NP-MRD: Showing NP-Card for Bilobalide A (NP0048582)

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Record Information

Version

2.0

Created at

2022-03-17 20:58:44 UTC

Updated at

2022-03-17 20:58:45 UTC

NP-MRD ID

NP0048582

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Bilobalide A

Description

Bilobalide A belongs to the class of organic compounds known as ginkgolides and bilobalides. These are diterpene lactones with a structure based either on the gingkolide or the bilobalide skeleton. The ginkgolide skeleton is a very rigid structure consisting of hexacyclic C20 trilactone. The cis-fused F/A/D/C ring junction forms an empty semi-ball hole, the D ring contains a cage form tetrahydrofuran ring which occupies the center of the empty hole, and the oxygen atoms of the D,C and F ring and 10-hydroxyl group consist of an analogous crown ether structure. Bilobalide A is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, bilobalide a has been detected, but not quantified in, fats and oils and ginkgo nuts. This could make bilobalide a a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 01101310022D          

 25 28  0  0  0  0            999 V2000
    0.3884   -1.1621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0609   -1.8540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4583   -2.4952    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2285   -2.1995    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0254   -2.4130    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4747   -1.7212    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1709   -0.0001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6860   -0.6675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1853   -1.3757    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7401   -0.0001    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9555   -0.2551    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9555   -1.0800    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7402   -1.3349    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2250   -0.6675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8847   -1.8972    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1390   -0.6617    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9555    0.5699    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0500   -0.6676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5652   -1.3349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2716   -1.9347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8872   -2.4356    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0685   -1.7212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0685   -2.1482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8550   -2.5181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2717   -3.0234    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  1  9  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
 12  6  1  0  0  0  0
  4  9  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
  9 12  1  0  0  0  0
 10 11  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
 11 12  1  0  0  0  0
  2 15  2  0  0  0  0
  8 16  2  0  0  0  0
 11 17  1  1  0  0  0
 14 18  2  0  0  0  0
 13 19  1  1  0  0  0
  6 20  1  6  0  0  0
  6 21  1  1  0  0  0
 20 22  1  0  0  0  0
 20 23  1  0  0  0  0
 20 24  1  0  0  0  0
  4 25  1  1  0  0  0
  9  8  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0048582

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C[C@@](O)(C(C)(C)C)[C@]34[C@H](O)C(=O)O[C@@]3([H])OC(=O)[C@]14CC(=O)O2

> <INCHI_IDENTIFIER>
InChI=1S/C15H18O8/c1-12(2,3)14(20)4-6-13(5-7(16)21-6)10(19)23-11-15(13,14)8(17)9(18)22-11/h6,8,11,17,20H,4-5H2,1-3H3/t6-,8+,11-,13-,14+,15+/m0/s1

> <INCHI_KEY>
MOLPUWBMSBJXER-NRSGSQFTSA-N

> <FORMULA>
C15H18O8

> <MOLECULAR_WEIGHT>
326.2986

> <EXACT_MASS>
326.100167552

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
29.39069790074211

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4R,7S,8S,9R,11S)-9-tert-butyl-7,9-dihydroxy-3,5,12-trioxatetracyclo[6.6.0.0¹,¹¹.0⁴,⁸]tetradecane-2,6,13-trione

> <ALOGPS_LOGP>
0.16

> <JCHEM_LOGP>
-0.5177614286666664

> <ALOGPS_LOGS>
-1.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.776747765035385

