MiMeDB: Showing metabocard for Gibberellin A38 (MMDBc0053288)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-05-16 21:19:46 UTC

Update Date

2024-04-30 20:47:57 UTC

Metabolite ID

MMDBc0053288

Metabolite Identification

Common Name

Gibberellin A38

Description

Gibberellin A38 (GA38) 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. Gibberellin A38 is found in chayote. Gibberellin A38 is isolated from immature seeds of Phaseolus vulgaris (French bean).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306222023522D          

 26 30  0  0  0  0            999 V2000
    0.2001    0.4019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7611   -0.9076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3592    2.4524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1138    0.6358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0154    1.2456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4994    2.3898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7132    0.3489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7540    1.3146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4178    1.8430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9425    0.7616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8060    1.7056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6128   -0.1569    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0215    0.3709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7674    0.7374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9118   -0.4467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0153    0.4405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4378   -0.1486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5929    1.8347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3846    0.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0958    1.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3047   -0.9222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1488   -0.7606    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1441   -1.2383    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7806    0.1325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3152    1.8857    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0070    1.2655    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
 10  1  2  0  0  0  0
 10  7  1  0  0  0  0
 11  3  1  0  0  0  0
 12  4  1  0  0  0  0
 14 13  1  0  0  0  0
 15 13  1  0  0  0  0
 17  2  1  0  0  0  0
 17 12  1  0  0  0  0
 17 14  1  0  0  0  0
 17 16  1  0  0  0  0
 18  5  1  0  0  0  0
 18  9  1  0  0  0  0
 18 11  1  0  0  0  0
 18 14  1  0  0  0  0
 19  7  1  0  0  0  0
 19  8  1  0  0  0  0
 19 11  1  0  0  0  0
 19 13  1  0  0  0  0
 20  6  1  0  0  0  0
 20  8  1  0  0  0  0
 20 10  1  0  0  0  0
 21 12  1  0  0  0  0
 22 15  2  0  0  0  0
 23 15  1  0  0  0  0
 24 16  2  0  0  0  0
 25 20  1  0  0  0  0
 26  9  1  0  0  0  0
 26 16  1  0  0  0  0
M  END


  Mrv1652306222023522D          

 26 30  0  0  0  0            999 V2000
    0.2001    0.4019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7611   -0.9076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3592    2.4524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1138    0.6358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0154    1.2456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4994    2.3898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7132    0.3489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7540    1.3146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4178    1.8430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9425    0.7616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8060    1.7056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6128   -0.1569    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0215    0.3709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7674    0.7374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9118   -0.4467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0153    0.4405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4378   -0.1486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5929    1.8347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3846    0.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0958    1.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3047   -0.9222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1488   -0.7606    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1441   -1.2383    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7806    0.1325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3152    1.8857    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0070    1.2655    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
 10  1  2  0  0  0  0
 10  7  1  0  0  0  0
 11  3  1  0  0  0  0
 12  4  1  0  0  0  0
 14 13  1  0  0  0  0
 15 13  1  0  0  0  0
 17  2  1  0  0  0  0
 17 12  1  0  0  0  0
 17 14  1  0  0  0  0
 17 16  1  0  0  0  0
 18  5  1  0  0  0  0
 18  9  1  0  0  0  0
 18 11  1  0  0  0  0
 18 14  1  0  0  0  0
 19  7  1  0  0  0  0
 19  8  1  0  0  0  0
 19 11  1  0  0  0  0
 19 13  1  0  0  0  0
 20  6  1  0  0  0  0
 20  8  1  0  0  0  0
 20 10  1  0  0  0  0
 21 12  1  0  0  0  0
 22 15  2  0  0  0  0
 23 15  1  0  0  0  0
 24 16  2  0  0  0  0
 25 20  1  0  0  0  0
 26  9  1  0  0  0  0
 26 16  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0053288

> <DATABASE_NAME>
MIME

> <SMILES>
CC12C3C(C(O)=O)C45CC(=C)C(O)(C4)CCC5C3(CCC1O)COC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H26O6/c1-10-7-19-8-20(10,25)6-3-11(19)18-5-4-12(21)17(2,16(24)26-9-18)14(18)13(19)15(22)23/h11-14,21,25H,1,3-9H2,2H3,(H,22,23)

> <INCHI_KEY>
GAQSCLQIDHHPEE-UHFFFAOYSA-N

> <FORMULA>
C20H26O6

> <MOLECULAR_WEIGHT>
362.4168

> <EXACT_MASS>
362.172938564

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
37.22892458323153

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,17-dihydroxy-11-methyl-6-methylidene-12-oxo-13-oxapentacyclo[9.3.3.1^{5,8}.0^{1,10}.0^{2,8}]octadecane-9-carboxylic acid

> <ALOGPS_LOGP>
0.46

> <JCHEM_LOGP>
0.579595748666666

> <ALOGPS_LOGS>
-2.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.453688965787581

