NP-MRD: Showing NP-Card for (1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid (NP0220314)

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Record Information

Version

2.0

Created at

2022-09-05 21:35:16 UTC

Updated at

2022-09-05 21:35:16 UTC

NP-MRD ID

NP0220314

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid

Description

(1R,2S,3S,4S,5S,8R,9R,11S,12R)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]Pentadecane-2,4,8-tricarboxylic acid belongs to the class of organic compounds known as c20-gibberellin 20-carboxylic acids. These are c20-gibberellins with a carboxyl group at the 6-position. (1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid is found in Cucurbita maxima. Based on a literature review very few articles have been published on (1R,2S,3S,4S,5S,8R,9R,11S,12R)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]Pentadecane-2,4,8-tricarboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052223352D          

 34 37  0  0  1  0            999 V2000
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   -0.0966    1.2252    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309052223352D          

 34 37  0  0  1  0            999 V2000
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 25 30  1  0  0  0  0
 30 11  1  1  0  0  0
 30 31  1  0  0  0  0
  4 31  1  0  0  0  0
 31 32  1  6  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0220314

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CC(=O)O[C@H]1CC[C@]2([C@@H]3C[C@H](O)[C@@H]4C[C@]3(CC4=C)[C@H]([C@@H]2[C@]1(C)C(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H34O9/c1-11(2)7-17(27)34-16-5-6-25(22(32)33)15-8-14(26)13-10-24(15,9-12(13)3)18(20(28)29)19(25)23(16,4)21(30)31/h11,13-16,18-19,26H,3,5-10H2,1-2,4H3,(H,28,29)(H,30,31)(H,32,33)/t13-,14+,15-,16+,18-,19-,23-,24+,25-/m1/s1

> <INCHI_KEY>
PGQPKTHMBIOFIN-WUWWEOQMSA-N

> <FORMULA>
C25H34O9

> <MOLECULAR_WEIGHT>
478.538

> <EXACT_MASS>
478.220282675

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
49.09969118603881

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2S,3S,4S,5S,8R,9R,11S,12R)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0^{1,9}.0^{3,8}]pentadecane-2,4,8-tricarboxylic acid

> <JCHEM_LOGP>
2.111372366333334

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
4.062645051728746

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.530669736324982

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8678811626342285

> <JCHEM_POLAR_SURFACE_AREA>
158.43

> <JCHEM_REFRACTIVITY>
116.75569999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,3S,4S,5S,8R,9R,11S,12R)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0^{1,9}.0^{3,8}]pentadecane-2,4,8-tricarboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.943  -1.180   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.500  -0.642   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.140  -1.543   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.210  -0.575   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.105   0.244   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.065   0.925   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.180   2.287   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.901   3.648   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.428   2.253   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.128   0.787   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.647   0.365   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.404   1.886   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.965   2.436   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.599   2.857   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.928   1.219   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.308   0.535   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.407  -1.002   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       7.787  -1.685   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       9.069  -0.831   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      10.449  -1.515   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       8.970   0.705   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.252   1.559   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.154   3.096   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.632   0.876   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.125  -1.855   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.212  -3.095   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.188  -2.969   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       7.684  -2.606   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       5.755  -4.447   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       3.745  -1.172   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.295  -1.731   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.952  -3.233   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       0.481  -3.687   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       3.081  -4.280   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10   31                                             
CONECT    5    4    6                                                       
CONECT    6    5    2    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10   12   15   30                                             
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   11   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   25                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   17   26   27   30                                             
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   25   11   31                                                  
CONECT   31   30    4   32                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Value	Source
(1R,2S,3S,4S,5S,8R,9R,11S,12R)-11-Hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0,.0,]pentadecane-2,4,8-tricarboxylate	Generator

Chemical Formula

C₂₅H₃₄O₉

Average Mass

478.5380 Da

Monoisotopic Mass

478.22028 Da

IUPAC Name

(1R,2S,3S,4S,5S,8R,9R,11S,12R)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0^{1,9}.0^{3,8}]pentadecane-2,4,8-tricarboxylic acid

Traditional Name

(1R,2S,3S,4S,5S,8R,9R,11S,12R)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0^{1,9}.0^{3,8}]pentadecane-2,4,8-tricarboxylic acid

CAS Registry Number

Not Available

SMILES

CC(C)CC(=O)O[C@H]1CC[C@]2([C@@H]3C[C@H](O)[C@@H]4C[C@]3(CC4=C)[C@H]([C@@H]2[C@]1(C)C(O)=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C25H34O9/c1-11(2)7-17(27)34-16-5-6-25(22(32)33)15-8-14(26)13-10-24(15,9-12(13)3)18(20(28)29)19(25)23(16,4)21(30)31/h11,13-16,18-19,26H,3,5-10H2,1-2,4H3,(H,28,29)(H,30,31)(H,32,33)/t13-,14+,15-,16+,18-,19-,23-,24+,25-/m1/s1

InChI Key

PGQPKTHMBIOFIN-WUWWEOQMSA-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
Cucurbita maxima	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as c20-gibberellin 20-carboxylic acids. These are c20-gibberellins with a carboxyl group at the 6-position.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

C20-gibberellin 20-carboxylic acids

Alternative Parents

Substituents

Gibberellane-20-carboxylic acid
Gibberellane-6-carboxylic acid
Tetracarboxylic acid or derivatives
Fatty acid ester
Fatty acyl
Cyclic alcohol
Carboxylic acid ester
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
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	2.11	ChemAxon
pKa (Strongest Acidic)	3.53	ChemAxon
pKa (Strongest Basic)	-0.87	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	158.43 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	116.76 m³·mol⁻¹	ChemAxon
Polarizability	49.1 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162883988

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid (NP0220314)

MOL for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)

3D MOL for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)

3D SDF for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)

3D-SDF for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)

PDB for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)

3D PDB for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)

SMILES for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)

INCHI for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)

Structure for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)

3D Structure for NP0220314 ((1r,2s,3s,4s,5s,8r,9r,11s,12r)-11-hydroxy-4-methyl-5-[(3-methylbutanoyl)oxy]-13-methylidenetetracyclo[10.2.1.0¹,⁹.0³,⁸]pentadecane-2,4,8-tricarboxylic acid)