Structure of PDB 1mkd Chain F Binding Site BS02

Receptor Information
>1mkd Chain F (length=328) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTF
KIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVF
TDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLA
VGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKT
MVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDR
IMEEFFPQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWA
DLVHPDAQDILDTLEDNREWYQSTIPQS
Ligand information
Ligand IDZAR
InChIInChI=1S/C12H10F2N2O3/c1-18-10-6-7(2-4-9(10)19-12(13)14)8-3-5-11(17)16-15-8/h2-6,12H,1H3,(H,16,17)
InChIKeyHJMQDJPMQIHLPB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1C=CC(=NN1)c2cc(OC)c(OC(F)F)cc2
CACTVS 3.341
OpenEye OEToolkits 1.5.0		COc1cc(ccc1OC(F)F)C2=NNC(=O)C=C2
FormulaC12 H10 F2 N2 O3
Name6-(4-DIFLUOROMETHOXY-3-METHOXY-PHENYL)-2H-PYRIDAZIN-3-ONE
ChEMBLCHEMBL313842
DrugBankDB02918
ZINCZINC000009230249
PDB chain1mkd Chain F Residue 3006 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1mkd Crystal structure of phosphodiesterase 4D and inhibitor complex
Resolution2.9 Å
Binding residue
(original residue number in PDB)		M370 Y426 W429 T430 M454 Q466 F469
Binding residue
(residue number reindexed from 1)		M188 Y244 W247 T248 M272 Q284 F287
Annotation score1
Binding affinityBindingDB: IC50=390nM
Enzymatic activity
Enzyme Commision number 3.1.4.53: 3',5'-cyclic-AMP phosphodiesterase.
Gene Ontology
Molecular Function
GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0008081 phosphoric diester hydrolase activity
Biological Process
GO:0007165 signal transduction

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1mkd, PDBe:1mkd, PDBj:1mkd
PDBsum1mkd
PubMed12387865
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

[Back to BioLiP]