Showing metabocard for Thermospermine (MMDBc0010742)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2021-05-15 02:50:03 UTC
Update Date2025-10-07 16:05:47 UTC
Metabolite IDMMDBc0010742
Metabolite Identification
Common NameThermospermine
DescriptionThermospermine is a polyamine metabolite belonging to the chemical class of aliphatic amines. It plays a significant role in plant biology, particularly in the regulation of xylem formation in Arabidopsis thaliana. Research indicates that thermospermine negatively regulates xylem differentiation by modulating the translation of mRNAs associated with the SAC51 gene family, which is crucial for proper xylem development (PMID:40946342 ). The balance between SAC51 and LHW family proteins is essential for the plant's response to thermospermine, as overaccumulation of SAC51 proteins leads to hypersensitivity to thermospermine, thereby repressing LHW protein function (PMID:40963835 ). Furthermore, the presence of an upstream open-reading-frame (uORF) in these mRNAs is conserved across species and its inhibitory effect on main ORF translation is alleviated by thermospermine (PMID:40963835 ). Mutations affecting uORFs in SAC51, SACL3, and SACL1 result in suppressed excessive xylem formation and dwarf phenotypes in thermospermine-deficient mutants, highlighting the complex regulatory mechanisms involved (PMID:40963835 ). Overall, thermospermine serves as a critical regulator of xylem development, influencing various genetic pathways in Arabidopsis thaliana.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007f2ad0c1c378>


  Mrv0541 05041411552D          

 14 13  0  0  0  0            999 V2000
    5.1927    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4783    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9072    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7638    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6217    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6664    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0493    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  1  0  0  0  0
 13  9  1  0  0  0  0
 14  8  1  0  0  0  0
 14 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f2ad0c1c378>

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3D SDF for #<Metabolite:0x00007f2ad0c1c378>

  Mrv0541 05041411552D          

 14 13  0  0  0  0            999 V2000
    5.1927    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4783    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9072    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7638    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6217    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6664    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0493    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  1  0  0  0  0
 13  9  1  0  0  0  0
 14  8  1  0  0  0  0
 14 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0010742

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCCNCCCNCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C10H26N4/c11-5-1-2-7-13-9-4-10-14-8-3-6-12/h13-14H,1-12H2

> <INCHI_KEY>
DODDBCGMRAFLEB-UHFFFAOYSA-N

> <FORMULA>
C10H26N4

> <MOLECULAR_WEIGHT>
202.3402

> <EXACT_MASS>
202.215746852

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
26.370670311482236

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4-aminobutyl)({3-[(3-aminopropyl)amino]propyl})amine

> <ALOGPS_LOGP>
-0.69

> <JCHEM_LOGP>
-1.4540076160000006

> <ALOGPS_LOGS>
-1.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_PKA_STRONGEST_BASIC>
11.080692199483746

> <JCHEM_POLAR_SURFACE_AREA>
76.1

> <JCHEM_REFRACTIVITY>
62.5582

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.24e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thermospermine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007f2ad0c1c378>
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PDB for #<Metabolite:0x00007f2ad0c1c378>
HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    7                                                       
CONECT    3    6    8                                                       
CONECT    4    9   10                                                       
CONECT    5    1   11                                                       
CONECT    6    3   12                                                       
CONECT    7    2   13                                                       
CONECT    8    3   14                                                       
CONECT    9    4   13                                                       
CONECT   10    4   14                                                       
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    7    9                                                       
CONECT   14    8   10                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

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3D PDB for #<Metabolite:0x00007f2ad0c1c378>
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SMILES for #<Metabolite:0x00007f2ad0c1c378>
NCCCCNCCCNCCCN
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INCHI for #<Metabolite:0x00007f2ad0c1c378>
InChI=1S/C10H26N4/c11-5-1-2-7-13-9-4-10-14-8-3-6-12/h13-14H,1-12H2
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Synonyms
ValueSource
1,12-Diamino-4,8-diazadodecaneChEBI
N1-(3-(3-Aminopropylamino)propyl)butane-1,4-diamineChEBI
Molecular FormulaC10H26N4
Average Mass202.3402
Monoisotopic Mass202.215746852
IUPAC Name(4-aminobutyl)({3-[(3-aminopropyl)amino]propyl})amine
Traditional Namethermospermine
CAS Registry NumberNot Available
SMILES
NCCCCNCCCNCCCN
InChI Identifier
InChI=1S/C10H26N4/c11-5-1-2-7-13-9-4-10-14-8-3-6-12/h13-14H,1-12H2
InChI KeyDODDBCGMRAFLEB-UHFFFAOYSA-N