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.974249820349915

> <JCHEM_PKA_STRONGEST_BASIC>
-3.37953725747988

> <JCHEM_POLAR_SURFACE_AREA>
119.36000000000001

> <JCHEM_REFRACTIVITY>
69.98790000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4R,7S,8S,9R,11S)-9-tert-butyl-7,9-dihydroxy-3,5,12-trioxatetracyclo[6.6.0.0¹,¹¹.0⁴,⁸]tetradecane-2,6,13-trione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-JAN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-JAN-13         0                                  
HETATM    1  C   UNK     0       0.725  -2.169   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.114  -3.461   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.855  -4.658   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.293  -4.106   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.781  -4.504   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.619  -3.213   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.186  -0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.281  -1.246   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.213  -2.568   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.115  -0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       3.650  -0.476   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.650  -2.016   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.115  -2.492   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.020  -1.246   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.651  -3.541   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -0.259  -1.235   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       3.650   1.064   0.000  0.00  0.00           H+0
HETATM   18  O   UNK     0       7.560  -1.246   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       6.655  -2.492   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       6.107  -3.611   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.389  -4.546   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       7.595  -3.213   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.595  -4.010   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.196  -4.700   0.000  0.00  0.00           C+0
HETATM   25  H   UNK     0       2.374  -5.644   0.000  0.00  0.00           H+0
CONECT    1    2    9                                                       
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9   25                                             
CONECT    5    4    6                                                       
CONECT    6    5   12   20   21                                             
CONECT    7    8   11                                                       
CONECT    8    7   16    9                                                  
CONECT    9    1    4   12    8                                             
CONECT   10   11   14                                                       
CONECT   11    7   10   12   17                                             
CONECT   12    6    9   13   11                                             
CONECT   13   12   14   19                                                  
CONECT   14   13   10   18                                                  
CONECT   15    2                                                            
CONECT   16    8                                                            
CONECT   17   11                                                            
CONECT   18   14                                                            
CONECT   19   13                                                            
CONECT   20    6   22   23   24                                             
CONECT   21    6                                                            
CONECT   22   20                                                            
CONECT   23   20                                                            
CONECT   24   20                                                            
CONECT   25    4                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END

View in JSmol

Synonyms

Value	Source
Bilobalide	HMDB
(-)-Bilobalide	MeSH

Chemical Formula

C₁₅H₁₈O₈

Average Mass

326.2986 Da

Monoisotopic Mass

326.10017 Da

IUPAC Name

(1S,4R,7S,8S,9R,11S)-9-tert-butyl-7,9-dihydroxy-3,5,12-trioxatetracyclo[6.6.0.0¹,¹¹.0⁴,⁸]tetradecane-2,6,13-trione

Traditional Name

(1S,4R,7S,8S,9R,11S)-9-tert-butyl-7,9-dihydroxy-3,5,12-trioxatetracyclo[6.6.0.0¹,¹¹.0⁴,⁸]tetradecane-2,6,13-trione

CAS Registry Number

33570-04-6

SMILES

[H][C@]12C[C@@](O)(C(C)(C)C)[C@]34[C@H](O)C(=O)O[C@@]3([H])OC(=O)[C@]14CC(=O)O2

InChI Identifier

InChI=1S/C15H18O8/c1-12(2,3)14(20)4-6-13(5-7(16)21-6)10(19)23-11-15(13,14)8(17)9(18)22-11/h6,8,11,17,20H,4-5H2,1-3H3/t6-,8+,11-,13-,14+,15+/m0/s1

InChI Key

MOLPUWBMSBJXER-NRSGSQFTSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Ginkgo biloba	FooDB	KNAPSACK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ginkgolides and bilobalides. These are diterpene lactones with a structure based either on the gingkolide or the bilobalide skeleton. The ginkgolide skeleton is a very rigid structure consisting of hexacyclic C20 trilactone. The cis-fused F/A/D/C ring junction forms an empty semi-ball hole, the D ring contains a cage form tetrahydrofuran ring which occupies the center of the empty hole, and the oxygen atoms of the D,C and F ring and 10-hydroxyl group consist of an analogous crown ether structure.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Ginkgolides and bilobalides

Alternative Parents

Substituents

Bilobalide
Diterpenoid
Tricarboxylic acid or derivatives
Furofuran
Acylal
Gamma butyrolactone
Cyclic alcohol
Tetrahydrofuran
Tertiary alcohol
Carboxylic acid ester
Lactone
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
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	0.16	ALOGPS
logP	-0.52	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	11.97	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	119.36 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.99 m³·mol⁻¹	ChemAxon
Polarizability	29.39 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0036735

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

11875005

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Bilobalide A (NP0048582)

MOL for NP0048582 (Bilobalide A)

3D MOL for NP0048582 (Bilobalide A)

3D SDF for NP0048582 (Bilobalide A)

3D-SDF for NP0048582 (Bilobalide A)

PDB for NP0048582 (Bilobalide A)

3D PDB for NP0048582 (Bilobalide A)

SMILES for NP0048582 (Bilobalide A)

INCHI for NP0048582 (Bilobalide A)

Structure for NP0048582 (Bilobalide A)

3D Structure for NP0048582 (Bilobalide A)