Structure of PDB 5y4p Chain B Binding Site BS02

Receptor Information
>5y4p Chain B (length=278) Species: 353153 (Trypanosoma cruzi strain CL Brener) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELISGGWFREENDQWPGQAMSLRVEKVLYDAPTKFQHLTIFESDPKGPWG
TVMALDGCIQVTDYDEFVYHEVLGHTSLCSHPKPERVLIIGGGDGGVLRE
VLRHGTVEHCDLVDIDGEVMEQSKQHFPQISRSLADPRATVRVGDGLAFV
RQTPDNTYDVVIIDTTAFYKDVLRILKPDGICCNQGESIWLDLELIEKMS
RFIRETGFASVQYALMHVPTYPCGSIGTLVCSKKAGVDVTKPLRPVEDMP
FAKDLKYYDSEMHKASFALPRFARHINN
Ligand information
Ligand ID8QO
InChIInChI=1S/C11H14N2O2/c1-7-6-12-11(13-7)9-4-3-8(15-2)5-10(9)14/h3-5,7,14H,6H2,1-2H3,(H,12,13)/t7-/m1/s1
InChIKeyGSHCIAWYWVRHMS-SSDOTTSWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@@H]1CN=C(N1)c2ccc(cc2O)OC
CACTVS 3.385COc1ccc(c(O)c1)C2=NC[CH](C)N2
CACTVS 3.385COc1ccc(c(O)c1)C2=NC[C@@H](C)N2
OpenEye OEToolkits 2.0.6CC1CN=C(N1)c2ccc(cc2O)OC
FormulaC11 H14 N2 O2
Name5-methoxy-2-[(5R)-5-methyl-4,5-dihydro-1H-imidazol-2-yl]phenol
ChEMBL
DrugBank
ZINCZINC000005530265
PDB chain5y4p Chain B Residue 302 [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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PDB5y4p Discovering a hidden allosteric binding site by combining molecular simulations and X-ray crystallography
Resolution2.16 Å
Binding residue
(original residue number in PDB)		E14 M24 L26 W53 I63 D69 Y73 Y237
Binding residue
(residue number reindexed from 1)		E10 M20 L22 W49 I59 D65 Y69 Y221
Annotation score1
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
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Biological Process
External links
PDB RCSB:5y4p, PDBe:5y4p, PDBj:5y4p
PDBsum5y4p
PubMed37521650
UniProtQ4DA73

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