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Showing NP-Card for Columbaridione (NP0049627)

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Record Information
Version2.0
Created at2022-03-17 21:15:32 UTC
Updated at2022-03-17 21:15:32 UTC
NP-MRD IDNP0049627
Secondary Accession NumbersNone
Natural Product Identification
Common NameColumbaridione
DescriptionColumbaridione belongs to the class of organic compounds known as diterpene lactones. These are diterpenoids containing a lactone moiety. Columbaridione is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, columbaridione has been detected, but not quantified in, a few different foods, such as beverages, common sages, and herbs and spices. Columbaridione is found in Salvia columbariae . This could make columbaridione a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0049627 (Columbaridione)


  Mrv0541 05061311482D          

 25 28  0  0  0  0            999 V2000
    7.0163    1.0217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9803   -0.4068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2497   -0.5444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1545   -1.0977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0679    1.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6375    0.4428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8926    1.1258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2509   -1.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.0756   -1.0482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8566   -0.3027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7612    0.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5060   -0.3443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1117    0.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3308   -0.3651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3668    1.0633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5421    1.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4227   -0.2799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0318   -0.2819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2870    0.4011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7251   -1.0898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7972    1.7672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1478    1.8088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8375   -0.8548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9418   -0.4686    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
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 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 13  2  0  0  0  0
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 19  3  1  0  0  0  0
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 18 25  1  0  0  0  0
 10 25  1  0  0  0  0
M  END
Download

3D MOL for NP0049627 (Columbaridione)

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3D SDF for NP0049627 (Columbaridione)

  Mrv0541 05061311482D          

 25 28  0  0  0  0            999 V2000
    7.0163    1.0217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9803   -0.4068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2497   -0.5444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1545   -1.0977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0679    1.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6375    0.4428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8926    1.1258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2509   -1.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5859    0.3179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0756   -1.0482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8566   -0.3027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7612    0.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5060   -0.3443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1117    0.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3308   -0.3651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3668    1.0633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5421    1.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4227   -0.2799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0318   -0.2819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2870    0.4011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7251   -1.0898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7972    1.7672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1478    1.8088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8375   -0.8548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9418   -0.4686    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 13  2  0  0  0  0
 15 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 12  2  0  0  0  0
 17 14  1  0  0  0  0
 17 16  1  0  0  0  0
 19  3  1  0  0  0  0
 19  4  1  0  0  0  0
 19  6  1  0  0  0  0
 19 11  1  0  0  0  0
 20  7  1  0  0  0  0
 20 11  1  0  0  0  0
 20 14  1  0  0  0  0
 20 18  1  0  0  0  0
 21 15  2  0  0  0  0
 22 16  1  0  0  0  0
 23 17  2  0  0  0  0
 24 18  2  0  0  0  0
 18 25  1  0  0  0  0
 10 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049627

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C1=C(O)C(=O)C2=C(C3CC4C(C)(C)CCCC24C(=O)O3)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H24O5/c1-9(2)12-15(21)13-10-8-11-19(3,4)6-5-7-20(11,18(24)25-10)14(13)17(23)16(12)22/h9-11,22H,5-8H2,1-4H3

> <INCHI_KEY>
ZGIOOTXNBWWRKD-UHFFFAOYSA-N

> <FORMULA>
C20H24O5

> <MOLECULAR_WEIGHT>
344.4016

> <EXACT_MASS>
344.162373878

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
36.46052079480931

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-hydroxy-11,11-dimethyl-5-(propan-2-yl)-16-oxatetracyclo[6.6.2.0¹,¹⁰.0²,⁷]hexadeca-2(7),4-diene-3,6,15-trione

> <ALOGPS_LOGP>
2.58

> <JCHEM_LOGP>
3.361022399666666

> <ALOGPS_LOGS>
-3.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.313823755185718

