SMTL ID : 1q9m.1

Three dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 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.2 ZN.2: 2 residues within 4Å: Chain A: 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.2, H2O.2, H2O.2 ZN.4: 5 residues within 4Å: Chain B: H.86, H.122, D.123, D.240 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.86, B:H.122, B:D.123, B:D.240, H2O.3 ZN.5: 2 residues within 4Å: Chain B: D.123 Ligands: ZN.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.123, H2O.3, H2O.3, H2O.4, H2O.4 ZN.7: 5 residues within 4Å: Chain C: H.86, H.122, D.123, D.240 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.86, C:H.122, C:D.123, C:D.240, H2O.5 ZN.8: 2 residues within 4Å: Chain C: D.123 Ligands: ZN.7 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.123, H2O.5, H2O.5, H2O.5, H2O.5 ZN.10: 5 residues within 4Å: Chain D: H.86, H.122, D.123, D.240 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.86, D:H.122, D:D.123, D:D.240, H2O.6 ZN.11: 4 residues within 4Å: Chain D: H.122, D.123, H.155 Ligands: ZN.10 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.123, H2O.6, H2O.7, H2O.7, H2O.7

4 x ROL: ROLIPRAM(Non-covalent)

ROL.3: 12 residues within 4Å: Chain A: Y.81, H.82, N.243, Y.251, T.255, I.258, M.259, F.262, M.279, S.290, Q.291, F.294 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.81, A:F.262, A:F.294 Hydrogen bonds: A:Q.291 pi-Stacking: A:F.294 ROL.6: 12 residues within 4Å: Chain B: Y.81, H.82, N.243, Y.251, T.255, I.258, M.259, F.262, M.279, S.290, Q.291, F.294 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.262, B:F.294, B:F.294 Hydrogen bonds: B:Q.291 ROL.9: 12 residues within 4Å: Chain C: Y.81, H.82, M.195, N.243, T.255, I.258, M.259, F.262, M.279, S.290, Q.291, F.294 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.262, C:F.294, C:F.294 Hydrogen bonds: C:Q.291 ROL.12: 10 residues within 4Å: Chain D: Y.81, H.82, N.243, T.255, I.258, F.262, M.279, S.290, Q.291, F.294 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.262, D:F.294, 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., Three dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity. Structure (2003)

Release Date

2003-09-02

Peptides

cAMP-specific phosphodiesterase PDE4D2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

cAMP-specific phosphodiesterase PDE4D2

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