MiMeDB: Showing metabocard for Gibberellin A9 (MMDBc0020516)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 10:39:06 UTC

Update Date

2022-08-31 06:46:55 UTC

Metabolite ID

MMDBc0020516

Metabolite Identification

Common Name

Gibberellin A9

Description

gibberellin A9, also known as GA9, belongs to the class of organic compounds known as c19-gibberellin 6-carboxylic acids. These are c19-gibberellins with a carboxyl group at the 6-position. Thus, gibberellin A9 is considered to be an isoprenoid lipid molecule. gibberellin A9 is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533007211515312D          
 
 25 29  0  0  1  0            999 V2000
   18.3310  -10.3277    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.3383  -11.1527    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.6168   -9.9137    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.0525   -9.9174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0452  -10.7387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9026  -11.1563    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.1080  -11.6046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9026  -10.3277    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.6205   -9.0888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0525   -9.0923    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.7588   -9.4954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1044  -12.5075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.5545   -9.2848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6132  -10.7387    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.2054  -11.6856    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.3318   -8.6758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2065   -9.9499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9029   -9.5485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2065  -11.5699    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.5130  -10.3468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5130  -11.1569    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2022  -12.3719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8946  -10.6514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5624  -10.6514    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.8765  -11.1531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  9 16  1  0  0  0  0
 11 13  2  0  0  0  0
  6  8  1  0  0  0  0
 10 11  1  1  0  0  0
  3 14  1  1  0  0  0
  1  2  1  0  0  0  0
  6 15  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  1  0  0  0
  2  6  1  0  0  0  0
  2  7  1  1  0  0  0
  3  8  1  0  0  0  0
  3  9  1  0  0  0  0
  4 10  1  0  0  0  0
  5 11  1  0  0  0  0
  8 17  1  0  0  0  0
  8 18  1  6  0  0  0
  6 19  1  0  0  0  0
 17 20  1  0  0  0  0
 19 21  1  0  0  0  0
 20 21  1  0  0  0  0
 19 22  1  1  0  0  0
 19 23  1  6  0  0  0
 23 18  1  0  0  0  0
 23 24  2  0  0  0  0
  7 12  2  0  0  0  0
  7 25  1  0  0  0  0
 16 10  1  0  0  0  0
M  END

 
  Mrv1533007211515312D          
 
 25 29  0  0  1  0            999 V2000
   18.3310  -10.3277    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.3383  -11.1527    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.6168   -9.9137    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.0525   -9.9174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0452  -10.7387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9026  -11.1563    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.1080  -11.6046    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9026  -10.3277    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.6205   -9.0888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0525   -9.0923    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.7588   -9.4954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1044  -12.5075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.5545   -9.2848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6132  -10.7387    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.2054  -11.6856    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.3318   -8.6758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2065   -9.9499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9029   -9.5485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2065  -11.5699    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.5130  -10.3468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5130  -11.1569    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2022  -12.3719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8946  -10.6514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5624  -10.6514    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.8765  -11.1531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  9 16  1  0  0  0  0
 11 13  2  0  0  0  0
  6  8  1  0  0  0  0
 10 11  1  1  0  0  0
  3 14  1  1  0  0  0
  1  2  1  0  0  0  0
  6 15  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  1  0  0  0
  2  6  1  0  0  0  0
  2  7  1  1  0  0  0
  3  8  1  0  0  0  0
  3  9  1  0  0  0  0
  4 10  1  0  0  0  0
  5 11  1  0  0  0  0
  8 17  1  0  0  0  0
  8 18  1  6  0  0  0
  6 19  1  0  0  0  0
 17 20  1  0  0  0  0
 19 21  1  0  0  0  0
 20 21  1  0  0  0  0
 19 22  1  1  0  0  0
 19 23  1  6  0  0  0
 23 18  1  0  0  0  0
 23 24  2  0  0  0  0
  7 12  2  0  0  0  0
  7 25  1  0  0  0  0
 16 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0020516

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CC[C@@H]3C[C@]1(CC3=C)[C@@H](C(O)=O)[C@]1([H])[C@]3(C)CCC[C@@]21OC3=O

> <INCHI_IDENTIFIER>
InChI=1S/C19H24O4/c1-10-8-18-9-11(10)4-5-12(18)19-7-3-6-17(2,16(22)23-19)14(19)13(18)15(20)21/h11-14H,1,3-9H2,2H3,(H,20,21)/t11-,12-,13-,14-,17-,18+,19-/m1/s1

> <INCHI_KEY>
MHVYWTXXZIFXDT-YGNOGLJPSA-N

> <FORMULA>
C19H24O4

> <MOLECULAR_WEIGHT>
316.397

> <EXACT_MASS>
316.167459253

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
0.0

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,5R,8R,9S,10R,11S)-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid

> <ALOGPS_LOGP>
2.82

> <JCHEM_LOGP>
2.7911308523333327

> <ALOGPS_LOGS>
-3.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.391547724572421

