Structure of PDB 6njj Chain A Binding Site BS02

Receptor Information
>6njj Chain A (length=334) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKI
PVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTD
LEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVG
FKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMV
ETKKVTVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEF
FRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHP
DAQDILDTLEDNREWYQSTIPNQVSEFISNTFLD
Ligand information
Ligand IDKR7
InChIInChI=1S/C21H15ClF3NO2/c22-17-3-1-2-16(12-17)18-9-15(10-19(26-18)21(23,24)25)8-13-4-6-14(7-5-13)11-20(27)28/h1-7,9-10,12H,8,11H2,(H,27,28)
InChIKeyLTSUMTMGJHPGFX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(c2cc(C(F)(F)F)nc(c1cccc(c1)Cl)c2)c3ccc(cc3)CC(=O)O
CACTVS 3.385OC(=O)Cc1ccc(Cc2cc(nc(c2)C(F)(F)F)c3cccc(Cl)c3)cc1
OpenEye OEToolkits 2.0.6c1cc(cc(c1)Cl)c2cc(cc(n2)C(F)(F)F)Cc3ccc(cc3)CC(=O)O
FormulaC21 H15 Cl F3 N O2
Name(4-{[2-(3-chlorophenyl)-6-(trifluoromethyl)pyridin-4-yl]methyl}phenyl)acetic acid
ChEMBLCHEMBL4541964
DrugBankDB14790
ZINC
PDB chain6njj Chain A Residue 703 [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]
PDB6njj Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors for the Treatment of Fragile X Syndrome and Other Brain Disorders.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		M439 N487 W498 T499 I502 Q535 F538 F599 T603
Binding residue
(residue number reindexed from 1)		M186 N231 W242 T243 I246 Q279 F282 F327 T331
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.99,IC50=1018nM
BindingDB: IC50=127nM
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:6njj, PDBe:6njj, PDBj:6njj
PDBsum6njj
PubMed31013090
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

[Back to BioLiP]