MiMeDB: Showing metabocard for Gibberellin A53 (MMDBc0053293)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-05-16 21:19:54 UTC

Update Date

2024-04-30 20:48:02 UTC

Metabolite ID

MMDBc0053293

Metabolite Identification

Common Name

Gibberellin A53

Description

Gibberellin A53 (GA53) belongs to the class of organic compounds known as C20-gibberellin 6-carboxylic acids. These are C20-gibberellins with a carboxyl group at the 6-position. Thus, gibberellin A53 is considered to be an isoprenoid lipid molecule. Gibberellin A53 is found in apple. Gibberellin A53 is isolated from Vicia faba and spinach (Spinacia oleracea).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306222023522D          

 25 28  0  0  0  0            999 V2000
    0.1513    0.5312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5510    2.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9866   -0.4932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1062    1.4539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4900    2.3744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3662    1.8187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1602    0.6306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6281    2.3911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6531    0.3392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7827    1.2970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9237    0.8210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8661    1.5895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9579    0.2407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7343    0.5370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7734   -0.5634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0449   -0.4237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6803    1.3602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4743    0.1722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3754    0.8595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1552    1.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9847   -0.8056    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3775   -1.1252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8462   -0.2275    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8141   -1.2157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4025    1.9982    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  4  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
 11  1  2  0  0  0  0
 11  9  1  0  0  0  0
 12  5  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  6  1  0  0  0  0
 17 12  1  0  0  0  0
 17 14  1  0  0  0  0
 18  3  1  0  0  0  0
 18  7  1  0  0  0  0
 18 14  1  0  0  0  0
 18 16  1  0  0  0  0
 19  9  1  0  0  0  0
 19 10  1  0  0  0  0
 19 12  1  0  0  0  0
 19 13  1  0  0  0  0
 20  8  1  0  0  0  0
 20 10  1  0  0  0  0
 20 11  1  0  0  0  0
 21 15  2  0  0  0  0
 22 15  1  0  0  0  0
 23 16  2  0  0  0  0
 24 16  1  0  0  0  0
 25 20  1  0  0  0  0
M  END


  Mrv1652306222023522D          

 25 28  0  0  0  0            999 V2000
    0.1513    0.5312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5510    2.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9866   -0.4932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1062    1.4539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4900    2.3744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3662    1.8187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1602    0.6306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6281    2.3911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6531    0.3392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7827    1.2970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9237    0.8210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8661    1.5895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9579    0.2407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7343    0.5370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7734   -0.5634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0449   -0.4237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6803    1.3602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4743    0.1722    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3754    0.8595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1552    1.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9847   -0.8056    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3775   -1.1252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8462   -0.2275    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8141   -1.2157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4025    1.9982    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  4  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
 11  1  2  0  0  0  0
 11  9  1  0  0  0  0
 12  5  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  6  1  0  0  0  0
 17 12  1  0  0  0  0
 17 14  1  0  0  0  0
 18  3  1  0  0  0  0
 18  7  1  0  0  0  0
 18 14  1  0  0  0  0
 18 16  1  0  0  0  0
 19  9  1  0  0  0  0
 19 10  1  0  0  0  0
 19 12  1  0  0  0  0
 19 13  1  0  0  0  0
 20  8  1  0  0  0  0
 20 10  1  0  0  0  0
 20 11  1  0  0  0  0
 21 15  2  0  0  0  0
 22 15  1  0  0  0  0
 23 16  2  0  0  0  0
 24 16  1  0  0  0  0
 25 20  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0053293

> <DATABASE_NAME>
MIME

> <SMILES>
CC12CCCC(C)(C1C(C(O)=O)C13CC(=C)C(O)(C1)CCC23)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O5/c1-11-9-19-10-20(11,25)8-5-12(19)17(2)6-4-7-18(3,16(23)24)14(17)13(19)15(21)22/h12-14,25H,1,4-10H2,2-3H3,(H,21,22)(H,23,24)

> <INCHI_KEY>
CZEMYYICWZPENF-UHFFFAOYSA-N

> <FORMULA>
C20H28O5

> <MOLECULAR_WEIGHT>
348.4333

> <EXACT_MASS>
348.193674006

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
37.21664720268062

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
12-hydroxy-4,8-dimethyl-13-methylidenetetracyclo[10.2.1.0^{1,9}.0^{3,8}]pentadecane-2,4-dicarboxylic acid

> <ALOGPS_LOGP>
1.77

> <JCHEM_LOGP>
2.4267068476666673

> <ALOGPS_LOGS>
-2.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.784908538755822

