NP-MRD: Showing NP-Card for Gardenolic acid B (NP0140751)

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Record Information

Version

2.0

Created at

2022-06-29 21:50:08 UTC

Updated at

2022-06-29 21:50:08 UTC

NP-MRD ID

NP0140751

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gardenolic acid B

Description

Gardenolic acid B, also known as gardenolate b, belongs to the class of organic compounds known as cycloartanols and derivatives. These are steroids containing a cycloartanol moiety. Gardenolic acid B is found in Gardenia jasminoides and Kleinhovia hospita. Gardenolic acid B was first documented in 2009 (PMID: 19489592). Based on a literature review very few articles have been published on Gardenolic acid B (PMID: 30518256).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306292223502D          

 35 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306292223502D          

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  7  9  1  0  0  0  0
 10  2  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 13 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 21 20  1  1  0  0  0
 21 22  1  0  0  0  0
 17 22  1  0  0  0  0
 22 23  1  1  0  0  0
 17 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 21 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  6  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 26 32  1  1  0  0  0
 24 33  1  6  0  0  0
 14 34  1  1  0  0  0
 13 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0140751

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CC(=O)C=C(C)C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@@H]4[C@]5(C[C@@]35CC[C@]12C)[C@@H](O)C[C@H](O)[C@@]4(C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H46O5/c1-17(2)13-19(31)14-18(3)20-9-10-27(5)21-7-8-22-28(6,25(34)35)23(32)15-24(33)30(22)16-29(21,30)12-11-26(20,27)4/h13,18,20-24,32-33H,7-12,14-16H2,1-6H3,(H,34,35)/t18-,20-,21+,22+,23+,24+,26-,27+,28+,29+,30-/m1/s1

> <INCHI_KEY>
TTYDGCKGPQOMOK-SESPQYOESA-N

> <FORMULA>
C30H46O5

> <MOLECULAR_WEIGHT>
486.693

> <EXACT_MASS>
486.334524581

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
55.78353658298071

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,3S,4S,6S,7S,8R,11S,12S,15R,16R)-4,6-dihydroxy-7,12,16-trimethyl-15-[(2R)-6-methyl-4-oxohept-5-en-2-yl]pentacyclo[9.7.0.0^{1,3}.0^{3,8}.0^{12,16}]octadecane-7-carboxylic acid

> <ALOGPS_LOGP>
4.27

> <JCHEM_LOGP>
4.616277326333334

> <ALOGPS_LOGS>
-5.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.310977175918254

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.460360924338091

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9785931003917456

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
135.84039999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.42e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3S,4S,6S,7S,8R,11S,12S,15R,16R)-4,6-dihydroxy-7,12,16-trimethyl-15-[(2R)-6-methyl-4-oxohept-5-en-2-yl]pentacyclo[9.7.0.0^{1,3}.0^{3,8}.0^{12,16}]octadecane-7-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0      11.969   4.447   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.549   3.020   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.075   2.809   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.020   4.025   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      14.440   5.452   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      16.545   3.815   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      17.126   2.388   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.651   2.177   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      16.181   1.172   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.604   1.804   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.032   0.325   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.757  -0.539   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.542   0.406   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.065   1.854   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.072   3.032   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.556   2.761   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.033   1.312   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.026   0.135   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.502  -1.314   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.986  -1.585   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.994  -0.407   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.517   1.041   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.040   2.489   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.524   2.218   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.008   1.947   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.485   0.499   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.478  -0.678   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.336  -1.712   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.696  -2.203   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       5.125  -2.776   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       2.485  -3.154   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       0.969   0.228   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       5.047   3.667   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      10.737   3.240   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       9.173  -1.089   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    2   11   14                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   18   35                                             
CONECT   14   13   10   15   34                                             
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   22   23                                             
CONECT   18   17   13   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   17   23   24                                             
CONECT   23   22   17                                                       
CONECT   24   22   25   33                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   32                                                  
CONECT   27   26   21   28   29                                             
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   26                                                            
CONECT   33   24                                                            
CONECT   34   14                                                            
CONECT   35   13                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Value	Source
Gardenolate b	Generator

