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Structure paper

TitleThiophene inhibitors of PDE4: Crystal structures show a second binding mode at the catalytic domain of PDE4D2.
Journal, issue, pagesBioorg. Med. Chem. Lett., Vol. 21, Page 7089-7093, Year 2011
Publish dateJun 24, 2011 (structure data deposition date)
AuthorsNankervis, J.L. / Feil, S.C. / Hancock, N.C. / Zheng, Z. / Ng, H.L. / Morton, C.J. / Holien, J.K. / Ho, P.W. / Frazzetto, M.M. / Jennings, I.G. ...Nankervis, J.L. / Feil, S.C. / Hancock, N.C. / Zheng, Z. / Ng, H.L. / Morton, C.J. / Holien, J.K. / Ho, P.W. / Frazzetto, M.M. / Jennings, I.G. / Manallack, D.T. / Martin, T.J. / Thompson, P.E. / Parker, M.W.
External linksBioorg. Med. Chem. Lett. / PubMed:22030030
MethodsX-ray diffraction
Resolution1.9 - 2.65 Å
Structure data

PDB-3sl3:
Crystal structure of the apo form of the catalytic domain of PDE4D2
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3sl4:
Crystal structure of the catalytic domain of PDE4D2 with compound 10D
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-3sl5:
Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-3sl6:
Crystal structure of the catalytic domain of PDE4D2 with compound 12c
Method: X-RAY DIFFRACTION / Resolution: 2.44 Å

PDB-3sl8:
Crystal structure of the catalytic domain of PDE4D2 with compound 10o
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

Chemicals

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-ZN:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

ChemComp-HOH:
WATER

ChemComp-JN4:
ethenyl 6-(ethenylcarbamoyl)-2-[(phenylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate

ChemComp-J25:
diethyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate

ChemComp-JN8:
cyclopentyl 6-(ethylcarbamoyl)-2-[(thiophen-2-ylacetyl)amino]-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate

ChemComp-JN7:
3-cyclopentyl 6-ethenyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate

Source
  • homo sapiens (human)
KeywordsHYDROLASE / catalytic mechanism / cAMP hydrolysis / Hydrolase/Inhibitor / Hydrolase-Inhibitor complex / Hydrolase/Hydrolase Inhibitor / Hydrolase-Hydrolase Inhibitor complex / catalytic domain

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