NP-MRD: Showing NP-Card for β-chlorogenin (NP0237434)

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Record Information

Version

1.0

Created at

2022-09-06 20:33:58 UTC

Updated at

2022-09-06 20:33:58 UTC

NP-MRD ID

NP0237434

Secondary Accession Numbers

None

Natural Product Identification

Common Name

β-chlorogenin

Description

B-Chlorogenin belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Thus, b-chlorogenin is considered to be a sterol lipid molecule. β-chlorogenin is found in Allium ampeloprasum and Allium rotundum. B-Chlorogenin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652307301920072D          

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M  END

     RDKit          3D

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M  END


  Mrv1652307301920072D          

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M  END
> <DATABASE_ID>
NP0237434

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4C[C@@H](O)[C@H]5C[C@@H](O)CC[C@]5(C)[C@H]4CC[C@]23C)O[C@]11CC[C@@H](C)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C27H44O4/c1-15-5-10-27(30-14-15)16(2)24-23(31-27)13-20-18-12-22(29)21-11-17(28)6-8-25(21,3)19(18)7-9-26(20,24)4/h15-24,28-29H,5-14H2,1-4H3/t15-,16+,17+,18-,19+,20+,21-,22-,23+,24+,25-,26+,27-/m1/s1

> <INCHI_KEY>
PZNPHSFXILSZTM-LHCNFSBLSA-N

> <FORMULA>
C27H44O4

> <MOLECULAR_WEIGHT>
432.645

> <EXACT_MASS>
432.323959897

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
52.002230498539504

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'R,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,16'S,18'S,19'R)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-16',19'-diol

> <JCHEM_LOGP>
4.024120138333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.42013912052768

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.751587014563686

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6909839223091847

> <JCHEM_POLAR_SURFACE_AREA>
58.92

> <JCHEM_REFRACTIVITY>
121.0084

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1'R,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,16'S,18'S,19'R)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-16',19'-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-19         0                                  
HETATM    1  C   UNK     0      -1.049  -9.055   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.373 -10.910   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.416 -10.021   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.664 -10.210   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.446  -9.996   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.491  -9.842   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.879 -10.110   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.954  -9.931   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.342 -10.200   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.966  -9.746   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.336  -7.179   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.415  -6.071   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.091  -6.454   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.014  -7.364   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.470  -8.805   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.605  -9.388   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      15.182  -8.466   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.724  -7.448   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.570  -8.734   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.187  -7.537   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.799  -7.269   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.953  -5.982   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.723  -7.161   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.973  -8.681   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      12.108  -8.645   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.495  -8.913   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.510  -8.306   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      16.720  -8.376   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      12.644  -4.606   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       2.534  -7.114   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       4.201  -6.929   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2   16                                                            
CONECT    3   25                                                            
CONECT    4   26                                                            
CONECT    5   10   15                                                       
CONECT    6    8   17                                                       
CONECT    7    9   19                                                       
CONECT    8    6   25                                                       
CONECT    9    7   26                                                       
CONECT   10    5   27                                                       
CONECT   11   17   21                                                       
CONECT   12   18   22                                                       
CONECT   13   20   23                                                       
CONECT   14   15   30                                                       
CONECT   15    1    5   14                                                  
CONECT   16    2   24   27                                                  
CONECT   17    6   11   28                                                  
CONECT   18   12   19   20                                                  
CONECT   19    7   18   25                                                  
CONECT   20   13   18   26                                                  
CONECT   21   11   22   25                                                  
CONECT   22   12   21   29                                                  
CONECT   23   13   24   31                                                  
CONECT   24   16   23   26                                                  
CONECT   25    3    8   19   21                                             
CONECT   26    4    9   20   24                                             
CONECT   27   10   16   30   31                                             
CONECT   28   17                                                            
CONECT   29   22                                                            
CONECT   30   14   27                                                       
CONECT   31   23   27                                                       
MASTER        0    0    0    0    0    0    0    0   31    0   72    0
END

View in JSmol

Synonyms

Value	Source
Ruizgenin	MeSH
Ruizgenin, (3beta,5alpha,6alpha,25R)-isomer	MeSH
Ruizgenin, (3beta,5alpha,6alpha,25S)-isomer	MeSH
5 beta-Spirostane-3 beta,6 alpha-diol	MeSH
Ruizgenin, (3beta,5alpha,6beta,25R)-isomer	MeSH

Chemical Formula

C₂₇H₄₄O₄

Average Mass

432.6450 Da

Monoisotopic Mass

432.32396 Da

IUPAC Name

(1'R,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,16'S,18'S,19'R)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-16',19'-diol

Traditional Name

(1'R,2R,2'S,4'S,5R,7'S,8'R,9'S,12'S,13'R,16'S,18'S,19'R)-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane]-16',19'-diol

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4C[C@@H](O)[C@H]5C[C@@H](O)CC[C@]5(C)[C@H]4CC[C@]23C)O[C@]11CC[C@@H](C)CO1

InChI Identifier

InChI=1S/C27H44O4/c1-15-5-10-27(30-14-15)16(2)24-23(31-27)13-20-18-12-22(29)21-11-17(28)6-8-25(21,3)19(18)7-9-26(20,24)4/h15-24,28-29H,5-14H2,1-4H3/t15-,16+,17+,18-,19+,20+,21-,22-,23+,24+,25-,26+,27-/m1/s1

InChI Key

PZNPHSFXILSZTM-LHCNFSBLSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Allium ampeloprasum	LOTUS Database	35616633
Allium rotundum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Spirostane skeleton
3-hydroxysteroid
6-hydroxysteroid
Hydroxysteroid
3-beta-hydroxysteroid
Steroid
Ketal
Oxane
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
Acetal
Organoheterocyclic compound
Oxacycle
Organic oxygen compound
Organooxygen compound
Alcohol
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Spirostanols and derivatives (LMST01080018 )

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	4.02	ChemAxon
pKa (Strongest Acidic)	14.75	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	58.92 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	121.01 m³·mol⁻¹	ChemAxon
Polarizability	52 Å³	ChemAxon
Number of Rings	6	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB021628

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

10717615

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for β-chlorogenin (NP0237434)

MOL for NP0237434 (β-chlorogenin)

3D MOL for NP0237434 (β-chlorogenin)

3D SDF for NP0237434 (β-chlorogenin)

3D-SDF for NP0237434 (β-chlorogenin)

PDB for NP0237434 (β-chlorogenin)

3D PDB for NP0237434 (β-chlorogenin)

SMILES for NP0237434 (β-chlorogenin)

INCHI for NP0237434 (β-chlorogenin)

Structure for NP0237434 (β-chlorogenin)

3D Structure for NP0237434 (β-chlorogenin)