Chemical Formula

C₃₀H₄₆O₅

Average Mass

486.6930 Da

Monoisotopic Mass

486.33452 Da

IUPAC Name

(1S,3S,4S,6S,7S,8R,11S,12S,15R,16R)-4,6-dihydroxy-7,12,16-trimethyl-15-[(2R)-6-methyl-4-oxohept-5-en-2-yl]pentacyclo[9.7.0.0^{1,3}.0^{3,8}.0^{12,16}]octadecane-7-carboxylic acid

Traditional Name

(1S,3S,4S,6S,7S,8R,11S,12S,15R,16R)-4,6-dihydroxy-7,12,16-trimethyl-15-[(2R)-6-methyl-4-oxohept-5-en-2-yl]pentacyclo[9.7.0.0^{1,3}.0^{3,8}.0^{12,16}]octadecane-7-carboxylic acid

CAS Registry Number

Not Available

SMILES

C[C@H](CC(=O)C=C(C)C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@@H]4[C@]5(C[C@@]35CC[C@]12C)[C@@H](O)C[C@H](O)[C@@]4(C)C(O)=O

InChI Identifier

InChI=1S/C30H46O5/c1-17(2)13-19(31)14-18(3)20-9-10-27(5)21-7-8-22-28(6,25(34)35)23(32)15-24(33)30(22)16-29(21,30)12-11-26(20,27)4/h13,18,20-24,32-33H,7-12,14-16H2,1-6H3,(H,34,35)/t18-,20-,21+,22+,23+,24+,26-,27+,28+,29+,30-/m1/s1

InChI Key

TTYDGCKGPQOMOK-SESPQYOESA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Gardenia jasminoides	LOTUS Database	35616633
Kleinhovia hospita	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cycloartanols and derivatives. These are steroids containing a cycloartanol moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Cycloartanols and derivatives

Direct Parent

Cycloartanols and derivatives

Alternative Parents

Substituents

Cycloartanol-skeleton
Cycloartane-skeleton
Triterpenoid
9b,19-cyclo-lanostane-skeleton
23-oxosteroid
4-carboxy steroid
Steroid acid
Hydroxysteroid
15-hydroxysteroid
3-beta-hydroxysteroid
11-hydroxysteroid
11-beta-hydroxysteroid
1-hydroxysteroid
Oxosteroid
3-hydroxysteroid
Beta-hydroxy acid
Hydroxy acid
Acryloyl-group
Cyclic alcohol
Alpha,beta-unsaturated ketone
Enone
Secondary alcohol
Ketone
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organic oxide
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	4.27	ALOGPS
logP	4.62	ChemAxon
logS	-5	ALOGPS
pKa (Strongest Acidic)	4.46	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	135.84 m³·mol⁻¹	ChemAxon
Polarizability	55.78 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

Not Available

Chemspider ID

24622189

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45273405

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Lu D, Zhang W, Jiang Y, Zhang Y, Pan D, Zhang D, Yao X, Yu Y: Two new triterpenoids from Gardenia jasminoides fruits. Nat Prod Res. 2019 Oct;33(19):2789-2794. doi: 10.1080/14786419.2018.1502764. Epub 2018 Dec 5. [PubMed:30518256 ]
Gan LS, Ren G, Mo JX, Zhang XY, Yao W, Zhou CX: Cycloartane triterpenoids from Kleinhovia hospita. J Nat Prod. 2009 Jun;72(6):1102-5. doi: 10.1021/np900029z. [PubMed:19489592 ]

Showing NP-Card for Gardenolic acid B (NP0140751)

MOL for NP0140751 (Gardenolic acid B)

3D MOL for NP0140751 (Gardenolic acid B)

3D SDF for NP0140751 (Gardenolic acid B)

3D-SDF for NP0140751 (Gardenolic acid B)

PDB for NP0140751 (Gardenolic acid B)

3D PDB for NP0140751 (Gardenolic acid B)

SMILES for NP0140751 (Gardenolic acid B)

INCHI for NP0140751 (Gardenolic acid B)

Structure for NP0140751 (Gardenolic acid B)

3D Structure for NP0140751 (Gardenolic acid B)