NP-MRD: Showing NP-Card for Pendulin (NP0053479)

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Record Information

Version

2.0

Created at

2022-04-28 00:07:28 UTC

Updated at

2022-04-28 00:07:28 UTC

NP-MRD ID

NP0053479

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pendulin

Description

Pendulin belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone. Thus, pendulin is considered to be a flavonoid. Pendulin is found in Aconitum japonicum, Brickellia pendula, Chrysosplenium flagelliferum, Chrysosplenium tetrandrum, Cocculus pendulus, Isopyrum thalictroides and Leptopus chinensis. Pendulin was first documented in 2007 (PMID: 19384428). Based on a literature review a small amount of articles have been published on Pendulin (PMID: 33921412) (PMID: 27295875) (PMID: 31965871) (PMID: 31091233).

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652304282202072D          

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M  END

     RDKit          3D

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M  END

  Mrv1652304282202072D          

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M  END
> <DATABASE_ID>
NP0053479

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(OC)C(O)=C2C(=O)C(OC)=C(OC2=C1)C1=CC=C(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C24H26O12/c1-31-13-8-12-15(17(27)22(13)32-2)18(28)23(33-3)21(35-12)10-4-6-11(7-5-10)34-24-20(30)19(29)16(26)14(9-25)36-24/h4-8,14,16,19-20,24-27,29-30H,9H2,1-3H3/t14-,16-,19+,20-,24-/m1/s1

> <INCHI_KEY>
ASCBRLGHWVZBMG-NPVWYNPDSA-N

> <FORMULA>
C24H26O12

> <MOLECULAR_WEIGHT>
506.46

> <EXACT_MASS>
506.142426277

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
50.31113481391316

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-hydroxy-3,6,7-trimethoxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-4H-chromen-4-one

> <ALOGPS_LOGP>
0.90

> <JCHEM_LOGP>
0.2928468719999998

> <ALOGPS_LOGS>
-3.12

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.200155139016278

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.734596575293835

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092343686506

> <JCHEM_POLAR_SURFACE_AREA>
173.6

> <JCHEM_REFRACTIVITY>
122.7224

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.89e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy-3,6,7-trimethoxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      10.669  -0.000   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      13.337  -3.080   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      14.670  -0.770   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      14.670   2.310   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      12.003   3.850   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    6   35                                                  
CONECT    2    1    3   33                                                  
CONECT    3    2    4   32                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10   12                                                  
CONECT   10    9    4   11                                                  
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12                                                            
CONECT   14    8   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18   14                                                       
CONECT   20   17   21                                                       
CONECT   21   20   22   26                                                  
CONECT   22   21   23   31                                                  
CONECT   23   22   24   30                                                  
CONECT   24   23   25   29                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25   21                                                       
CONECT   27   25   28                                                       
CONECT   28   27                                                            
CONECT   29   24                                                            
CONECT   30   23                                                            
CONECT   31   22                                                            
CONECT   32    3                                                            
CONECT   33    2   34                                                       
CONECT   34   33                                                            
CONECT   35    1   36                                                       
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₆O₁₂

Average Mass

506.4600 Da

Monoisotopic Mass

506.14243 Da

IUPAC Name

5-hydroxy-3,6,7-trimethoxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-4H-chromen-4-one

Traditional Name

5-hydroxy-3,6,7-trimethoxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one

CAS Registry Number

Not Available

SMILES

COC1=C(OC)C(O)=C2C(=O)C(OC)=C(OC2=C1)C1=CC=C(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C=C1

InChI Identifier

InChI=1S/C24H26O12/c1-31-13-8-12-15(17(27)22(13)32-2)18(28)23(33-3)21(35-12)10-4-6-11(7-5-10)34-24-20(30)19(29)16(26)14(9-25)36-24/h4-8,14,16,19-20,24-27,29-30H,9H2,1-3H3/t14-,16-,19+,20-,24-/m1/s1

