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Showing NP-Card for Syndesine (NP0336319)

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Record Information
Version2.0
Created at2024-09-11 05:41:27 UTC
Updated at2024-09-11 05:41:27 UTC
NP-MRD IDNP0336319
Secondary Accession NumbersNone
Natural Product Identification
Common NameSyndesine
Description Based on a literature review very few articles have been published on Syndesine.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0336319 (Syndesine)


  Mrv2104 05262308132D          

 21 20  0  0  0  0            999 V2000
    6.5408    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2552    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6842    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3987    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6842    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  7  1  1  0  0  0  0
  7  5  1  0  0  0  0
  8  2  1  0  0  0  0
  8  6  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15  5  2  0  0  0  0
 15  6  1  0  0  0  0
 16  7  1  0  0  0  0
 17  8  1  0  0  0  0
 18 11  2  0  0  0  0
 19 11  1  0  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
M  END
Download

3D MOL for NP0336319 (Syndesine)

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3D SDF for NP0336319 (Syndesine)

  Mrv2104 05262308132D          

 21 20  0  0  0  0            999 V2000
    6.5408    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2552    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6842    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3987    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6842    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  7  1  1  0  0  0  0
  7  5  1  0  0  0  0
  8  2  1  0  0  0  0
  8  6  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15  5  2  0  0  0  0
 15  6  1  0  0  0  0
 16  7  1  0  0  0  0
 17  8  1  0  0  0  0
 18 11  2  0  0  0  0
 19 11  1  0  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0336319

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CCC(O)C\N=C\C(O)CCC(N)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1/C12H23N3O6/c13-9(11(18)19)3-1-7(16)5-15-6-8(17)2-4-10(14)12(20)21/h5,7-10,16-17H,1-4,6,13-14H2,(H,18,19)(H,20,21)/b15-5+

> <INCHI_KEY>
QWGIOMIEVFVREE-PJQLUOCWNA-N

> <FORMULA>
C12H23N3O6

> <MOLECULAR_WEIGHT>
305.331

> <EXACT_MASS>
305.158685473

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
31.011774692991924

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-6-[(E)-(5-amino-5-carboxy-2-hydroxypentylidene)amino]-5-hydroxyhexanoic acid

> <JCHEM_LOGP>
-6.997975083583922

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.1804416180392368

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5797347904238284

> <JCHEM_PKA_STRONGEST_BASIC>
9.524607174647098

> <JCHEM_POLAR_SURFACE_AREA>
179.45999999999998

> <JCHEM_REFRACTIVITY>
72.66149999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-6-[(E)-(5-amino-5-carboxy-2-hydroxypentylidene)amino]-5-hydroxyhexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0336319 (Syndesine)
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PDB for NP0336319 (Syndesine)
HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  C   UNK     0      12.209   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.543   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.542   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.875   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.876   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.541   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.877   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      16.211   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      14.877  -1.540   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       1.540  -1.540   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       8.208   0.770   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      10.876   2.310   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.541   2.310   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      17.544   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      16.211   2.310   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -1.127   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.206   2.310   0.000  0.00  0.00           O+0
CONECT    1    3    7                                                       
CONECT    2    4    8                                                       
CONECT    3    1    9                                                       
CONECT    4    2   10                                                       
CONECT    5    7   15                                                       
CONECT    6    8   15                                                       
CONECT    7    1    5   16                                                  
CONECT    8    2    6   17                                                  
CONECT    9    3   11   13                                                  
CONECT   10    4   12   14                                                  
CONECT   11    9   18   19                                                  
CONECT   12   10   20   21                                                  
CONECT   13    9                                                            
CONECT   14   10                                                            
CONECT   15    5    6                                                       
CONECT   16    7                                                            
CONECT   17    8                                                            
CONECT   18   11                                                            
CONECT   19   11                                                            
CONECT   20   12                                                            
CONECT   21   12                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   40    0
END

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3D PDB for NP0336319 (Syndesine)
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SMILES for NP0336319 (Syndesine)
NC(CCC(O)C\N=C\C(O)CCC(N)C(O)=O)C(O)=O
Download
INCHI for NP0336319 (Syndesine)
InChI=1/C12H23N3O6/c13-9(11(18)19)3-1-7(16)5-15-6-8(17)2-4-10(14)12(20)21/h5,7-10,16-17H,1-4,6,13-14H2,(H,18,19)(H,20,21)/b15-5+
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View in JSmol
SynonymsNot Available
Chemical FormulaC12H23N3O6
Average Mass305.3310 Da
Monoisotopic Mass305.15869 Da
IUPAC Name2-amino-6-[(E)-(5-amino-5-carboxy-2-hydroxypentylidene)amino]-5-hydroxyhexanoic acid
Traditional Name2-amino-6-[(E)-(5-amino-5-carboxy-2-hydroxypentylidene)amino]-5-hydroxyhexanoic acid
CAS Registry NumberNot Available
SMILES
NC(CCC(O)C\N=C\C(O)CCC(N)C(O)=O)C(O)=O
InChI Identifier
InChI=1/C12H23N3O6/c13-9(11(18)19)3-1-7(16)5-15-6-8(17)2-4-10(14)12(20)21/h5,7-10,16-17H,1-4,6,13-14H2,(H,18,19)(H,20,21)/b15-5+
InChI KeyQWGIOMIEVFVREE-PJQLUOCWNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-7ChemAxon
pKa (Strongest Acidic)1.58ChemAxon
pKa (Strongest Basic)9.52ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area179.46 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity72.66 m³·mol⁻¹ChemAxon
Polarizability31.01 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available