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Showing NP-Card for senkyunolide b (NP0299726)

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Record Information
Version2.0
Created at2022-09-10 11:43:16 UTC
Updated at2022-09-10 11:43:16 UTC
NP-MRD IDNP0299726
Secondary Accession NumbersNone
Natural Product Identification
Common Namesenkyunolide b
Description(Z)-3-butylidene-7-hydroxyphthalide, also known as 7-hydroxy-3-butylidenephthalide or senkyunolide b, belongs to the class of organic compounds known as isobenzofuranones. Isobenzofuranones are compounds containing a 2-benzofuran moiety that carries an oxo group at the 1 position. senkyunolide b is found in Angelica sinensis, Cnidium officinale, Levisticum officinale, Ligusticum jeholense and Ligusticum sinense. senkyunolide b was first documented in 2005 (PMID: 16132135). Based on a literature review very few articles have been published on (Z)-3-butylidene-7-hydroxyphthalide (PMID: 21823452).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0299726 (senkyunolide b)


  Mrv1652309102213432D          

 15 16  0  0  0  0            999 V2000
   -0.9851   -3.2777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.7541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  9 15  1  0  0  0  0
  5 15  1  0  0  0  0
M  END
Download

3D MOL for NP0299726 (senkyunolide b)

     RDKit          3D

 27 28  0  0  0  0  0  0  0  0999 V2000
   -3.1925    0.1887    1.4517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6674   -0.3313    0.1183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6838    0.0121   -0.9916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3489   -0.5907   -0.7099 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2590    0.1566   -0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2359    1.5476   -0.6750 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0857    1.9848   -0.4744 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4162    3.1938   -0.5074 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8914    0.7981   -0.2421 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2527    0.6898    0.0068 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0509    1.8300    0.0616 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8261   -0.5576    0.2026 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0297   -1.6692    0.1459 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6802   -1.5470   -0.1020 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0901   -0.3204   -0.2991 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8937    1.2583    1.3717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3368   -0.4518    1.7590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0331    0.1127    2.1702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6933   -1.4404    0.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6515    0.1046   -0.0771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0307   -0.3745   -1.9647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5922    1.1037   -1.0712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2060   -1.6545   -0.6042 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0359    1.7077    0.2451 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8924   -0.6662    0.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4945   -2.6534    0.3026 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0790   -2.4316   -0.1413 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  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15  5  1  0
 15  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
 11 24  1  0
 12 25  1  0
 13 26  1  0
 14 27  1  0
M  END
Download

3D SDF for NP0299726 (senkyunolide b)


  Mrv1652309102213432D          

 15 16  0  0  0  0            999 V2000
   -0.9851   -3.2777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.7541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  9 15  1  0  0  0  0
  5 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0299726

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC\C=C1/OC(=O)C2=C(O)C=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C12H12O3/c1-2-3-7-10-8-5-4-6-9(13)11(8)12(14)15-10/h4-7,13H,2-3H2,1H3/b10-7-

> <INCHI_KEY>
XLFDJKJEYMKLJX-YFHOEESVSA-N

> <FORMULA>
C12H12O3

> <MOLECULAR_WEIGHT>
204.225

> <EXACT_MASS>
204.078644246

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
21.898039133438367

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3Z)-3-butylidene-7-hydroxy-1,3-dihydro-2-benzofuran-1-one

> <JCHEM_LOGP>
3.370362906333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.372953795817539

> <JCHEM_PKA_STRONGEST_BASIC>
-4.317697061446624

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
58.25700000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
senkyunolide B

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0299726 (senkyunolide b)

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PDB for NP0299726 (senkyunolide b)
HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.839  -6.118   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.333  -5.798   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.220  -1.303   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.650   1.408   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.924   1.777   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   15                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   15                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    9    5                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

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3D PDB for NP0299726 (senkyunolide b)
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SMILES for NP0299726 (senkyunolide b)
CCC\C=C1/OC(=O)C2=C(O)C=CC=C12
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INCHI for NP0299726 (senkyunolide b)
InChI=1S/C12H12O3/c1-2-3-7-10-8-5-4-6-9(13)11(8)12(14)15-10/h4-7,13H,2-3H2,1H3/b10-7-
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View in JSmol
Synonyms
ValueSource
(3Z)-3-Butylidene-7-hydroxyisobenzofuran-1(3H)-oneChEBI
3-Butylidene-7-hydroxyphthalideChEBI
7-Hydroxy-3-butylidenephthalideChEBI
Senkyunolide bChEBI
Chemical FormulaC12H12O3
Average Mass204.2250 Da
Monoisotopic Mass204.07864 Da
IUPAC Name(3Z)-3-butylidene-7-hydroxy-1,3-dihydro-2-benzofuran-1-one
Traditional Namesenkyunolide B
CAS Registry NumberNot Available
SMILES
CCC\C=C1/OC(=O)C2=C(O)C=CC=C12
InChI Identifier
InChI=1S/C12H12O3/c1-2-3-7-10-8-5-4-6-9(13)11(8)12(14)15-10/h4-7,13H,2-3H2,1H3/b10-7-
InChI KeyXLFDJKJEYMKLJX-YFHOEESVSA-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
Angelica sinensisLOTUS Database
Cnidium officinaleLOTUS Database
Levisticum officinaleLOTUS Database
Ligusticum jeholenseLOTUS Database
Ligusticum sinenseLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as isobenzofuranones. Isobenzofuranones are compounds containing a 2-benzofuran moiety that carries an oxo group at the 1 position.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassIsocoumarans  
Sub ClassIsobenzofuranones  
Direct ParentIsobenzofuranones  
Alternative Parents
Substituents
  • Isobenzofuranone
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Benzenoid
    • 

  • Enol ester
    • 

  • Vinylogous acid
    • 

  • Carboxylic acid ester
    • 

  • Lactone
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Oxacycle
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
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
logP3.37ChemAxon
pKa (Strongest Acidic)9.37ChemAxon
pKa (Strongest Basic)-4.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area46.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity58.26 m³·mol⁻¹ChemAxon
Polarizability21.9 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00002983  
Chemspider ID4444884  
KEGG Compound IDC09921  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5281559  
PDB IDNot Available
ChEBI ID1458  
Good Scents IDNot Available
References
General References
  1. Wang J, Yang JB, Wang AG, Ji TF, Su YL: [Studies on the chemical constituents of Ligusticum sinense]. Zhong Yao Cai. 2011 Mar;34(3):378-80. [PubMed:21823452  ] 
  2. Wang YL, Liang YZ, Chen BM, He YK, Li BY, Hu QN: LC-DAD-APCI-MS-based screening and analysis of the absorption and metabolite components in plasma from a rabbit administered an oral solution of danggui. Anal Bioanal Chem. 2005 Sep;383(2):247-54. doi: 10.1007/s00216-005-0008-7. Epub  2005 Oct 12. [PubMed:16132135  ] 
  3. LOTUS database [Link]