Structure of PDB 4yv0 Chain B Binding Site BS02

Receptor Information

>4yv0 Chain B (length=290) Species: 353153 (Trypanosoma cruzi strain CL Brener)

ELISGGWFREENDQWPGQAMSLRVEKVLYDAPTKFQHLTIFESDPKGPWG
TVMALDGCIQVTDYDEFVYHEVLGHTSLCSHPKPERVLIIGGGDGGVLRE
VLRHGTVEHCDLVDIDGEVMEQSKQHFPQISRSLADPRATVRVGDGLAFV
RQTPDNTYDVVIIDTTDPAGPASKLFGEAFYKDVLRILKPDGICCNQGES
IWLDLELIEKMSRFIRETGFASVQYALMHVPTYPCGSIGTLVCSKKAGVD
VTKPLRPVEDMPFAKDLKYYDSEMHKASFALPRFARHINN

Ligand information

• Ligand ID: 4JW
• InChI: InChI=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
• InChIKey: NKHFUWXPKFRIAY-HNNXBMFYSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: CN(c1ccccc1)C(=O)[C@@H]2COc3ccccc3O2
  OpenEye OEToolkits 1.9.2: CN(c1ccccc1)C(=O)C2COc3ccccc3O2
  CACTVS 3.385: CN(C(=O)[C@@H]1COc2ccccc2O1)c3ccccc3
  ACDLabs 12.01: c1ccc(cc1)N(C(=O)C3COc2ccccc2O3)C
  CACTVS 3.385: CN(C(=O)[CH]1COc2ccccc2O1)c3ccccc3
• Formula: C16 H15 N O3
• Name: (2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine-2-carboxamide
• ZINC: ZINC000011612156
• PDB chain: 4yv0 Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yv0 Structural insights into the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): E14 Q22 A23 M24 Y237 P238 C239
• Binding residue (residue number reindexed from 1): E10 Q18 A19 M20 Y233 P234 C235
• Annotation score: 1
• Binding affinity: MOAD: ic50=530uM
  PDBbind-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

External links

• PDB: RCSB:4yv0, PDBe:4yv0, PDBj:4yv0
• PDBsum: 4yv0
• PubMed: 26327378
• UniProt: Q4DA73