NP-MRD: Showing NP-Card for Dimethyl lithospermate (NP0075297)

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Record Information

Version

2.0

Created at

2022-04-28 20:35:40 UTC

Updated at

2022-04-28 20:35:40 UTC

NP-MRD ID

NP0075297

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dimethyl lithospermate

Description

Dimethyl Lithospermate belongs to the class of organic compounds known as 2-arylbenzofuran flavonoids. These are phenylpropanoids containing the 2-phenylbenzofuran moiety. Dimethyl lithospermate is found in Salvia miltiorrhiza . Dimethyl lithospermate was first documented in 2011 (PMID: 22124203). Based on a literature review a small amount of articles have been published on Dimethyl Lithospermate (PMID: 23947137) (PMID: 33668538) (PMID: 29124660) (PMID: 24469601).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282222352D          

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 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 18 23  1  0  0  0  0
 22 24  1  0  0  0  0
 21 25  1  0  0  0  0
  5 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
  4 28  1  0  0  0  0
 27 29  1  6  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 29 34  1  0  0  0  0
 33 35  1  0  0  0  0
 32 36  1  0  0  0  0
 26 37  1  1  0  0  0
 37 38  2  0  0  0  0
 37 39  1  0  0  0  0
 39 40  1  0  0  0  0
  3 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0075297

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)[C@@H](CC1=CC=C(O)C(O)=C1)OC(=O)\C=C\C1=C2[C@@H]([C@H](OC2=C(O)C=C1)C1=CC=C(O)C(O)=C1)C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C29H26O12/c1-38-28(36)22(12-14-3-7-17(30)20(33)11-14)40-23(35)10-6-15-4-9-19(32)27-24(15)25(29(37)39-2)26(41-27)16-5-8-18(31)21(34)13-16/h3-11,13,22,25-26,30-34H,12H2,1-2H3/b10-6+/t22-,25+,26-/m1/s1

> <INCHI_KEY>
YAXTXMBBIHBGPZ-ZBBBDWFHSA-N

> <FORMULA>
C29H26O12

> <MOLECULAR_WEIGHT>
566.515

> <EXACT_MASS>
566.142426277

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
55.31813480736801

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (2S,3S)-2-(3,4-dihydroxyphenyl)-4-[(1E)-3-{[(2R)-3-(3,4-dihydroxyphenyl)-1-methoxy-1-oxopropan-2-yl]oxy}-3-oxoprop-1-en-1-yl]-7-hydroxy-2,3-dihydro-1-benzofuran-3-carboxylate

> <ALOGPS_LOGP>
3.71

> <JCHEM_LOGP>
4.037458472666667

> <ALOGPS_LOGS>
-4.88

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.396381393232659

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.879199423156834

> <JCHEM_PKA_STRONGEST_BASIC>
-4.961636718212665

> <JCHEM_POLAR_SURFACE_AREA>
189.28

> <JCHEM_REFRACTIVITY>
142.61070000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.52e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2S,3S)-2-(3,4-dihydroxyphenyl)-4-[(1E)-3-{[(2R)-3-(3,4-dihydroxyphenyl)-1-methoxy-1-oxopropan-2-yl]oxy}-3-oxoprop-1-en-1-yl]-7-hydroxy-2,3-dihydro-1-benzofuran-3-carboxylate

> <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       1.334  -0.770   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   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       9.336 -11.550   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      12.003 -10.010   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       3.812   2.570   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.185   3.977   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       1.654   3.816   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       3.955   5.311   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.185   6.645   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.955   7.978   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.495   7.978   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.265   6.645   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       5.495   5.311   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       7.805   6.645   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       6.265   9.312   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       5.318   2.250   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       5.794   0.786   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       6.349   3.395   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       7.855   3.075   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   41                                                  
CONECT    4    3    5   28                                                  
CONECT    5    4    6   26                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15                                                            
CONECT   17   12   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   25                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22   18                                                       
CONECT   24   22                                                            
CONECT   25   21                                                            
CONECT   26    5   27   37                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27    4                                                       
CONECT   29   27   30   34                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   36                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33   29                                                       
CONECT   35   33                                                            
CONECT   36   32                                                            
CONECT   37   26   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40                                                       
CONECT   40   39                                                            
CONECT   41    3                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   88    0
END

View in JSmol

Synonyms

Value	Source
Dimethyl lithospermic acid	Generator

Chemical Formula

C₂₉H₂₆O₁₂

Average Mass

566.5150 Da

Monoisotopic Mass

566.14243 Da

IUPAC Name

methyl (2S,3S)-2-(3,4-dihydroxyphenyl)-4-[(1E)-3-{[(2R)-3-(3,4-dihydroxyphenyl)-1-methoxy-1-oxopropan-2-yl]oxy}-3-oxoprop-1-en-1-yl]-7-hydroxy-2,3-dihydro-1-benzofuran-3-carboxylate

