SMTL ID : 3sl3.2 (3 other biounits)

Crystal structure of the apo form of the catalytic domain of PDE4D2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: Q.132, I.135 Ligands: DMS.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.132 EDO.2: 5 residues within 4Å: Chain A: D.256, M.259, E.260, F.263, V.287 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: A.105, V.106, T.108 Ligands: EDO.16 No protein-ligand interaction detected (PLIP) EDO.4: 7 residues within 4Å: Chain A: M.208, T.211, K.212, K.213, L.220, L.221, D.227 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.211, A:T.211, A:K.213, A:K.213 EDO.5: 6 residues within 4Å: Chain A: N.37, A.77, N.83, N.84, I.85, R.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.37, A:N.37, A:N.84, A:R.257 EDO.6: 5 residues within 4Å: Chain A: L.97, T.100, W.306, D.313, I.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.97, A:T.100, A:D.313 EDO.7: 2 residues within 4Å: Chain A: D.296, H.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.296 Water bridges: A:H.300 EDO.8: 8 residues within 4Å: Chain A: H.82, H.126, G.128, V.129, E.261, F.262, Q.265 Ligands: DMS.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.82, A:E.261, A:Q.265 Water bridges: A:Q.265 EDO.12: 1 residues within 4Å: Chain A: E.140 No protein-ligand interaction detected (PLIP) EDO.13: 7 residues within 4Å: Chain A: I.276, S.277, P.278, M.279, C.280, D.281, N.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.276, A:M.279, A:D.281, A:N.284 EDO.16: 3 residues within 4Å: Chain A: T.108, D.109 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.109

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 3 residues within 4Å: Chain A: D.123 Ligands: ZN.10, PO4.11 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.123, H2O.1, H2O.1, H2O.1, H2O.3 ZN.10: 6 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 Ligands: ZN.9, PO4.11 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

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 6 residues within 4Å: Chain A: H.82, H.86, D.123, D.240 Ligands: ZN.9, ZN.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.123, A:T.193 Salt bridges: A:H.82, A:H.86

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

DMS.14: 6 residues within 4Å: Chain A: S.130, F.262, Q.265, P.278, C.280 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.130 Water bridges: A:Q.265 pi-Cation interactions: A:F.262 DMS.15: 4 residues within 4Å: Chain A: N.131, Q.132, S.196 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.131, A:Q.132

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 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

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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