Brand  (β version)

PDB ID: 3SL5

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Select hetatm:   

close
information
centroid:
interaction residue:

Select chain:   Sequence  

Data format:   

Color scheme of protein:

Ligands
Code Name Style Show Link
ZN Zinc ion PoSSuM
J25 Diethyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-C]pyridine-3,6(5h)-dicarboxylate PoSSuM
EDO 1,2-ethanediol PoSSuM
DMS Dimethyl sulfoxide PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 3SL5   PDBj   RCSB PDB   PDBe
Header : Hydrolase/Hydrolase Inhibitor
Title : Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d
Release Data : 2011-10-26
Compound :
mol_id molecule chains synonym
1 cAMP-specific 3',5'-cyclic phosphodiesterase 4D A,B,C,D DPDE3, PDE43
ec: 3.1.4.17
fragment: Catalytic domain, UNP residues 385-714
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:469008)
gene: DPDE3, PDE4D
expression_system_strain: BL21(DE3) Star Rosetta
expression_system_vector_type: plasmid
expression_system_plasmid: pET15b
Authors : Feil, S.F.
Keywords : catalytic mechanism, cAMP hydrolysis, Hydrolase-Hydrolase Inhibitor complex
Exp. method : X-RAY DIFFRACTION ( 2.650 Å )
Citation :

Thiophene inhibitors of PDE4: Crystal structures show a second binding mode at the catalytic domain of PDE4D2.

Nankervis, J.L.,Feil, S.C.,Hancock, N.C.  et al.
(2011)  Bioorg.Med.Chem.Lett.  21 : 7089 - 7093

PubMed: 22030030
DOI: 10.1016/j.bmcl.2011.09.109

Reaction

Chain : A, B, C, D
UniProt : Q08499 (PDE4D_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
3',5'-cyclic AMP + H2O = AMP + H(+) 3.1.4.53 PubMed:9371713
left-to-right
Cofactor: Evidence: Note:
Zn(2+) ECO:0000269 | PubMed:14609333
ECO:0000269 | PubMed:15260978
ECO:0000269 | PubMed:15576036
ECO:0000269 | PubMed:17582435
Binds 2 divalent metal cations per subunit. Site 1 may preferentially bind zinc ions.
Mn(2+) ECO:0000269 | PubMed:15260978
ECO:0000269 | PubMed:15576036
ECO:0000250 | UniProtKB:Q07343
Binds 2 divalent metal cations per subunit (PubMed:15260978, PubMed:15576036). Site 2 has a preference for magnesium and/or manganese ions (By similarity).