Structure of PDB 5y4p Chain D Binding Site BS01

Receptor Information

>5y4p Chain D (length=274) Species: 353153 (Trypanosoma cruzi strain CL Brener)

ELISGGWFREENDQWPGQAMSLRVEKVLYDAPTKFQHLTIFESDPKGPWG
TVMALDGCIQVTDYDEFVYHEVLGHTSLCSHPKPERVLIIGGGDGGVLRE
VLRHGTVEHCDLVDIDGEVMEQSKQHFPQISRSLADPRATVRVGDGLAFV
RQTPDNTYDVVIIDTEAFYKDVLRILKPDGICCNQGESIWLDLELIEKMS
RFIRETGFASVQYALMHVPTYIGTLVCSKKAGVDVTKPLRPVEDMPFAKD
LKYYDSEMHKASFALPRFARHINN

Ligand information

• Ligand ID: S4M
• InChI: InChI=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
• InChIKey: KIZZALRCMBIHBH-IDTAVKCVSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CS(CCCN)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  OpenEye OEToolkits 1.5.0: C[S@@H](CCCN)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.341: C[SH](CCCN)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  ACDLabs 10.04: n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CS(CCCN)C)N
  CACTVS 3.341: C[SH](CCCN)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
• Formula: C14 H24 N6 O3 S
• Name: 5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE
• PDB chain: 5y4p Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5y4p Discovering a hidden allosteric binding site by combining molecular simulations and X-ray crystallography
• Resolution: 2.16 Å
• Binding residue (original residue number in PDB): Q64 H74 G95 D98 D118 I119 G150 D168 T169
• Binding residue (residue number reindexed from 1): Q60 H70 G91 D94 D114 I115 G146 D164 T165
• Annotation score: 3

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:5y4p, PDBe:5y4p, PDBj:5y4p
• PDBsum: 5y4p
• PubMed: 37521650
• UniProt: Q4DA73