SMTL ID : 2fm5.1

Crystal structure of PDE4D2 in complex with inhibitor L-869299

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 Ligands: MG.2 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.1 ZN.4: 5 residues within 4Å: Chain B: H.86, H.122, D.123, D.240 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.86, B:H.122, B:D.123, B:D.240, H2O.4, H2O.4 ZN.7: 5 residues within 4Å: Chain C: H.86, H.122, D.123, D.240 Ligands: MG.8 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.86, C:H.122, C:D.123, C:D.240, H2O.7, H2O.7 ZN.10: 5 residues within 4Å: Chain D: H.86, H.122, D.123, D.240 Ligands: MG.11 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.86, D:H.122, D:D.123, D:D.240, H2O.10, H2O.10

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.123 Ligands: ZN.1 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.1 MG.5: 3 residues within 4Å: Chain B: H.122, D.123 Ligands: ZN.4 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.123, H2O.4, H2O.4, H2O.4, H2O.4, H2O.4 MG.8: 2 residues within 4Å: Chain C: D.123 Ligands: ZN.7 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.123, H2O.7, H2O.7, H2O.7, H2O.7, H2O.7 MG.11: 4 residues within 4Å: Chain D: H.122, D.123, H.155 Ligands: ZN.10 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.123, H2O.10, H2O.10, H2O.10, H2O.10, H2O.10

4 x M99: (R)-3-(2-(3-CYCLOPROPOXY-4-(DIFLUOROMETHOXY)PHENYL)-2-(5-(1,1,1,3,3,3-HEXAFLUORO-2-HYDROXYPROPAN-2-YL)THIAZOL-2-YL)ETHYL)PYRIDINE 1-OXIDE(Non-covalent)

M99.3: 17 residues within 4Å: Chain A: Y.81, H.82, T.193, M.195, D.240, L.241, N.243, P.244, Y.251, W.254, T.255, I.258, F.262, M.279, Q.291, F.294, I.298 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.241, A:I.258, A:F.294 Hydrogen bonds: A:Q.291 pi-Stacking: A:F.294 M99.6: 17 residues within 4Å: Chain B: H.82, T.193, M.195, D.240, L.241, N.243, P.244, Y.251, W.254, T.255, I.258, F.262, M.279, S.290, Q.291, F.294, I.298 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.241, B:I.258, B:F.294 Hydrogen bonds: B:Q.291 pi-Stacking: B:F.294 M99.9: 17 residues within 4Å: Chain C: Y.81, H.82, T.193, M.195, D.240, L.241, N.243, P.244, Y.251, W.254, T.255, I.258, F.262, M.279, Q.291, F.294, I.298 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.241, C:I.258, C:F.294 Hydrogen bonds: C:Q.291 Water bridges: C:E.152 pi-Stacking: C:F.294 M99.12: 17 residues within 4Å: Chain D: Y.81, H.82, T.193, M.195, D.240, L.241, N.243, P.244, Y.251, W.254, T.255, I.258, F.262, M.279, Q.291, F.294, I.298 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.241, D:I.258, D:F.294 Hydrogen bonds: D:Q.291 pi-Stacking: D:F.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huai, Q. et al., Enantiomer Discrimination Illustrated by the High Resolution Crystal Structures of Type 4 Phosphodiesterase. J.Med.Chem. (2006)

Release Date

2006-03-28

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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