Structure of PDB 5g5v Chain A Binding Site BS02

Receptor Information
>5g5v Chain A (length=335) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKRVTAITKVEREAVLVCELPSFDVTDVEFDLFRARESTDKPLDVAAAIA
YRLLLGSGLPQKFGCSDEVLLNFILQCRKKYRNVPYHNFYHVVDVCQTIH
TFLYRGNVYEKLTELECFVLLITALVHDLDHMGLNNSFYLKTESPLGILS
SASGNTSVLEVHHCNLAVEILSDPESDVFDGLEGAERTLAFRSMIDCVLA
TDMAKHGSALEAFLASAADQSSDEAAFHRMTMEIILKAGDISNVTKPFDI
SRQWAMAVTEEFYRQGDMEKERGVEVLPMFDRSKNMELAKGQIGFIDFVA
APFFQKIVDACLQGMQWTVDRIKSNRAQWERVLET
Ligand information
Ligand ID8Z4
InChIInChI=1S/C29H33N3O4/c1-18(2)32-29(35)24-7-5-4-6-23(24)27(30-32)21-12-13-26(36-3)25(16-21)19-8-10-20(11-9-19)28(34)31-15-14-22(33)17-31/h4-5,8-13,16,18,22-24,33H,6-7,14-15,17H2,1-3H3/t22-,23+,24-/m1/s1
InChIKeyUNEWFLJRNQWALM-TZRRMPRUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)N1C(=O)C2CC=CCC2C(=N1)c3ccc(c(c3)c4ccc(cc4)C(=O)N5CCC(C5)O)OC
OpenEye OEToolkits 1.7.6CC(C)N1C(=O)[C@@H]2CC=CC[C@@H]2C(=N1)c3ccc(c(c3)c4ccc(cc4)C(=O)N5CC[C@H](C5)O)OC
CACTVS 3.385COc1ccc(cc1c2ccc(cc2)C(=O)N3CC[CH](O)C3)C4=NN(C(C)C)C(=O)[CH]5CC=CC[CH]45
CACTVS 3.385COc1ccc(cc1c2ccc(cc2)C(=O)N3CC[C@@H](O)C3)C4=NN(C(C)C)C(=O)[C@@H]5CC=CC[C@H]45
FormulaC29 H33 N3 O4
Name(4AS,8AR)-4-(3-{4-[(3R)-3-HYDROXYPYRROLIDINE-1-
ChEMBLCHEMBL4208363
DrugBank
ZINC
PDB chain5g5v Chain A Residue 1936 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5g5v Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		M785 D822 V840 T841 Y845 M861 N867 G873 Q874 F877
Binding residue
(residue number reindexed from 1)		M203 D240 V258 T259 Y263 M279 N285 G291 Q292 F295
Annotation score1
Binding affinityMOAD: Ki=200nM
PDBbind-CN: -logKd/Ki=6.70,Ki=199nM
BindingDB: Ki=200nM
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:5g5v, PDBe:5g5v, PDBj:5g5v
PDBsum5g5v
PubMed29672041
UniProtQ8WQX9

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