InChI Key

ASCBRLGHWVZBMG-NPVWYNPDSA-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
Aconitum japonicum	LOTUS Database	35616633
Brickellia pendula	Plant	KNApSAcK
Chrysosplenium flagelliferum	Plant	KNApSAcK
Chrysosplenium tetrandrum	Plant	KNApSAcK
Cocculus pendulus	LOTUS Database	35616633
Isopyrum thalictroides	LOTUS Database	35616633
Leptopus chinensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid O-glycosides

Alternative Parents

Substituents

Flavonoid o-glycoside
Flavonoid-4p-o-glycoside
3-methoxyflavonoid-skeleton
7-methoxyflavonoid-skeleton
6-methoxyflavonoid-skeleton
Flavone
Hydroxyflavonoid
5-hydroxyflavonoid
Phenolic glycoside
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
3-methoxychromone
Alkyl glycoside
Hexose monosaccharide
Chromone
O-glycosyl compound
Glycosyl compound
Benzopyran
1-benzopyran
Phenol ether
Anisole
Phenoxy compound
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
Pyranone
Monosaccharide
Pyran
Oxane
Monocyclic benzene moiety
Fatty acyl
Benzenoid
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Oxacycle
Ether
Acetal
Organoheterocyclic compound
Polyol
Organooxygen compound
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	0.9	ALOGPS
logP	0.29	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	7.73	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	173.6 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	122.72 m³·mol⁻¹	ChemAxon
Polarizability	50.31 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00010299

Chemspider ID

65791437

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12314045

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Velasco-Azorsa R, Cruz-Santiago H, Cid Del Prado-Vera I, Ramirez-Mares MV, Gutierrez-Ortiz MDR, Santos-Sanchez NF, Salas-Coronado R, Villanueva-Canongo C, Lira-de Leon KI, Hernandez-Carlos B: Chemical Characterization of Plant Extracts and Evaluation of their Nematicidal and Phytotoxic Potential. Molecules. 2021 Apr 12;26(8). pii: molecules26082216. doi: 10.3390/molecules26082216. [PubMed:33921412 ]
Domokos Erzsebet, Kursinszki L, Kelemen H, Varga E: [Phytopharmacological review of bathurst burr (Xanthium spinosum L.)]. Acta Pharm Hung. 2016;86(1):35-40. [PubMed:27295875 ]
Serway CN, Dunkelberger BS, Del Padre D, Nolan NWC, Georges S, Freer S, Andres AJ, de Belle JS: Importin-alpha2 mediates brain development, learning and memory consolidation in Drosophila. J Neurogenet. 2020 Mar;34(1):69-82. doi: 10.1080/01677063.2019.1709184. Epub 2020 Jan 22. [PubMed:31965871 ]
Asaoka M, Hanyu-Nakamura K, Nakamura A, Kobayashi S: Maternal Nanos inhibits Importin-alpha2/Pendulin-dependent nuclear import to prevent somatic gene expression in the Drosophila germline. PLoS Genet. 2019 May 15;15(5):e1008090. doi: 10.1371/journal.pgen.1008090. eCollection 2019 May. [PubMed:31091233 ]
Holt JE, Ly-Huynh JD, Efthymiadis A, Hime GR, Loveland KL, Jans DA: Regulation of Nuclear Import During Differentiation; The IMP alpha Gene Family and Spermatogenesis. Curr Genomics. 2007 Aug;8(5):323-34. doi: 10.2174/138920207782446151. [PubMed:19384428 ]

Showing NP-Card for Pendulin (NP0053479)

MOL for NP0053479 (Pendulin)

3D MOL for NP0053479 (Pendulin)

3D SDF for NP0053479 (Pendulin)

3D-SDF for NP0053479 (Pendulin)

PDB for NP0053479 (Pendulin)

3D PDB for NP0053479 (Pendulin)

SMILES for NP0053479 (Pendulin)

INCHI for NP0053479 (Pendulin)

Structure for NP0053479 (Pendulin)

3D Structure for NP0053479 (Pendulin)