SMTL ID : 1xon.1 (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: 2 residues within 4Å: Chain A: D.137 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: 17 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 Ligands: EDO.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.276, A:F.308 Hydrogen bonds: A:Q.305 Water bridges: A:Y.95, A:H.96, A:M.209, A:D.254 pi-Stacking: A:F.308

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.4: 6 residues within 4Å: Chain A: K.30, E.31, E.33, D.34, H.41, R.44 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.34, A:H.41, A:R.44 Water bridges: A:D.34

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

EDO.5: 3 residues within 4Å: Chain A: K.198, I.201, D.202 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: N.145, Q.146, S.210 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: G.50, N.51, R.52 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Chain A: D.87 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: P.115, A.116, H.325, P.326, D.327 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: N.51, A.91, N.97, N.98, I.99 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: V.110, L.111, T.114, W.320, V.324, D.327, A.328, I.331 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: A.119, V.120, L.234, L.235, L.236, R.242 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: F.174, F.185, R.193, R.197 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: S.144, F.276, S.291, P.292, C.294 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: D.92, V.93, A.94, P.141, E.275, R.278 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: M.209, F.308, I.312 Ligands: PIL.3, EDO.17 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: F.308, I.312 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: E.154, L.155, M.158 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: D.87, H.88, Y.89, H.90 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: V.306, G.307, D.310, Y.311 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: I.149, N.152, S.153, A.156, L.157, D.161 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: H.90, D.139, P.141, L.155, H.168 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: E.274, F.277, D.281, K.296 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: Q.263, R.266, Q.267 Ligand excluded by PLIP

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
A

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

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