NP-MRD: Showing NP-Card for Citrobilin (NP0084701)

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Record Information

Version

2.0

Created at

2022-04-29 05:22:21 UTC

Updated at

2022-04-29 05:22:21 UTC

NP-MRD ID

NP0084701

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Citrobilin

Description

Citrobilin is found in Citrus nobilis . Based on a literature review very few articles have been published on acetyl 2-[(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(2-hydroxy-5-oxo-2,5-dihydrofuran-3-yl)-1,8,12,15,15-pentamethyl-5,18-dioxo-3,6,14-trioxapentacyclo[9.7.0.0²,⁴.0²,⁸.0¹²,¹⁶]Octadecan-13-yl]acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292207222D          

 43 48  0  0  1  0            999 V2000
   -1.2899    1.6873    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6386    2.1937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  4 43  2  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292207222D          

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    2.0872   -1.2846    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9660    1.8191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5266    0.2673    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8069   -0.5086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9948   -0.3634    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8496   -1.1755    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1827   -0.2182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0976    0.5577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3492   -0.8489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3398    4.0910    0.0000 O   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
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  2  0  0  0  0
 16 21  2  0  0  0  0
 14 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 13 26  1  6  0  0  0
 13 27  1  0  0  0  0
 23 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
 12 30  1  1  0  0  0
 12 31  1  0  0  0  0
 31 32  1  6  0  0  0
 31 33  1  0  0  0  0
 29 33  1  0  0  0  0
 33 34  2  0  0  0  0
  9 35  1  1  0  0  0
  9 36  1  0  0  0  0
 31 36  1  0  0  0  0
 36 37  1  6  0  0  0
 36 38  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  1  0  0  0
 38 40  1  0  0  0  0
 40 41  1  0  0  0  0
  7 41  1  0  0  0  0
 40 42  2  0  0  0  0
  4 43  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0084701

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12O[C@@]11[C@@](C)(CC[C@]3([H])[C@@]4(C)[C@H](CC(=O)OC(C)=O)OC(C)(C)[C@]4([H])CC(=O)[C@@]13C)[C@@]([H])(OC2=O)C1=CC(=O)OC1O

> <INCHI_IDENTIFIER>
InChI=1S/C28H34O11/c1-12(29)35-19(32)11-17-26(5)14-7-8-25(4)20(13-9-18(31)36-22(13)33)37-23(34)21-28(25,39-21)27(14,6)16(30)10-15(26)24(2,3)38-17/h9,14-15,17,20-22,33H,7-8,10-11H2,1-6H3/t14-,15+,17+,20+,21-,22?,25+,26-,27+,28-/m1/s1

> <INCHI_KEY>
JQAPXGJZJGADHN-SYIQFVMMSA-N

> <FORMULA>
C28H34O11

> <MOLECULAR_WEIGHT>
546.569

> <EXACT_MASS>
546.210111915

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
54.83897886263608

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
acetyl 2-[(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(2-hydroxy-5-oxo-2,5-dihydrofuran-3-yl)-1,8,12,15,15-pentamethyl-5,18-dioxo-3,6,14-trioxapentacyclo[9.7.0.0^{2,4}.0^{2,8}.0^{12,16}]octadecan-13-yl]acetate

> <ALOGPS_LOGP>
2.38

> <JCHEM_LOGP>
1.773157662

> <ALOGPS_LOGS>
-4.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.730228744952939

