Structure of PDB 5y4p Chain A Binding Site BS01

Receptor Information
>5y4p Chain A (length=266) Species: 353153 (Trypanosoma cruzi strain CL Brener) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GWFREENDQPGQAMSLRVEKVLYDAPTKFQHLTIFESDPKGPWGTVMALD
GCIQVTDYDEFVYHEVLGHTSLCSHPKPERVLIIGGGDGGVLREVLRHGT
VEHCDLVDIDGEVMEQSKQHFPQISRSLADPRATVRVGDGLAFVRQTPDN
TYDVVIIDTAFYKDVLRILKPDGICCNQGESIWLDLELIEKMSRFIRETG
FASVQYALMHVPTYIGTLVCSKKAGVDVTKPLRPVEDMPFAKDLKYYDSE
MHKASFALPRFARHIN
Ligand information
Ligand IDS4M
InChIInChI=1S/C14H24N6O3S/c1-24(4-2-3-15)5-8-10(21)11(22)14(23-8)20-7-19-9-12(16)17-6-18-13(9)20/h6-8,10-11,14,21-22,24H,2-5,15H2,1H3,(H2,16,17,18)/t8-,10-,11-,14-/m1/s1
InChIKeyKIZZALRCMBIHBH-IDTAVKCVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CS(CCCN)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
OpenEye OEToolkits 1.5.0C[S@@H](CCCN)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[SH](CCCN)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CS(CCCN)C)N
CACTVS 3.341C[SH](CCCN)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
FormulaC14 H24 N6 O3 S
Name5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE
ChEMBL
DrugBank
ZINC
PDB chain5y4p Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		Q40 L59 Q64 H74 G95 D98 D118 I119 V123 D149 D168 T169
Binding residue
(residue number reindexed from 1)		Q30 L49 Q54 H64 G85 D88 D108 I109 V113 D139 D158 T159
Annotation score3
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:5y4p, PDBe:5y4p, PDBj:5y4p
PDBsum5y4p
PubMed37521650
UniProtQ4DA73

[Back to BioLiP]