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Ligand · SPD

SPD · Spermidine

SPD, Spermidine (C7 H19 N3, 145.2 g/mol), in the MolNFT structures on GenesisL1: bound in 147 records (132 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands found with it.

Component
SPD
Formula
C7 H19 N3
Class
ligand
Structures
147
PDB entries
132

Binding sites

SPD in 147 structures; the first of them:

  • 4YBB · High-resolution structure of the Escherichia coli ribosome · SPD DA3183 · binds G855, G856, G857, G858
  • 5FOI · Crystal structure of mycinamicin VIII C21 methyl hydroxylase MycCI from Micromonospora… · SPD A1391 · binds ASP153, PHE156, GLU178, GLU181, TYR182
  • 5IT8 · High-resolution structure of the Escherichia coli ribosome · SPD DA3181 · binds G855, G856, G857, G858
  • 5J5B · Structure of the WT E coli ribosome bound to tetracycline · SPD DA3183 · binds G855, G856, G857, G858
  • 5J7L · Structure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to… · SPD DA3183 · binds G855, G856, G857, G858
  • 5JC9 · Structure of the Escherichia coli ribosome with the U1052G mutation in the 16S rRNA · SPD DA3186 · binds G855, G856, G857, G858
  • 5JVG · The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin · SPD X3320 · binds G219, G231, C602, THR6
  • 5NRG · The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex… · SPD X3286 · binds G2570, G2571, G2669, G2670, A2671, G2672, LYS86
  • 6DY5 · Crystal structure of double-stranded DNA AGGGATCCCT in complex with Zn2+ · SPD A101 · binds DA4, DT5
  • 6HIW · Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains… · SPD CA736 · binds ARG292, MET387, A452, A453, G454, G466, A467, A468 and 2 more
  • 6HIY · Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains… · SPD CA733 · binds ARG572, ASP578, ASN581, TYR13, GLY14, PRO15, A218, U259 and 4 more
  • 6HIZ · Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains… · SPD DL401 · binds HIS267, GLY19, U398, A399, U457, U458, A459
  • 6IKM · Crystal structure of SpuE-Spermidine in complex with ScFv5 · SPD A404 · binds TRP34, THR35, TYR37, SER82, GLU181, TYR239, ASP242, ASN269 and 3 more

Residues it binds most

G 416, A 405, C 370, U 341, TYR 138, ASP 109, TRP 84, GLU 110, GLN 69, ARG 95 (residue and the binding sites it lines).

Found with

  • MG · Magnesium ion
  • ZN · Zinc ion
  • K · Potassium ion
  • PUT · 1,4-diaminobutane
  • SPM · Spermine
  • EDO · 1,2-ethanediol
  • CL · Chloride ion
  • PEG · Di(hydroxyethyl)ether
  • GDP · Guanosine-5'-diphosphate
  • ATP · Adenosine-5'-triphosphate
  • GTP · Guanosine-5'-triphosphate
  • MPD · (4S)-2-methyl-2,4-pentanediol

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