Traditional Name

methyl (2S,3S)-2-(3,4-dihydroxyphenyl)-4-[(1E)-3-{[(2R)-3-(3,4-dihydroxyphenyl)-1-methoxy-1-oxopropan-2-yl]oxy}-3-oxoprop-1-en-1-yl]-7-hydroxy-2,3-dihydro-1-benzofuran-3-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)[C@@H](CC1=CC=C(O)C(O)=C1)OC(=O)\C=C\C1=C2[C@@H]([C@H](OC2=C(O)C=C1)C1=CC=C(O)C(O)=C1)C(=O)OC

InChI Identifier

InChI=1S/C29H26O12/c1-38-28(36)22(12-14-3-7-17(30)20(33)11-14)40-23(35)10-6-15-4-9-19(32)27-24(15)25(29(37)39-2)26(41-27)16-5-8-18(31)21(34)13-16/h3-11,13,22,25-26,30-34H,12H2,1-2H3/b10-6+/t22-,25+,26-/m1/s1

InChI Key

YAXTXMBBIHBGPZ-ZBBBDWFHSA-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
Salvia miltiorrhiza	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2-arylbenzofuran flavonoids. These are phenylpropanoids containing the 2-phenylbenzofuran moiety.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

2-arylbenzofuran flavonoids

Sub Class

Not Available

Direct Parent

2-arylbenzofuran flavonoids

Alternative Parents

Substituents

2-arylbenzofuran flavonoid
Cinnamic acid or derivatives
Coumaric acid or derivatives
Cinnamic acid ester
Coumaran
Tricarboxylic acid or derivatives
Catechol
Styrene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Fatty acid ester
Fatty acyl
Benzenoid
Monocyclic benzene moiety
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Carboxylic acid ester
Ether
Oxacycle
Carboxylic acid derivative
Organoheterocyclic compound
Organic oxygen compound
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	3.71	ALOGPS
logP	4.04	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	8.88	ChemAxon
pKa (Strongest Basic)	-5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	189.28 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	142.61 m³·mol⁻¹	ChemAxon
Polarizability	55.32 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00037059

Chemspider ID

28505722

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70688393

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gao JF, Ding L, Zhang P, Liu JX: [Chemical constituents of Salvia chinensis]. Zhongguo Zhong Yao Za Zhi. 2013 May;38(10):1556-9. [PubMed:23947137 ]
Han YK, Lee JS, Yang SY, Lee KY, Kim YH: In Vitro and In Silico Studies of Soluble Epoxide Hydrolase Inhibitors from the Roots of Lycopus lucidus. Plants (Basel). 2021 Feb 13;10(2). pii: plants10020356. doi: 10.3390/plants10020356. [PubMed:33668538 ]
Choi HG, Tran PT, Lee JH, Min BS, Kim JA: Anti-inflammatory activity of caffeic acid derivatives isolated from the roots of Salvia miltiorrhiza Bunge. Arch Pharm Res. 2018 Jan;41(1):64-70. doi: 10.1007/s12272-017-0983-1. Epub 2017 Nov 9. [PubMed:29124660 ]
Lim E, Ricci J, Jung M: Synthesis of a dual-labeled probe of dimethyl lithospermate B with photochemical and fluorescent properties. Molecules. 2011 Nov 28;16(12):9886-99. doi: 10.3390/molecules16129886. [PubMed:22124203 ]
Choi YJ, Kim HS, Lee J, Chung J, Lee JS, Choi JS, Yoon TR, Kim HK, Chung HY: Down-regulation of oxidative stress and COX-2 and iNOS expressions by dimethyl lithospermate in aged rat kidney. Arch Pharm Res. 2014 Aug;37(8):1032-8. doi: 10.1007/s12272-014-0332-6. Epub 2014 Jan 29. [PubMed:24469601 ]

Showing NP-Card for Dimethyl lithospermate (NP0075297)

MOL for NP0075297 (Dimethyl lithospermate)

3D MOL for NP0075297 (Dimethyl lithospermate)

3D SDF for NP0075297 (Dimethyl lithospermate)

3D-SDF for NP0075297 (Dimethyl lithospermate)

PDB for NP0075297 (Dimethyl lithospermate)

3D PDB for NP0075297 (Dimethyl lithospermate)

SMILES for NP0075297 (Dimethyl lithospermate)

INCHI for NP0075297 (Dimethyl lithospermate)

Structure for NP0075297 (Dimethyl lithospermate)

3D Structure for NP0075297 (Dimethyl lithospermate)