Structure of PDB 5l8c Chain B Binding Site BS02

Receptor Information
>5l8c Chain B (length=332) 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
FQKIVDACLQGMQWTVDRIKSNRAQWERVLET
Ligand information
Ligand ID908
InChIInChI=1S/C27H30N4O4/c1-16(2)31-27(34)21-7-5-4-6-20(21)25(30-31)19-12-13-23(35-3)22(14-19)17-8-10-18(11-9-17)26(33)29-15-24(28)32/h4-5,8-14,16,20-21H,6-7,15H2,1-3H3,(H2,28,32)(H,29,33)/t20-,21+/m0/s1
InChIKeySTNWAGAHKRPYDJ-LEWJYISDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5CC(C)N1C(=O)[C@@H]2CC=CC[C@@H]2C(=N1)c3ccc(c(c3)c4ccc(cc4)C(=O)NCC(=O)N)OC
CACTVS 3.385COc1ccc(cc1c2ccc(cc2)C(=O)NCC(N)=O)C3=NN(C(C)C)C(=O)[CH]4CC=CC[CH]34
OpenEye OEToolkits 2.0.5CC(C)N1C(=O)C2CC=CCC2C(=N1)c3ccc(c(c3)c4ccc(cc4)C(=O)NCC(=O)N)OC
CACTVS 3.385COc1ccc(cc1c2ccc(cc2)C(=O)NCC(N)=O)C3=NN(C(C)C)C(=O)[C@@H]4CC=CC[C@H]34
FormulaC27 H30 N4 O4
Name4-[5-[(4~{a}~{R},8~{a}~{S})-4-oxidanylidene-3-propan-2-yl-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(2-azanyl-2-oxidanylidene-ethyl)benzamide
ChEMBLCHEMBL4204999
DrugBank
ZINC
PDB chain5l8c Chain B Residue 1007 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5l8c Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		M785 V840 T841 Y845 M861 E869 Q874 F877
Binding residue
(residue number reindexed from 1)		M200 V255 T256 Y260 M276 E284 Q289 F292
Annotation score1
Binding affinityMOAD: Ki=100nM
BindingDB: Ki=100nM
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:5l8c, PDBe:5l8c, PDBj:5l8c
PDBsum5l8c
PubMed29672041
UniProtQ8WQX9

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