NP-MRD: Showing NP-Card for Senkyunolide I (NP0074161)

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Record Information

Version

2.0

Created at

2022-04-28 19:19:30 UTC

Updated at

2022-04-28 19:19:31 UTC

NP-MRD ID

NP0074161

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Senkyunolide I

Description

Senkyunolide I belongs to the class of organic compounds known as isobenzofurans. These are organic aromatic compounds containing an isobenzofuran moiety. Senkyunolide I is found in Angelica acutiloba (Hokkado) , Angelica acutiloba (Toyama) , Angelica gigas , Angelica sinensis , Larix kaempferi, Ligusticum porteri, Meum athamanticum and Pseudolarix kaempferi Gord. . Senkyunolide I was first documented in 2021 (PMID: 34951246). Based on a literature review a small amount of articles have been published on senkyunolide I (PMID: 35463086) (PMID: 34857480) (PMID: 34224996) (PMID: 34185967).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    4.2533    0.8221    1.0301 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9458    0.8004   -0.4616 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1114   -0.4311   -0.7196 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8347   -0.3829    0.0723 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6443   -0.4026   -0.5049 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4674   -0.4680   -1.8648 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8991   -0.4690   -2.0881 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5079   -0.5196   -3.2097 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5942   -0.4015   -0.8165 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6760   -0.3621    0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9619   -0.2887    1.5790 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4039   -0.1135    1.9079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0901    0.6070    0.7661 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.3778    0.9582    1.0788 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0310   -0.3709   -0.4151 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8573    0.0196   -1.4479 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3218    0.9575    1.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6861    1.6723    1.4783 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9226   -0.0953    1.5354 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3412    1.6791   -0.7562 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8722    0.6972   -1.0515 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8896   -0.5873   -1.7950 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7015   -1.3020   -0.3385 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8721   -0.3306    1.1445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6003   -1.2344    2.0453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3939    0.5453    2.0415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5329    0.4180    2.8694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8621   -1.1427    1.9467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4726    1.4898    0.4312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0235    0.3992    0.6030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3193   -1.3571   -0.0057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2602   -0.8065   -1.8264 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
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 10  5  1  0
 15  9  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
 11 25  1  0
 11 26  1  0
 12 27  1  0
 12 28  1  0
 13 29  1  6
 14 30  1  0
 15 31  1  1
 16 32  1  0
M  END


  Mrv1652304282221192D          

 16 17  0  0  1  0            999 V2000
    3.3523    1.9354    0.0000 C   0  0  1  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    0.6979    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
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -0.8853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -1.0568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    2.3479    0.0000 O   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
  1  6  1  0  0  0  0
  6  7  1  6  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  1 16  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0074161

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC\C=C1/OC(=O)C2=C1CC[C@H](O)[C@H]2O

> <INCHI_IDENTIFIER>
InChI=1S/C12H16O4/c1-2-3-4-9-7-5-6-8(13)11(14)10(7)12(15)16-9/h4,8,11,13-14H,2-3,5-6H2,1H3/b9-4-/t8-,11+/m0/s1

> <INCHI_KEY>
DQNGMIQSXNGHOA-JXQVETIVSA-N

> <FORMULA>
C12H16O4

> <MOLECULAR_WEIGHT>
224.256

> <EXACT_MASS>
224.104858995

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.90115369533284

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3Z,6S,7S)-3-butylidene-6,7-dihydroxy-1,3,4,5,6,7-hexahydro-2-benzofuran-1-one

> <ALOGPS_LOGP>
1.20

> <JCHEM_LOGP>
0.7912022496666669

> <ALOGPS_LOGS>
-1.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.00799082307816

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.228125607865369

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1886830578134164

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
59.8015

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.30e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3Z,6S,7S)-3-butylidene-6,7-dihydroxy-4,5,6,7-tetrahydro-2-benzofuran-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.924   5.923   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.650   5.553   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.220   2.843   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.333  -1.652   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.839  -1.973   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       7.591   4.383   0.000  0.00  0.00           O+0
CONECT    1    2    6   16                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10    4   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16    1                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₆O₄