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.1110265656957665

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9048835073802236

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
90.53059999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.39e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
12-hydroxy-4,8-dimethyl-13-methylidenetetracyclo[10.2.1.0^{1,9}.0^{3,8}]pentadecane-2,4-dicarboxylic 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       0.282   0.992   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.629   4.060   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.442  -0.921   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.532   2.714   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.648   4.432   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.150   3.395   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.632   1.177   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.039   4.463   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.086   0.633   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.328   2.421   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.724   1.533   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.350   2.967   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.521   0.449   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.971   1.002   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.177  -1.052   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.417  -0.791   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.870   2.539   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.352   0.321   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.434   1.604   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.156   3.100   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       3.705  -1.504   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       6.305  -2.100   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      10.913  -0.425   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       8.986  -2.269   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.751   3.730   0.000  0.00  0.00           O+0
CONECT    1   11                                                            
CONECT    2   17                                                            
CONECT    3   18                                                            
CONECT    4    6    7                                                       
CONECT    5    8   12                                                       
CONECT    6    4   17                                                       
CONECT    7    4   18                                                       
CONECT    8    5   20                                                       
CONECT    9   11   19                                                       
CONECT   10   19   20                                                       
CONECT   11    1    9   20                                                  
CONECT   12    5   17   19                                                  
CONECT   13   14   15   19                                                  
CONECT   14   13   17   18                                                  
CONECT   15   13   21   22                                                  
CONECT   16   18   23   24                                                  
CONECT   17    2    6   12   14                                             
CONECT   18    3    7   14   16                                             
CONECT   19    9   10   12   13                                             
CONECT   20    8   10   11   25                                             
CONECT   21   15                                                            
CONECT   22   15                                                            
CONECT   23   16                                                            
CONECT   24   16                                                            
CONECT   25   20                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

Synonyms

Value	Source
GA53	HMDB
Gibberellin 53	HMDB

Molecular Formula

C₂₀H₂₈O₅

Average Mass

348.4333

Monoisotopic Mass

348.193674006

IUPAC Name

12-hydroxy-4,8-dimethyl-13-methylidenetetracyclo[10.2.1.0^{1,9}.0^{3,8}]pentadecane-2,4-dicarboxylic acid

Traditional Name

12-hydroxy-4,8-dimethyl-13-methylidenetetracyclo[10.2.1.0^{1,9}.0^{3,8}]pentadecane-2,4-dicarboxylic acid

CAS Registry Number

Not Available

SMILES

CC12CCCC(C)(C1C(C(O)=O)C13CC(=C)C(O)(C1)CCC23)C(O)=O

InChI Identifier

InChI=1S/C20H28O5/c1-11-9-19-10-20(11,25)8-5-12(19)17(2)6-4-7-18(3,16(23)24)14(17)13(19)15(21)22/h12-14,25H,1,4-10H2,2-3H3,(H,21,22)(H,23,24)

InChI Key

CZEMYYICWZPENF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as c20-gibberellin 6-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 6-carboxylic acids

Alternative Parents

Substituents

Gibberellane-6-carboxylic acid
Dicarboxylic acid or derivatives
Tertiary alcohol
Cyclic alcohol
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.54 g/L	ALOGPS
logP	1.77	ALOGPS
logP	2.43	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	4.11	ChemAxon
pKa (Strongest Basic)	-0.9	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	90.53 m³·mol⁻¹	ChemAxon
Polarizability	37.22 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	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fz9-0219000000-a3a32b5b1958eaf43854	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-002b-4021790000-be27b9ca49c8b719a502	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-0029000000-c96aeeb9e91b4028c07a	2015-05-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01q0-0179000000-9a1ffa403e54886ddd84	2015-05-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052r-2692000000-2028bd409181d9869708	2015-05-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f6t-0029000000-4b508b38191430bae1f1	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0zg1-0079000000-3cb7e1465f14fd5a603f	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4r-1094000000-ba4002cfdf21089dc56e	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

HMDB0036895

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5253706

PDB ID

Not Available

ChEBI ID

27433

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 A53 (MMDBc0053293)

MOL for #<Metabolite:0x00007fed17633100>

3D MOL for #<Metabolite:0x00007fed17633100>

3D SDF for #<Metabolite:0x00007fed17633100>

3D-SDF for #<Metabolite:0x00007fed17633100>

PDB for #<Metabolite:0x00007fed17633100>

3D PDB for #<Metabolite:0x00007fed17633100>

SMILES for #<Metabolite:0x00007fed17633100>

INCHI for #<Metabolite:0x00007fed17633100>

Structure for #<Metabolite:0x00007fed17633100>

3D Structure for #<Metabolite:0x00007fed17633100>