Structure of PDB 4yv0 Chain A Binding Site BS02

Receptor Information
>4yv0 Chain A (length=269) Species: 353153 (Trypanosoma cruzi strain CL Brener) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GWFREEPGQAMSLRVEKVLYDAPTKFQHLTIFESDPKGPWGTVMALDGCI
QVTDYDEFVYHEVLGHTSLCSHPKPERVLIIGGGDGGVLREVLRHGTVEH
CDLVDIDGEVMEQSKQHFPQISRSLADPRATVRVGDGLAFVRQTPDNTYD
VVIIDTTAFYKDVLRILKPDGICCNQGESIWLDLELIEKMSRFIRETGFA
SVQYALMHVPTYPCGSIGTLVCSKKAGVDVTKPLRPVEDMPFAKDLKYYD
SEMHKASFALPRFARHINN
Ligand information
Ligand ID4JW
InChIInChI=1S/C16H15NO3/c1-17(12-7-3-2-4-8-12)16(18)15-11-19-13-9-5-6-10-14(13)20-15/h2-10,15H,11H2,1H3/t15-/m0/s1
InChIKeyNKHFUWXPKFRIAY-HNNXBMFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CN(c1ccccc1)C(=O)[C@@H]2COc3ccccc3O2
OpenEye OEToolkits 1.9.2CN(c1ccccc1)C(=O)C2COc3ccccc3O2
CACTVS 3.385CN(C(=O)[C@@H]1COc2ccccc2O1)c3ccccc3
ACDLabs 12.01c1ccc(cc1)N(C(=O)C3COc2ccccc2O3)C
CACTVS 3.385CN(C(=O)[CH]1COc2ccccc2O1)c3ccccc3
FormulaC16 H15 N O3
Name(2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine-2-carboxamide
ChEMBL
DrugBank
ZINCZINC000011612156
PDB chain4yv0 Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yv0 Structural insights into the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase
Resolution1.95 Å
Binding residue
(original residue number in PDB)		E14 M24 L26 W53 P235 T236
Binding residue
(residue number reindexed from 1)		E5 M11 L13 W40 P210 T211
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.28,IC50=530uM
Enzymatic activity
Enzyme Commision number 2.5.1.16: spermidine synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004766 spermidine synthase activity
GO:0016740 transferase activity
Biological Process
GO:0006596 polyamine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4yv0, PDBe:4yv0, PDBj:4yv0
PDBsum4yv0
PubMed26327378
UniProtQ4DA73

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