SMTL ID : 3sl5.4 (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

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

EDO.1: 2 residues within 4Å: Chain A: H.74, E.165 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.70, A:E.165 EDO.2: 2 residues within 4Å: Chain A: N.138, L.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.138 EDO.6: 6 residues within 4Å: Chain A: L.98, L.103, A.105, V.106, F.107, I.112 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.103, A:A.105, A:V.106, A:F.107 Water bridges: A:R.51, A:L.98 EDO.7: 1 residues within 4Å: Chain A: E.104 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: L.97, T.100, W.306, V.310, D.313, I.317 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.100, A:W.306 EDO.9: 2 residues within 4Å: Chain A: P.101, D.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.313 EDO.10: 7 residues within 4Å: Chain A: N.37, R.38, E.72, D.73, Y.75, A.77, N.84 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain A: N.37, I.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.32 Water bridges: A:E.33, A:R.257

2 x ZN: ZINC ION(Non-covalent)

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

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

J25.5: 15 residues within 4Å: Chain A: Y.81, M.195, L.241, N.243, P.244, Y.251, T.255, I.258, M.259, F.262, M.279, S.290, Q.291, F.294, I.298 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.243, A:P.244, A:Y.251, A:F.294, A:F.294 Hydrogen bonds: A:Q.291 pi-Stacking: A:F.294

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
D

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

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