SMTL ID : 3sl5.2 (3 other biounits)

Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.86, A:H.122, A:D.123, A:D.240, H2O.3 ZN.2: 3 residues within 4Å: Chain A: H.122, D.123 Ligands: ZN.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.123, H2O.2, H2O.3, H2O.4, H2O.4

1 x J25: diethyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate(Non-covalent)

J25.3: 13 residues within 4Å: Chain A: Y.81, M.195, L.241, N.243, P.244, Y.251, T.255, M.259, F.262, M.279, S.290, Q.291, F.294 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.244, A:Y.251, A:F.262, A:M.279, A:F.294, A:F.294, A:F.294 Hydrogen bonds: A:Q.291 pi-Stacking: A:F.262, A:F.294

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

EDO.4: 1 residues within 4Å: Chain A: E.140 No protein-ligand interaction detected (PLIP) EDO.5: 8 residues within 4Å: Chain A: H.82, H.126, G.128, V.129, S.130, E.261, F.262, Q.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.261 Water bridges: A:H.82, A:H.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nankervis, J.L. et al., Thiophene inhibitors of PDE4: Crystal structures show a second binding mode at the catalytic domain of PDE4D2. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-10-26

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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