NP-MRD: Showing NP-Card for Spathodic acid (NP0077182)

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Record Information

Version

2.0

Created at

2022-04-28 22:19:46 UTC

Updated at

2022-04-28 22:19:46 UTC

NP-MRD ID

NP0077182

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Spathodic acid

Description

Spathodic acid, also known as spathodate, belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Spathodic acid is found in Diospyros kaki , Rubia yunnanensis and Spathodea campanulata. Spathodic acid was first documented in 2005 (PMID: 16252920). Based on a literature review a small amount of articles have been published on spathodic acid (PMID: 29318764) (PMID: 35416746) (PMID: 24047122) (PMID: 18058383).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292200192D          

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M  END

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M  END


  Mrv1652304292200192D          

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    5.2520    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4895    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8395   -1.0164    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  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  2 12  1  1  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  6  0  0  0
 15 16  1  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 19 18  1  6  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 19 24  1  0  0  0  0
 24 25  1  6  0  0  0
 25 26  1  0  0  0  0
 24 27  1  1  0  0  0
 23 28  1  6  0  0  0
 20 29  1  6  0  0  0
 16 30  1  6  0  0  0
 11 31  1  1  0  0  0
  3 32  1  6  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
  1 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0077182

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@H](O)[C@](C)(CO)[C@@H]5CC[C@@]34C)[C@@H]2[C@@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H48O5/c1-25(2)13-15-30(24(34)35)16-14-28(5)18(22(30)23(25)33)7-8-20-26(3)11-10-21(32)27(4,17-31)19(26)9-12-29(20,28)6/h7,19-23,31-33H,8-17H2,1-6H3,(H,34,35)/t19-,20-,21+,22-,23+,26+,27-,28-,29-,30+/m1/s1

> <INCHI_KEY>
TUOYZAJHBIXONX-CGSJAQJOSA-N

> <FORMULA>
C30H48O5

> <MOLECULAR_WEIGHT>
488.709

> <EXACT_MASS>
488.350174646

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
83

> <JCHEM_AVERAGE_POLARIZABILITY>
56.63588351676425

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4aR,6aS,6bR,8aR,9S,10S,12aR,12bR,14bS)-1,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid

> <ALOGPS_LOGP>
4.96

> <JCHEM_LOGP>
4.161204939666668

> <ALOGPS_LOGS>
-4.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.152523355233832

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.643560791431459

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7854425934406057

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
136.8377

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.33e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4aR,6aS,6bR,8aR,9S,10S,12aR,12bR,14bS)-1,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       9.804  -0.564   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.034   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.804   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.344   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.114   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.344  -0.564   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.397  -2.103   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.650  -1.380   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.034   3.437   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.494   3.437   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.724   2.104   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.184   2.104   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.414   3.437   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.874   3.437   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.104   2.104   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.510   3.643   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -0.850   4.366   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -0.742   2.920   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -1.746   0.770   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       3.644  -0.564   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.885   3.635   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.574   3.437   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       9.804   4.771   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      12.114   3.437   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       9.034  -1.897   0.000  0.00  0.00           O+0
CONECT    1    2    6   35                                                  
CONECT    2    1    3   12                                                  
CONECT    3    2    4    9   32                                             
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1    7    8                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    3   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16   31                                             
CONECT   12   11    2   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   11   17   30                                             
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   15   21   29                                             
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   19   25   27                                             
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27   24                                                            
CONECT   28   23                                                            
CONECT   29   20                                                            
CONECT   30   16                                                            
CONECT   31   11                                                            
CONECT   32    3   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35    1                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Value	Source
Spathodate	Generator

Chemical Formula

C₃₀H₄₈O₅

Average Mass

488.7090 Da

Monoisotopic Mass

488.35017 Da

IUPAC Name

(1S,4aR,6aS,6bR,8aR,9S,10S,12aR,12bR,14bS)-1,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid

Traditional Name

(1S,4aR,6aS,6bR,8aR,9S,10S,12aR,12bR,14bS)-1,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@H](O)[C@](C)(CO)[C@@H]5CC[C@@]34C)[C@@H]2[C@@H]1O)C(O)=O

InChI Identifier

InChI=1S/C30H48O5/c1-25(2)13-15-30(24(34)35)16-14-28(5)18(22(30)23(25)33)7-8-20-26(3)11-10-21(32)27(4,17-31)19(26)9-12-29(20,28)6/h7,19-23,31-33H,8-17H2,1-6H3,(H,34,35)/t19-,20-,21+,22-,23+,26+,27-,28-,29-,30+/m1/s1

InChI Key

TUOYZAJHBIXONX-CGSJAQJOSA-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
Diospyros kaki	Plant	KNApSAcK
Rubia yunnanensis	LOTUS Database	35616633
Spathodea campanulata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Steroid
Cyclic alcohol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

hydroxy monocarboxylic acid (CHEBI:69529 )
pentacyclic triterpenoid (CHEBI:69529 )
sapogenin (CHEBI:69529 )

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	4.96	ALOGPS
logP	4.16	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	4.64	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	136.84 m³·mol⁻¹	ChemAxon
Polarizability	56.64 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

C00040339

Chemspider ID

10217347

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21594148

PDB ID

Not Available

ChEBI ID

69529

Good Scents ID

Not Available

References

General References

Zhang AL, Ye Q, Li BG, Qi HY, Zhang GL: Phenolic and triterpene glycosides from the stems of Ilex litseaefolia. J Nat Prod. 2005 Oct;68(10):1531-5. doi: 10.1021/np050285z. [PubMed:16252920 ]
Zhang X, Zhou Y, Wei Z, Shen J, Wang L, Ma Z, Zhang X: Antiphytoviral toxins of Actinidia chinensis root bark (ACRB) extract: laboratory and semi-field trials. Pest Manag Sci. 2018 Jul;74(7):1630-1636. doi: 10.1002/ps.4854. Epub 2018 Feb 23. [PubMed:29318764 ]
Mahmoud AH, Mahmoud BK, Samy MN, Fouad MA, Kamel MS, Matsunami K: Cytotoxic and antileishmanial triterpenes of Tabebuia aurea (Silva Manso) leaves. Nat Prod Res. 2022 Apr 13:1-5. doi: 10.1080/14786419.2022.2062350. [PubMed:35416746 ]
Pan ZH, Ning DS, Liu JL, Pan B, Li DP: A new triterpenoid saponin from the root of Croton lachnocarpus Benth. Nat Prod Res. 2014;28(1):48-51. doi: 10.1080/14786419.2013.838238. Epub 2013 Sep 18. [PubMed:24047122 ]
Feng F, Zhu MX, Xie N, Liu WY, Chen DJ, You QD: Two new triterpenoid saponins from the root of Ilex pubescens. J Asian Nat Prod Res. 2008 Jan-Feb;10(1-2):71-5. doi: 10.1080/10286020701273874. [PubMed:18058383 ]

Showing NP-Card for Spathodic acid (NP0077182)

MOL for NP0077182 (Spathodic acid)

3D MOL for NP0077182 (Spathodic acid)

3D SDF for NP0077182 (Spathodic acid)

3D-SDF for NP0077182 (Spathodic acid)

PDB for NP0077182 (Spathodic acid)

3D PDB for NP0077182 (Spathodic acid)

SMILES for NP0077182 (Spathodic acid)

INCHI for NP0077182 (Spathodic acid)

Structure for NP0077182 (Spathodic acid)

3D Structure for NP0077182 (Spathodic acid)