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Showing NP-Card for sarmentose (NP0245296)

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Record Information
Version1.0
Created at2022-09-07 06:19:41 UTC
Updated at2022-09-07 06:19:41 UTC
NP-MRD IDNP0245296
Secondary Accession NumbersNone
Natural Product Identification
Common Namesarmentose
Description sarmentose is found in Nerium oleander. It was first documented in 2013 (PMID: 23359438). Based on a literature review a small amount of articles have been published on sarmentose (PMID: 28233998) (PMID: 33818079).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0245296 (sarmentose)


  Mrv1652309072208192D          

 11 10  0  0  1  0            999 V2000
    4.6184    0.1914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  1  0  0  0
M  END
Download

3D MOL for NP0245296 (sarmentose)

     RDKit          3D

 25 24  0  0  0  0  0  0  0  0999 V2000
   -1.1153    1.9754   -1.0629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0999    0.5831   -1.0707 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7282    0.1054    0.1584 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8714   -0.6418    0.8082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3468   -1.7943    0.0335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2368   -2.5148    0.4312 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5187   -0.7218    0.1668 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3844   -1.8263   -0.6469 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7635    0.0051   -0.2213 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0885    1.1746    0.6796 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8195   -0.9230   -0.0403 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1071    2.3245   -0.8205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7836    2.3048   -0.2297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4638    2.4000   -2.0192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5209    0.9635    0.8717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5363   -0.9373    1.8452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7346    0.0579    0.9298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9085   -2.0270   -0.9188 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6999   -1.1272    1.2059 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8563   -2.6021   -0.2756 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7992    0.3210   -1.2669 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0847    2.1496    0.1226 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1322    1.1112    1.0895 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3922    1.1696    1.5350 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9140   -1.5300   -0.7897 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  3  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  1
  4 16  1  0
  4 17  1  0
  5 18  1  0
  7 19  1  1
  8 20  1  0
  9 21  1  6
 10 22  1  0
 10 23  1  0
 10 24  1  0
 11 25  1  0
M  END
Download

3D SDF for NP0245296 (sarmentose)


  Mrv1652309072208192D          

 11 10  0  0  1  0            999 V2000
    4.6184    0.1914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0245296

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H](CC=O)[C@@H](O)[C@@H](C)O

> <INCHI_IDENTIFIER>
InChI=1S/C7H14O4/c1-5(9)7(10)6(11-2)3-4-8/h4-7,9-10H,3H2,1-2H3/t5-,6+,7+/m1/s1

> <INCHI_KEY>
GOYBREOSJSERKM-VQVTYTSYSA-N

> <FORMULA>
C7H14O4

> <MOLECULAR_WEIGHT>
162.185

> <EXACT_MASS>
162.089208931

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.600017102133183

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S,5R)-4,5-dihydroxy-3-methoxyhexanal

> <JCHEM_LOGP>
-1.1631656320000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.41733817363243

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.091590488471269

> <JCHEM_PKA_STRONGEST_BASIC>
-3.047103879110124

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
39.2149

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
sarmentose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0245296 (sarmentose)

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PDB for NP0245296 (sarmentose)
HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       8.621   0.357   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    3    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0245296 (sarmentose)
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SMILES for NP0245296 (sarmentose)
CO[C@@H](CC=O)[C@@H](O)[C@@H](C)O
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INCHI for NP0245296 (sarmentose)
InChI=1S/C7H14O4/c1-5(9)7(10)6(11-2)3-4-8/h4-7,9-10H,3H2,1-2H3/t5-,6+,7+/m1/s1
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View in JSmol
Synonyms
ValueSource
D-SarmentoseChEBI
Chemical FormulaC7H14O4
Average Mass162.1850 Da
Monoisotopic Mass162.08921 Da
IUPAC Name(3S,4S,5R)-4,5-dihydroxy-3-methoxyhexanal
Traditional Namesarmentose
CAS Registry NumberNot Available
SMILES
CO[C@@H](CC=O)[C@@H](O)[C@@H](C)O
InChI Identifier
InChI=1S/C7H14O4/c1-5(9)7(10)6(11-2)3-4-8/h4-7,9-10H,3H2,1-2H3/t5-,6+,7+/m1/s1
InChI KeyGOYBREOSJSERKM-VQVTYTSYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Nerium oleanderLOTUS Database
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-1.2ChemAxon
pKa (Strongest Acidic)13.09ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.76 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity39.21 m³·mol⁻¹ChemAxon
Polarizability16.6 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
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 ID4574161  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSarmentose  
METLIN IDNot Available
PubChem Compound5460676  
PDB IDNot Available
ChEBI ID33982  
Good Scents IDNot Available
References
General References
  1. Mestre J, Matheu MI, Diaz Y, Castillon S, Boutureira O: Chemical Access to d-Sarmentose Units Enables the Total Synthesis of Cardenolide Monoglycoside N-1 from Nerium oleander. J Org Chem. 2017 Mar 17;82(6):3327-3333. doi: 10.1021/acs.joc.7b00210. Epub 2017  Mar 7. [PubMed:28233998  ] 
  2. Singh Y, Nimoriya R, Rawat P, Mishra DK, Kanojiya S: Structural Analysis of Diastereomeric Cardiac Glycosides and Their Genins Using Ultraperformance Liquid Chromatography-Tandem Mass Spectrometry. J Am Soc Mass Spectrom. 2021 May 5;32(5):1205-1214. doi: 10.1021/jasms.1c00017.  Epub 2021 Apr 5. [PubMed:33818079  ] 
  3. de Carvalho AL, Nelson BW, Bianchini MC, Plagnol D, Kuplich TM, Daly DC: Bamboo-dominated forests of the southwest Amazon: detection, spatial extent, life cycle length and flowering waves. PLoS One. 2013;8(1):e54852. doi: 10.1371/journal.pone.0054852. Epub 2013 Jan 24. [PubMed:23359438  ] 
  4. LOTUS database [Link]