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.303217314884126

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9479392941827007

> <JCHEM_POLAR_SURFACE_AREA>
155.03

> <JCHEM_REFRACTIVITY>
128.82169999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.38e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
acetyl [(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(2-hydroxy-5-oxo-2H-furan-3-yl)-1,8,12,15,15-pentamethyl-5,18-dioxo-3,6,14-trioxapentacyclo[9.7.0.0^{2,4}.0^{2,8}.0^{12,16}]octadecan-13-yl]acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  O   UNK     0      -2.408   3.150   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.192   4.095   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.242   5.634   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.206   6.157   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.151   4.941   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.287   3.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.810   2.218   0.000  0.00  0.00           C+0
HETATM    8  H   UNK     0      -0.706   2.489   0.000  0.00  0.00           H+0
HETATM    9  C   UNK     0       2.326   1.947   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.319   3.125   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.835   2.854   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.358   1.405   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.874   1.134   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.090   2.079   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.040   3.618   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.348   4.431   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       9.298   5.971   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      10.606   6.784   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.556   8.323   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      11.964   6.057   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      10.706   3.705   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       9.365   1.215   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       8.937  -0.264   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.453  -0.535   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.826  -1.800   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.505   2.629   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.398  -0.314   0.000  0.00  0.00           C+0
HETATM   28  H   UNK     0       8.069  -1.700   0.000  0.00  0.00           H+0
HETATM   29  C   UNK     0       6.405  -1.492   0.000  0.00  0.00           C+0
HETATM   30  H   UNK     0       5.882  -0.043   0.000  0.00  0.00           H+0
HETATM   31  C   UNK     0       4.366   0.228   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.254  -1.308   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.889  -1.221   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       3.896  -2.398   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       1.803   3.396   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.850   0.499   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       3.373  -0.949   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       1.857  -0.678   0.000  0.00  0.00           C+0
HETATM   39  H   UNK     0       1.586  -2.194   0.000  0.00  0.00           H+0
HETATM   40  C   UNK     0       0.341  -0.407   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -0.182   1.041   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      -0.652  -1.585   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       0.634   7.637   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   43                                                  
CONECT    5    4    6                                                       
CONECT    6    5    2    7                                                  
CONECT    7    6    8    9   41                                             
CONECT    8    7                                                            
CONECT    9    7   10   35   36                                             
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   30   31                                             
CONECT   13   12   14   26   27                                             
CONECT   14   13   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   16                                                            
CONECT   22   14   23                                                       
CONECT   23   22   24   25   27                                             
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   13                                                            
CONECT   27   13   23   28   29                                             
CONECT   28   27                                                            
CONECT   29   27   33                                                       
CONECT   30   12                                                            
CONECT   31   12   32   33   36                                             
CONECT   32   31                                                            
CONECT   33   31   29   34                                                  
CONECT   34   33                                                            
CONECT   35    9                                                            
CONECT   36    9   31   37   38                                             
CONECT   37   36   38                                                       
CONECT   38   36   37   39   40                                             
CONECT   39   38                                                            
CONECT   40   38   41   42                                                  
CONECT   41   40    7                                                       
CONECT   42   40                                                            
CONECT   43    4                                                            
MASTER        0    0    0    0    0    0    0    0   43    0   96    0
END

View in JSmol

Synonyms

Value	Source
Acetyl 2-[(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(2-hydroxy-5-oxo-2,5-dihydrofuran-3-yl)-1,8,12,15,15-pentamethyl-5,18-dioxo-3,6,14-trioxapentacyclo[9.7.0.0,.0,.0,]octadecan-13-yl]acetic acid	Generator

Chemical Formula

C₂₈H₃₄O₁₁

Average Mass

546.5690 Da

Monoisotopic Mass

546.21011 Da

IUPAC Name

acetyl 2-[(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(2-hydroxy-5-oxo-2,5-dihydrofuran-3-yl)-1,8,12,15,15-pentamethyl-5,18-dioxo-3,6,14-trioxapentacyclo[9.7.0.0^{2,4}.0^{2,8}.0^{12,16}]octadecan-13-yl]acetate

Traditional Name

acetyl [(1R,2R,4S,7R,8S,11R,12R,13S,16R)-7-(2-hydroxy-5-oxo-2H-furan-3-yl)-1,8,12,15,15-pentamethyl-5,18-dioxo-3,6,14-trioxapentacyclo[9.7.0.0^{2,4}.0^{2,8}.0^{12,16}]octadecan-13-yl]acetate

CAS Registry Number

Not Available

SMILES

[H][C@]12O[C@@]11[C@@](C)(CC[C@]3([H])[C@@]4(C)[C@H](CC(=O)OC(C)=O)OC(C)(C)[C@]4([H])CC(=O)[C@@]13C)[C@@]([H])(OC2=O)C1=CC(=O)OC1O

InChI Identifier

InChI=1S/C28H34O11/c1-12(29)35-19(32)11-17-26(5)14-7-8-25(4)20(13-9-18(31)36-22(13)33)37-23(34)21-28(25,39-21)27(14,6)16(30)10-15(26)24(2,3)38-17/h9,14-15,17,20-22,33H,7-8,10-11H2,1-6H3/t14-,15+,17+,20+,21-,22?,25+,26-,27+,28-/m1/s1

InChI Key

JQAPXGJZJGADHN-SYIQFVMMSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Citrus nobilis	Plant	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	2.38	ALOGPS
logP	1.77	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	5.3	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	155.03 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	128.82 m³·mol⁻¹	ChemAxon
Polarizability	54.84 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

Not Available

KNApSAcK ID

C00054253

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

163183809

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Citrobilin (NP0084701)

MOL for NP0084701 (Citrobilin)

3D MOL for NP0084701 (Citrobilin)

3D SDF for NP0084701 (Citrobilin)

3D-SDF for NP0084701 (Citrobilin)

PDB for NP0084701 (Citrobilin)

3D PDB for NP0084701 (Citrobilin)

SMILES for NP0084701 (Citrobilin)

INCHI for NP0084701 (Citrobilin)

Structure for NP0084701 (Citrobilin)

3D Structure for NP0084701 (Citrobilin)