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.246711152826593

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9048824169630426

> <JCHEM_POLAR_SURFACE_AREA>
104.06

> <JCHEM_REFRACTIVITY>
90.32859999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.99e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,17-dihydroxy-11-methyl-6-methylidene-12-oxo-13-oxapentacyclo[9.3.3.1^{5,8}.0^{1,10}.0^{2,8}]octadecane-9-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  C   UNK     0       0.374   0.750   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.887  -1.694   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.404   4.578   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.812   1.187   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.629   2.325   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.799   4.461   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.198   0.651   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.274   2.454   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.247   3.440   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.759   1.422   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.238   3.184   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.744  -0.293   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.640   0.692   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.032   1.376   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.435  -0.834   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.362   0.822   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.284  -0.277   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.707   3.425   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.451   1.743   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.045   3.022   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       6.169  -1.721   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.011  -1.420   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       5.869  -2.311   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      10.790   0.247   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.588   3.520   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       9.346   2.362   0.000  0.00  0.00           O+0
CONECT    1   10                                                            
CONECT    2   17                                                            
CONECT    3    6   11                                                       
CONECT    4    5   12                                                       
CONECT    5    4   18                                                       
CONECT    6    3   20                                                       
CONECT    7   10   19                                                       
CONECT    8   19   20                                                       
CONECT    9   18   26                                                       
CONECT   10    1    7   20                                                  
CONECT   11    3   18   19                                                  
CONECT   12    4   17   21                                                  
CONECT   13   14   15   19                                                  
CONECT   14   13   17   18                                                  
CONECT   15   13   22   23                                                  
CONECT   16   17   24   26                                                  
CONECT   17    2   12   14   16                                             
CONECT   18    5    9   11   14                                             
CONECT   19    7    8   11   13                                             
CONECT   20    6    8   10   25                                             
CONECT   21   12                                                            
CONECT   22   15                                                            
CONECT   23   15                                                            
CONECT   24   16                                                            
CONECT   25   20                                                            
CONECT   26    9   16                                                       
MASTER        0    0    0    0    0    0    0    0   26    0   60    0
END

Synonyms

Value	Source
3,13-Dihydroxygibberellin a15	HMDB
GA38	HMDB

Molecular Formula

C₂₀H₂₆O₆

Average Mass

362.4168

Monoisotopic Mass

362.172938564

IUPAC Name

5,17-dihydroxy-11-methyl-6-methylidene-12-oxo-13-oxapentacyclo[9.3.3.1^{5,8}.0^{1,10}.0^{2,8}]octadecane-9-carboxylic acid

Traditional Name

5,17-dihydroxy-11-methyl-6-methylidene-12-oxo-13-oxapentacyclo[9.3.3.1^{5,8}.0^{1,10}.0^{2,8}]octadecane-9-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC12C3C(C(O)=O)C45CC(=C)C(O)(C4)CCC5C3(CCC1O)COC2=O

InChI Identifier

InChI=1S/C20H26O6/c1-10-7-19-8-20(10,25)6-3-11(19)18-5-4-12(21)17(2,16(24)26-9-18)14(18)13(19)15(22)23/h11-14,21,25H,1,3-9H2,2H3,(H,22,23)

InChI Key

GAQSCLQIDHHPEE-UHFFFAOYSA-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
Delta valerolactone
Delta_valerolactone
Dicarboxylic acid or derivatives
Oxane
Cyclic alcohol
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Lactone
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Carbonyl group
Alcohol
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.99 g/L	ALOGPS
logP	0.46	ALOGPS
logP	0.58	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	4.25	ChemAxon
pKa (Strongest Basic)	-0.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	104.06 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	90.33 m³·mol⁻¹	ChemAxon
Polarizability	37.23 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 (Non-derivatized) - 70eV, Positive	splash10-00m1-1009000000-1365634ac7f166456b71	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0470-6100390000-b36a0b4e76a0c021a651	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0019000000-88fc183f1811698a12d9	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-002b-0339000000-32a54f62b1c25cfc4d31	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00kb-1974000000-b06a34683331a378f01c	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0019000000-6e1e9772cfa8edbd35ba	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0295-0049000000-e1798c00bb09080eca3d	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-1074-2197000000-ebd57fb7f6c302916cde	2015-05-27	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

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	Basidiomycota	8	Human feces
Eukaryota/Fungi	Ascomycota	2

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

HMDB0036902

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB015865

KNApSAcK ID

C00000038

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

14833724

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. doi: 10.1038/35036052. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. doi: 10.1194/jlr.R600022-JLR200. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. doi: 10.1194/jlr.R700005-JLR200. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
Yannai, Shmuel (2004). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. Boca Raton: Chapman & Hall/CRC..
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for Gibberellin A38 (MMDBc0053288)

MOL for #<Metabolite:0x00005634c28bd308>

3D MOL for #<Metabolite:0x00005634c28bd308>

3D SDF for #<Metabolite:0x00005634c28bd308>

3D-SDF for #<Metabolite:0x00005634c28bd308>

PDB for #<Metabolite:0x00005634c28bd308>

3D PDB for #<Metabolite:0x00005634c28bd308>

SMILES for #<Metabolite:0x00005634c28bd308>

INCHI for #<Metabolite:0x00005634c28bd308>

Structure for #<Metabolite:0x00005634c28bd308>

3D Structure for #<Metabolite:0x00005634c28bd308>