SMTL ID : 4ogb.2 (3 other biounits)

Crystal structure of the catalytic domain of PDE4D2 with compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

1 x 2SR: (2R)-8-(3,4-dimethoxyphenyl)-6-methyl-2-(tetrahydro-2H-pyran-4-yl)-2H-chromen-4-ol(Non-covalent)

2SR.1: 9 residues within 4Å: Chain A: H.82, M.195, L.241, F.262, M.279, S.290, Q.291, F.294 Ligands: DMS.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.241, A:F.294 Hydrogen bonds: A:Q.291 pi-Stacking: A:F.294

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 Ligands: ZN.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.86, A:H.122, A:D.123, A:D.240, H2O.1, H2O.4 ZN.3: 2 residues within 4Å: Chain A: D.123 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.123, H2O.1, H2O.1, H2O.1, H2O.1, H2O.4

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

EDO.4: 4 residues within 4Å: Chain A: S.130, F.262, P.278, C.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.130, A:S.130, A:P.278 Water bridges: A:Q.265 EDO.5: 4 residues within 4Å: Chain A: F.29, Q.253, D.256, R.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.256, A:R.257 EDO.6: 3 residues within 4Å: Chain A: N.136, M.274 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.7: 7 residues within 4Å: Chain A: F.133, N.136, E.269, M.274, E.275, S.277 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.265, A:E.269 Water bridges: A:S.130, A:E.275, A:S.277 EDO.8: 3 residues within 4Å: Chain A: A.105, F.107, T.108 No protein-ligand interaction detected (PLIP) EDO.9: 9 residues within 4Å: Chain A: K.23, W.24, G.25, L.26, V.28, D.89, Q.92, S.93, K.246 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.25, A:L.26, A:Q.92, A:K.246, A:K.246 EDO.11: 3 residues within 4Å: Chain A: D.62, T.63, N.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.62, A:T.63

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 9 residues within 4Å: Chain A: Y.81, N.243, P.244, Y.251, T.255, I.258, Q.291, F.294 Ligands: 2SR.1 No protein-ligand interaction detected (PLIP) DMS.12: 2 residues within 4Å: Chain A: E.271, R.272 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Howard, B.L. et al., The PDE inhibition profile of LY294002 and tetrahydropyranyl analogues reveals a chromone motif for the development of PDE inhibitors. To be Published

Release Date

2015-01-21

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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