MiMeDB: Showing metabocard for gibberellin A4 (MMDBc0053289)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-05-16 21:19:47 UTC

Update Date

2022-09-01 02:19:49 UTC

Metabolite ID

MMDBc0053289

Metabolite Identification

Common Name

gibberellin A4

Description

gibberellin A4 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 A4 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303082008112D          

 24 28  0  0  1  0            999 V2000
    7.2513   -0.3371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6961   -1.6489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8679    1.3845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0475    1.4189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4977    0.3138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0989    0.8300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7314   -0.5961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6133    0.3157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4465   -0.1556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2467    0.6485    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6474    0.6862    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5266   -0.4780    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4309   -0.5974    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7244   -0.2227    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6877   -1.4817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9294   -0.7448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1638   -0.9491    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0492   -0.0660    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8772    0.6820    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7507   -0.7630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4367   -1.8849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0674   -2.1768    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0430   -1.5636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2469   -0.0188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  9  1  2  0  0  0  0
  9  7  1  0  0  0  0
 10  3  1  0  0  0  0
 10  8  1  6  0  0  0
 10  9  1  0  0  0  0
 11  4  1  6  0  0  0
 12  5  1  0  0  0  0
 14 13  1  6  0  0  0
 13 15  1  1  0  0  0
 17  2  1  6  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  7  1  0  0  0  0
 18  8  1  6  0  0  0
 18 11  1  0  0  0  0
 18 13  1  0  0  0  0
 19  6  1  0  0  0  0
 19 11  1  0  0  0  0
 19 14  1  0  0  0  0
 12 20  1  1  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
 19 24  1  6  0  0  0
M  CHG  1  22  -1
M  END
> <DATABASE_ID>
MMDBc0053289

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@@]12[C@H]3[C@H](C([O-])=O)[C@@]45C[C@@H](CC[C@H]4[C@@]3(CC[C@@H]1O)OC2=O)C(=C)C5

> <INCHI_IDENTIFIER>
InChI=1S/C19H24O5/c1-9-7-18-8-10(9)3-4-11(18)19-6-5-12(20)17(2,16(23)24-19)14(19)13(18)15(21)22/h10-14,20H,1,3-8H2,2H3,(H,21,22)/p-1/t10-,11-,12+,13-,14-,17+,18+,19-/m1/s1

> <INCHI_KEY>
RSQSQJNRHICNNH-UKJRIFTCSA-M

> <FORMULA>
C19H23O5

> <MOLECULAR_WEIGHT>
331.389

> <EXACT_MASS>
331.155097421

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
37.39557499526541

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,5R,8R,9S,10R,11R,12S)-12-hydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadecane-9-carboxylate

> <ALOGPS_LOGP>
1.84

> <JCHEM_LOGP>
1.5603197853333337

> <ALOGPS_LOGS>
-2.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.445587590324653

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.288334110545963

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0419589762960797

> <JCHEM_POLAR_SURFACE_AREA>
86.66000000000001

> <JCHEM_REFRACTIVITY>
94.91589999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.30e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5R,8R,9S,10R,11R,12S)-12-hydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadecane-9-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0      13.536  -0.629   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.033  -3.078   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.953   2.584   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.422   2.649   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.662   0.586   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.785   1.549   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.699  -1.113   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.478   0.589   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.033  -0.290   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.661   1.211   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.675   1.281   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.716  -0.892   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.271  -1.115   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.952  -0.416   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.750  -2.766   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.335  -1.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.906  -1.772   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.425  -0.123   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.237   1.273   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       3.268  -1.424   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      10.149  -3.518   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       7.592  -4.063   0.000  0.00  0.00           O-1
HETATM   23  O   UNK     0       7.547  -2.919   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       7.928  -0.035   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2   17                                                            
CONECT    3    4   10                                                       
CONECT    4    3   11                                                       
CONECT    5    6   12                                                       
CONECT    6    5   19                                                       
CONECT    7    9   18                                                       
CONECT    8   10   18                                                       
CONECT    9    1    7   10                                                  
CONECT   10    3    8    9                                                  
CONECT   11    4   18   19                                                  
CONECT   12    5   17   20                                                  
CONECT   13   14   15   18                                                  
CONECT   14   13   17   19                                                  
CONECT   15   13   21   22                                                  
CONECT   16   17   23   24                                                  
CONECT   17    2   12   14   16                                             
CONECT   18    7    8   11   13                                             
CONECT   19    6   11   14   24                                             
CONECT   20   12                                                            
CONECT   21   15                                                            
CONECT   22   15                                                            
CONECT   23   16                                                            
CONECT   24   16   19                                                       
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

Synonyms

Value	Source
(1R,2R,5R,8R,9S,10R,11R,12S)-12-Hydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid	Generator

Molecular Formula

C₁₉H₂₃O₅

Average Mass

331.389

Monoisotopic Mass

331.155097421

IUPAC Name

(1R,2R,5R,8R,9S,10R,11R,12S)-12-hydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadecane-9-carboxylate

Traditional Name

(1R,2R,5R,8R,9S,10R,11R,12S)-12-hydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadecane-9-carboxylate

CAS Registry Number

Not Available

SMILES

C[C@@]12[C@H]3[C@H](C([O-])=O)[C@@]45C[C@@H](CC[C@H]4[C@@]3(CC[C@@H]1O)OC2=O)C(=C)C5

InChI Identifier

InChI=1S/C19H24O5/c1-9-7-18-8-10(9)3-4-11(18)19-6-5-12(20)17(2,16(23)24-19)14(19)13(18)15(21)22/h10-14,20H,1,3-8H2,2H3,(H,21,22)/p-1/t10-,11-,12+,13-,14-,17+,18+,19-/m1/s1

InChI Key

RSQSQJNRHICNNH-UKJRIFTCSA-M

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
Gamma butyrolactone
Dicarboxylic acid or derivatives
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Organic anion
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	0.53 g/L	ALOGPS
logP	1.84	ALOGPS
logP	1.56	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	4.29	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	86.66 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	94.92 m³·mol⁻¹	ChemAxon
Polarizability	37.4 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	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	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
Bacteria	Firmicutes	2
Eukaryota/Fungi	Ascomycota	8	Human feces
Bacteria	Proteobacteria	1

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

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

25245706

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for gibberellin A4 (MMDBc0053289)

MOL for #<Metabolite:0x00007fecc54960b0>

3D MOL for #<Metabolite:0x00007fecc54960b0>

3D SDF for #<Metabolite:0x00007fecc54960b0>

3D-SDF for #<Metabolite:0x00007fecc54960b0>

PDB for #<Metabolite:0x00007fecc54960b0>

3D PDB for #<Metabolite:0x00007fecc54960b0>

SMILES for #<Metabolite:0x00007fecc54960b0>

INCHI for #<Metabolite:0x00007fecc54960b0>

Structure for #<Metabolite:0x00007fecc54960b0>

3D Structure for #<Metabolite:0x00007fecc54960b0>