> <JCHEM_PKA_STRONGEST_BASIC>
-7.130963497507645

> <JCHEM_POLAR_SURFACE_AREA>
63.60000000000001

> <JCHEM_REFRACTIVITY>
82.56329999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.18e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gibberellin A9

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-JUL-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JUL-15         0                                  
HETATM    1  C   UNK     0      34.218 -19.278   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      34.231 -20.818   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      32.885 -18.506   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      35.565 -18.512   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      35.551 -20.046   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      31.552 -20.825   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      35.668 -21.662   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      31.552 -19.278   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      32.892 -16.966   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      35.565 -16.972   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      36.883 -17.725   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      35.662 -23.347   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      38.368 -17.332   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0      32.878 -20.046   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0      32.117 -21.813   0.000  0.00  0.00           H+0
HETATM   16  C   UNK     0      34.219 -16.195   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      30.252 -18.573   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      31.552 -17.824   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      30.252 -21.597   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      28.958 -19.314   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      28.958 -20.826   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      30.244 -23.094   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      29.670 -19.883   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      30.917 -19.883   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      37.103 -20.819   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6    7                                                  
CONECT    3   14    1    8    9                                             
CONECT    4    1   10                                                       
CONECT    5    1   11                                                       
CONECT    6    8   15    2   19                                             
CONECT    7    2   12   25                                                  
CONECT    8    6    3   17   18                                             
CONECT    9   16    3                                                       
CONECT   10   11    4   16                                                  
CONECT   11   13   10    5                                                  
CONECT   12    7                                                            
CONECT   13   11                                                            
CONECT   14    3                                                            
CONECT   15    6                                                            
CONECT   16    9   10                                                       
CONECT   17    8   20                                                       
CONECT   18    8   23                                                       
CONECT   19    6   21   22   23                                             
CONECT   20   17   21                                                       
CONECT   21   19   20                                                       
CONECT   22   19                                                            
CONECT   23   19   18   24                                                  
CONECT   24   23                                                            
CONECT   25    7                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   58    0
END

Synonyms

Value	Source
GA9	ChEBI

Molecular Formula

C₁₉H₂₄O₄

Average Mass

316.397

Monoisotopic Mass

316.167459253

IUPAC Name

(1R,2R,5R,8R,9S,10R,11S)-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid

Traditional Name

gibberellin A9

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC[C@@H]3C[C@]1(CC3=C)[C@@H](C(O)=O)[C@]1([H])[C@]3(C)CCC[C@@]21OC3=O

InChI Identifier

InChI=1S/C19H24O4/c1-10-8-18-9-11(10)4-5-12(18)19-7-3-6-17(2,16(22)23-19)14(19)13(18)15(20)21/h11-14H,1,3-9H2,2H3,(H,20,21)/t11-,12-,13-,14-,17-,18+,19-/m1/s1

InChI Key

MHVYWTXXZIFXDT-YGNOGLJPSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as c19-gibberellin 6-carboxylic acids. These are c19-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

C19-gibberellin 6-carboxylic acids

Alternative Parents

Substituents

20-norgibberellane-6-carboxylic acid
Diterpene lactone
Caprolactone
Oxepane
Dicarboxylic acid or derivatives
Gamma butyrolactone
Tetrahydrofuran
Carboxylic acid ester
Lactone
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Organoheterocyclic compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

lactone (CHEBI:29605 )
C19-gibberellin (CHEBI:29605 )
gibberellin monocarboxylic acid (CHEBI:29605 )
Gibberellins (C11863 )
Gibberellins (LMPR0104170020 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.12 g/L	ALOGPS
logP	2.82	ALOGPS
logP	2.79	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	4.39	ChemAxon
pKa (Strongest Basic)	-7.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.6 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	82.56 m³·mol⁻¹	ChemAxon
Polarizability	0 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01ba-0095000000-b5ae963d9271fbf62c46	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01ba-0791000000-557eb098353ded32ef54	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-014i-4950000000-b58543238ebce914043b	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01b9-0079000000-3cac46e9db42eab92e9e	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00xr-0092000000-1761e51e0f92d388e694	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05di-1290000000-03bbe72d3ae4056e8ae3	2019-02-23	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	6	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00000009

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

CPD1F-134

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5281984

PDB ID

Not Available

ChEBI ID

29605

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Gibberellin A9 (MMDBc0020516)

MOL for #<Metabolite:0x00007fecf06810c0>

3D MOL for #<Metabolite:0x00007fecf06810c0>

3D SDF for #<Metabolite:0x00007fecf06810c0>

3D-SDF for #<Metabolite:0x00007fecf06810c0>

PDB for #<Metabolite:0x00007fecf06810c0>

3D PDB for #<Metabolite:0x00007fecf06810c0>

SMILES for #<Metabolite:0x00007fecf06810c0>

INCHI for #<Metabolite:0x00007fecf06810c0>

Structure for #<Metabolite:0x00007fecf06810c0>

3D Structure for #<Metabolite:0x00007fecf06810c0>