A: L.262, W.341 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain A: P.261, L.262, T.334, D.337, N.338 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.262, A:N.338 EDO.15: 5 residues within 4Å: Chain A: D.92, V.93, A.94, E.275, R.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.94, A:R.278 Water bridges: A:R.282 EDO.16: 5 residues within 4Å: Chain A: N.51, A.91, N.97, N.98, I.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.51, A:N.98 Water bridges: A:H.90, A:N.98 EDO.17: 4 residues within 4Å: Chain A: K.303, V.306, Q.343, I.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.343 EDO.18: 3 residues within 4Å: Chain A: N.145, Q.146, I.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.145 Water bridges: A:Q.146, A:Q.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Card, G.L. et al., Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases. STRUCTURE (2004)

Release Date

2004-12-14

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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