NP-MRD: Showing NP-Card for 5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid (NP0240502)

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Record Information

Version

2.0

Created at

2022-09-07 00:20:46 UTC

Updated at

2022-09-07 00:20:46 UTC

NP-MRD ID

NP0240502

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid

Description

Gibberellin A3 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. 5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid is found in Carica papaya, Prunus avium and Prunus cerasus. Gibberellin A3 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305221920252D          

 25 29  0  0  0  0            999 V2000
    3.2160    2.6388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4579    3.7866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0063    0.5972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6850    1.7646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8660    0.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0641    1.2214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6513    2.7011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6109    1.7354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4221    2.2888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5591    1.3439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6474    2.5887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3430    2.6784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4028    2.3115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6385    3.6056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1845    2.8531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796    3.0732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9802    2.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2693    1.4315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2522    1.3681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4430    2.9217    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4159    4.1027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0116    4.3838    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0098    3.7087    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0888    1.1370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1392    2.0943    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  3  1  0  0  0  0
  6  4  2  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
 11  4  1  0  0  0  0
 13 12  1  0  0  0  0
 14 12  1  0  0  0  0
 16  2  1  0  0  0  0
 16 11  1  0  0  0  0
 16 13  1  0  0  0  0
 16 15  1  0  0  0  0
 17  7  1  0  0  0  0
 17  8  1  0  0  0  0
 17 10  1  0  0  0  0
 17 12  1  0  0  0  0
 18  5  1  0  0  0  0
 18  8  1  0  0  0  0
 18  9  1  0  0  0  0
 19  6  1  0  0  0  0
 19 10  1  0  0  0  0
 19 13  1  0  0  0  0
 20 11  1  0  0  0  0
 21 14  2  0  0  0  0
 22 14  1  0  0  0  0
 23 15  2  0  0  0  0
 24 18  1  0  0  0  0
 25 15  1  0  0  0  0
 25 19  1  0  0  0  0
M  END


  Mrv1652305221920252D          

 25 29  0  0  0  0            999 V2000
    3.2160    2.6388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4579    3.7866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0063    0.5972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6850    1.7646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8660    0.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0641    1.2214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6513    2.7011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6109    1.7354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4221    2.2888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5591    1.3439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6474    2.5887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3430    2.6784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4028    2.3115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6385    3.6056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1845    2.8531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796    3.0732    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9802    2.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2693    1.4315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2522    1.3681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4430    2.9217    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4159    4.1027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0116    4.3838    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0098    3.7087    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0888    1.1370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1392    2.0943    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  3  1  0  0  0  0
  6  4  2  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
 11  4  1  0  0  0  0
 13 12  1  0  0  0  0
 14 12  1  0  0  0  0
 16  2  1  0  0  0  0
 16 11  1  0  0  0  0
 16 13  1  0  0  0  0
 16 15  1  0  0  0  0
 17  7  1  0  0  0  0
 17  8  1  0  0  0  0
 17 10  1  0  0  0  0
 17 12  1  0  0  0  0
 18  5  1  0  0  0  0
 18  8  1  0  0  0  0
 18  9  1  0  0  0  0
 19  6  1  0  0  0  0
 19 10  1  0  0  0  0
 19 13  1  0  0  0  0
 20 11  1  0  0  0  0
 21 14  2  0  0  0  0
 22 14  1  0  0  0  0
 23 15  2  0  0  0  0
 24 18  1  0  0  0  0
 25 15  1  0  0  0  0
 25 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0240502

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC12C3C(C(O)=O)C45CC(=C)C(O)(C4)CCC5C3(OC1=O)C=CC2O

> <INCHI_IDENTIFIER>
InChI=1S/C19H22O6/c1-9-7-17-8-18(9,24)5-3-10(17)19-6-4-11(20)16(2,15(23)25-19)13(19)12(17)14(21)22/h4,6,10-13,20,24H,1,3,5,7-8H2,2H3,(H,21,22)

> <INCHI_KEY>
IXORZMNAPKEEDV-UHFFFAOYSA-N

> <FORMULA>
C19H22O6

> <MOLECULAR_WEIGHT>
346.3744

> <EXACT_MASS>
346.141638436

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
34.862666573449815

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadec-13-ene-9-carboxylic acid

> <ALOGPS_LOGP>
0.66

> <JCHEM_LOGP>
0.3509132836666674

> <ALOGPS_LOGS>
-2.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.06512209173422

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.163467082979854

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9049344149234976

> <JCHEM_POLAR_SURFACE_AREA>
104.06

> <JCHEM_REFRACTIVITY>
86.41549999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.95e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadec-13-ene-9-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       6.003   4.926   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.721   7.068   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.878   1.115   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.145   3.294   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.483   1.232   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.986   2.280   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.082   5.042   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.007   3.239   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.521   4.272   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.044   2.509   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.075   4.832   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.640   5.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.752   4.315   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.192   6.730   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.344   5.326   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.829   5.737   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.830   3.950   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.236   2.672   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.471   2.554   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -4.560   5.454   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.643   7.658   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -0.022   8.183   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -0.018   6.923   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       5.766   2.122   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.260   3.909   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2   16                                                            
CONECT    3    5   10                                                       
CONECT    4    6   11                                                       
CONECT    5    3   18                                                       
CONECT    6    4   19                                                       
CONECT    7    9   17                                                       
CONECT    8   17   18                                                       
CONECT    9    1    7   18                                                  
CONECT   10    3   17   19                                                  
CONECT   11    4   16   20                                                  
CONECT   12   13   14   17                                                  
CONECT   13   12   16   19                                                  
CONECT   14   12   21   22                                                  
CONECT   15   16   23   25                                                  
CONECT   16    2   11   13   15                                             
CONECT   17    7    8   10   12                                             
CONECT   18    5    8    9   24                                             
CONECT   19    6   10   13   25                                             
CONECT   20   11                                                            
CONECT   21   14                                                            
CONECT   22   14                                                            
CONECT   23   15                                                            
CONECT   24   18                                                            
CONECT   25   15   19                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₂₂O₆

Average Mass

346.3744 Da

Monoisotopic Mass

346.14164 Da

IUPAC Name

5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadec-13-ene-9-carboxylic acid

Traditional Name

5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadec-13-ene-9-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC12C3C(C(O)=O)C45CC(=C)C(O)(C4)CCC5C3(OC1=O)C=CC2O

InChI Identifier

InChI=1S/C19H22O6/c1-9-7-17-8-18(9,24)5-3-10(17)19-6-4-11(20)16(2,15(23)25-19)13(19)12(17)14(21)22/h4,6,10-13,20,24H,1,3,5,7-8H2,2H3,(H,21,22)

InChI Key

IXORZMNAPKEEDV-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Carica papaya	LOTUS Database	35616633
Prunus avium	LOTUS Database	35616633
Prunus cerasus	LOTUS Database	35616633

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
Dicarboxylic acid or derivatives
Gamma butyrolactone
Cyclic alcohol
Tetrahydrofuran
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

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	0.66	ALOGPS
logP	0.35	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	4.16	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	86.42 m³·mol⁻¹	ChemAxon
Polarizability	34.86 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB013644

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Gibberellic acid

METLIN ID

Not Available

PubChem Compound

522636

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid (NP0240502)

MOL for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)

3D MOL for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)

3D SDF for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)

3D-SDF for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)

PDB for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)

3D PDB for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)

SMILES for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)

INCHI for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)

Structure for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)

3D Structure for NP0240502 (5,12-dihydroxy-11-methyl-6-methylidene-16-oxo-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadec-13-ene-9-carboxylic acid)