> <JCHEM_PKA_STRONGEST_BASIC>
-4.091793489481767

> <JCHEM_POLAR_SURFACE_AREA>
80.67

> <JCHEM_REFRACTIVITY>
92.35319999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.36e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-hydroxy-5-isopropyl-11,11-dimethyl-16-oxatetracyclo[6.6.2.0¹,¹⁰.0²,⁷]hexadeca-2(7),4-diene-3,6,15-trione

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0049627 (Columbaridione)
Download
PDB for NP0049627 (Columbaridione)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      13.097   1.907   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.030  -0.759   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.333  -1.016   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.022  -2.049   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.860   2.140   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.057   0.827   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.400   2.101   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.068  -1.918   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.294   0.593   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.608  -1.957   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.332  -0.565   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.754   0.632   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.411  -0.643   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.675   0.710   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.951  -0.682   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.018   1.985   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.479   2.024   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.389  -0.522   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.793  -0.526   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.136   0.749   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      10.687  -2.034   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      10.821   3.299   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       7.743   3.376   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       5.297  -1.596   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       7.358  -0.875   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3   19                                                            
CONECT    4   19                                                            
CONECT    5    6    7                                                       
CONECT    6    5   19                                                       
CONECT    7    5   20                                                       
CONECT    8   10   11                                                       
CONECT    9    1    2   12                                                  
CONECT   10    8   13   25                                                  
CONECT   11    8   19   20                                                  
CONECT   12    9   15   16                                                  
CONECT   13   10   14   15                                                  
CONECT   14   13   17   20                                                  
CONECT   15   12   13   21                                                  
CONECT   16   12   17   22                                                  
CONECT   17   14   16   23                                                  
CONECT   18   20   24   25                                                  
CONECT   19    3    4    6   11                                             
CONECT   20    7   11   14   18                                             
CONECT   21   15                                                            
CONECT   22   16                                                            
CONECT   23   17                                                            
CONECT   24   18                                                            
CONECT   25   18   10                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

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3D PDB for NP0049627 (Columbaridione)
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SMILES for NP0049627 (Columbaridione)
CC(C)C1=C(O)C(=O)C2=C(C3CC4C(C)(C)CCCC24C(=O)O3)C1=O
Download
INCHI for NP0049627 (Columbaridione)
InChI=1S/C20H24O5/c1-9(2)12-15(21)13-10-8-11-19(3,4)6-5-7-20(11,18(24)25-10)14(13)17(23)16(12)22/h9-11,22H,5-8H2,1-4H3
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View in JSmol
SynonymsNot Available
Chemical FormulaC20H24O5
Average Mass344.4016 Da
Monoisotopic Mass344.16237 Da
IUPAC Name4-hydroxy-11,11-dimethyl-5-(propan-2-yl)-16-oxatetracyclo[6.6.2.0¹,¹⁰.0²,⁷]hexadeca-2(7),4-diene-3,6,15-trione
Traditional Name4-hydroxy-5-isopropyl-11,11-dimethyl-16-oxatetracyclo[6.6.2.0¹,¹⁰.0²,⁷]hexadeca-2(7),4-diene-3,6,15-trione
CAS Registry Number156162-09-3
SMILES
CC(C)C1=C(O)C(=O)C2=C(C3CC4C(C)(C)CCCC24C(=O)O3)C1=O
InChI Identifier
InChI=1S/C20H24O5/c1-9(2)12-15(21)13-10-8-11-19(3,4)6-5-7-20(11,18(24)25-10)14(13)17(23)16(12)22/h9-11,22H,5-8H2,1-4H3
InChI KeyZGIOOTXNBWWRKD-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Salvia columbariaePlant
Salvia officinalisFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diterpene lactones. These are diterpenoids containing a lactone moiety.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene lactones
Direct ParentDiterpene lactones
Alternative ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.58ALOGPS
logP3.36ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)8.31ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area80.67 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity92.35 m³·mol⁻¹ChemAxon
Polarizability36.46 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0040388  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB020120  
KNApSAcK IDC00036922  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References