Structure of PDB 5l9h Chain A Binding Site BS02

Receptor Information
>5l9h Chain A (length=333) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTAITKVEREAVLVCELPSFDVTDVEFDLFRARESTDKPLDVAAAIAYRL
LLGSGLPQKFGCSDEVLLNFILQCRKKYRNVPYHNFYHVVDVCQTIHTFL
YRGNVYEKLTELECFVLLITALVHDLDHMGLNNSFYLKTESPLGILSSAS
GNTSVLEVHHCNLAVEILSDPESDVFDGLEGAERTLAFRSMIDCVLATDM
AKHGSALEAFLASAADQSSDEAAFHRMTMEIILKAGDISNVTKPFDISRQ
WAMAVTEEFYRQGDMEKERGVEVLPMFDRSKNMELAKGQIGFIDFVAAPF
FQKIVDACLQGMQWTVDRIKSNRAQWERVLETR
Ligand information
Ligand IDCVL
InChIInChI=1S/C26H32N6O4/c1-17(2)32-25(33)26(3,4)23(29-32)19-10-13-21(34-5)22(16-19)36-15-7-6-14-35-20-11-8-18(9-12-20)24-27-30-31-28-24/h8-13,16-17H,6-7,14-15H2,1-5H3,(H,27,28,30,31)
InChIKeyLSMMVMRAIOYJHV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(cc1OCCCCOc2ccc(cc2)c3[nH]nnn3)C4=NN(C(C)C)C(=O)C4(C)C
OpenEye OEToolkits 2.0.5CC(C)N1C(=O)C(C(=N1)c2ccc(c(c2)OCCCCOc3ccc(cc3)c4[nH]nnn4)OC)(C)C
FormulaC26 H32 N6 O4
Name5-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy]phenyl]-4,4-dimethyl-2-propan-2-yl-pyrazol-3-one
ChEMBLCHEMBL2171456
DrugBank
ZINCZINC000095556359
PDB chain5l9h Chain A Residue 1005 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5l9h Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		N825 A837 M861 Q874 F877 F880
Binding residue
(residue number reindexed from 1)		N240 A252 M276 Q289 F292 F295
Annotation score1
Binding affinityMOAD: ic50=0.4uM
PDBbind-CN: -logKd/Ki=6.40,IC50=0.4uM
BindingDB: IC50=400nM
Enzymatic activity
Enzyme Commision number 3.1.4.-
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:5l9h, PDBe:5l9h, PDBj:5l9h
PDBsum5l9h
PubMed29672041
UniProtQ8WQX9

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