Average Mass

224.2560 Da

Monoisotopic Mass

224.10486 Da

IUPAC Name

(3Z,6S,7S)-3-butylidene-6,7-dihydroxy-1,3,4,5,6,7-hexahydro-2-benzofuran-1-one

Traditional Name

(3Z,6S,7S)-3-butylidene-6,7-dihydroxy-4,5,6,7-tetrahydro-2-benzofuran-1-one

CAS Registry Number

Not Available

SMILES

CCC\C=C1/OC(=O)C2=C1CC[C@H](O)[C@H]2O

InChI Identifier

InChI=1S/C12H16O4/c1-2-3-4-9-7-5-6-8(13)11(14)10(7)12(15)16-9/h4,8,11,13-14H,2-3,5-6H2,1H3/b9-4-/t8-,11+/m0/s1

InChI Key

DQNGMIQSXNGHOA-JXQVETIVSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Angelica acutiloba (Hokkado)	Plant	KNApSAcK
Angelica acutiloba (Toyama)	Plant	KNApSAcK
Angelica gigas	Plant	KNApSAcK
Angelica sinensis	Plant	KNApSAcK
Larix kaempferi	LOTUS Database	35616633
Ligusticum porteri	LOTUS Database	35616633
Meum athamanticum	LOTUS Database	35616633
Pseudolarix kaempferi Gord.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isobenzofurans. These are organic aromatic compounds containing an isobenzofuran moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Isobenzofurans

Sub Class

Not Available

Direct Parent

Isobenzofurans

Alternative Parents

Substituents

Isobenzofuran
2-furanone
Dihydrofuran
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Enol ester
1,2-diol
Carboxylic acid ester
Secondary alcohol
Lactone
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organic oxide
Alcohol
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	1.2	ALOGPS
logP	0.79	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	13.23	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	59.8 m³·mol⁻¹	ChemAxon
Polarizability	23.9 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00035161

Chemspider ID

9696215

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11521428

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Chang N, Wang Y, Jiang M, Bai G: Integrated Network Pharmacology and UPLC/Q-TOF-MS Screen System to Exploring Anti-Inflammatory Active Components and Mechanism of Shunaoxin Pills. Evid Based Complement Alternat Med. 2022 Apr 14;2022:2868767. doi: 10.1155/2022/2868767. eCollection 2022. [PubMed:35463086 ]
Lu CN, Ye X, Liu XQ, Feng WH, Liang YH, Li C, Wang ZM: [Content determination and transferring rules of seven components in Angelicae Sinensis Radix and its processed products]. Zhongguo Zhong Yao Za Zhi. 2021 Dec;46(23):6196-6203. doi: 10.19540/j.cnki.cjcmm.20210727.201. [PubMed:34951246 ]
Zhu YL, Huang J, Chen XY, Xie J, Yang Q, Wang JF, Deng XM: Senkyunolide I alleviates renal Ischemia-Reperfusion injury by inhibiting oxidative stress, endoplasmic reticulum stress and apoptosis. Int Immunopharmacol. 2022 Jan;102:108393. doi: 10.1016/j.intimp.2021.108393. Epub 2021 Nov 30. [PubMed:34857480 ]
Zha YF, Xie J, Ding P, Zhu CL, Li P, Zhao ZZ, Li YH, Wang JF: Senkyunolide I protect against lung injury via inhibiting formation of neutrophil extracellular trap in a murine model of cecal ligation and puncture. Int Immunopharmacol. 2021 Oct;99:107922. doi: 10.1016/j.intimp.2021.107922. Epub 2021 Jul 2. [PubMed:34224996 ]
Li J, Chen W, Wang Y, Yin H: An LC-MS/MS method for simultaneous quantification of 11 components of Xian-Xiong-Gu-Kang in the plasma of osteoarthritic rats and pharmacokinetic analysis. J Sep Sci. 2021 Sep;44(18):3386-3397. doi: 10.1002/jssc.202100132. Epub 2021 Jul 8. [PubMed:34185967 ]

Showing NP-Card for Senkyunolide I (NP0074161)

MOL for NP0074161 (Senkyunolide I)

3D MOL for NP0074161 (Senkyunolide I)

3D SDF for NP0074161 (Senkyunolide I)

3D-SDF for NP0074161 (Senkyunolide I)

PDB for NP0074161 (Senkyunolide I)

3D PDB for NP0074161 (Senkyunolide I)

SMILES for NP0074161 (Senkyunolide I)

INCHI for NP0074161 (Senkyunolide I)

Structure for NP0074161 (Senkyunolide I)

3D Structure for NP0074161 (Senkyunolide I)