- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.2: 7 residues within 4Å:- Chain A: N.22, K.23, W.24, V.96, D.316, I.317
- Ligands: EDO.8
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:W.24
- Water bridges: A:I.317
PEG.13: 5 residues within 4Å:- Chain A: Q.180, K.184, I.187, D.188
- Ligands: EDO.12
1 PLIP interactions:1 interactions with chain A- Water bridges: A:D.188
PEG.17: 5 residues within 4Å:- Chain A: P.247, L.248, T.320, D.323, N.324
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.248, A:D.323
PEG.20: 7 residues within 4Å:- Chain A: D.78, V.79, A.80, P.127, E.261, R.264, R.268
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:A.80, A:R.268
- Water bridges: A:Q.265
- 2 x ZN: ZINC ION(Non-covalent)
ZN.3: 6 residues within 4Å:- Chain A: H.86, H.122, D.123, D.240
- Ligands: ZN.4, PO4.25
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
ZN.4: 3 residues within 4Å:- Chain A: D.123
- Ligands: ZN.3, PO4.25
5 PLIP interactions:1 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:D.123, H2O.1, H2O.3, H2O.5, H2O.6
- 4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.9: 4 residues within 4Å:- Chain A: S.99, T.100, P.101, E.104
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:E.104
DMS.10: 3 residues within 4Å:- Chain A: D.62, I.65, T.66
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:D.62
DMS.14: 6 residues within 4Å:- Chain A: N.37, E.72, D.73, Y.75, N.84
- Ligands: EDO.18
No protein-ligand interaction detected (PLIP)DMS.24: 7 residues within 4Å:- Chain A: H.27, V.28, F.29, R.30, Q.249, L.250, Q.253
No protein-ligand interaction detected (PLIP)- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- 1 x JN4: ethenyl 6-(ethenylcarbamoyl)-2-[(phenylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate(Non-covalent)
JN4.26: 16 residues within 4Å:- Chain A: Y.81, M.195, L.241, N.243, P.244, Y.251, W.254, T.255, I.258, M.259, F.262, M.279, S.290, Q.291, F.294
- Ligands: PO4.25
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:Y.81, A:N.243, A:P.244, A:Y.251, A:I.258, A:I.258, A:F.262, A:F.262, 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
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 2 x ZN: ZINC ION(Non-covalent)
- 4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- 1 x JN4: ethenyl 6-(ethenylcarbamoyl)-2-[(phenylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate(Non-covalent)
- 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