NP-MRD: Showing NP-Card for deoxypumiloside (NP0286731)

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Record Information

Version

2.0

Created at

2022-09-09 15:26:23 UTC

Updated at

2022-09-09 15:26:23 UTC

NP-MRD ID

NP0286731

Secondary Accession Numbers

None

Natural Product Identification

Common Name

deoxypumiloside

Description

Deoxypumiloside belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Deoxypumiloside is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. deoxypumiloside is found in Mostuea brunonis and Ophiorrhiza pumila. deoxypumiloside was first documented in 2013 (PMID: 22652243). Based on a literature review a small amount of articles have been published on Deoxypumiloside (PMID: 31537116) (PMID: 32021647) (PMID: 30823523) (PMID: 24882065).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092217262D          

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M  END

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M  END


  Mrv1652309092217262D          

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M  END
> <DATABASE_ID>
NP0286731

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2OC=C3[C@@H](C[C@@H]4N(CC5=C4N=C4C=CC=CC4=C5)C3=O)[C@H]2C=C)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28N2O8/c1-2-14-15-8-18-20-13(7-12-5-3-4-6-17(12)27-20)9-28(18)24(33)16(15)11-34-25(14)36-26-23(32)22(31)21(30)19(10-29)35-26/h2-7,11,14-15,18-19,21-23,25-26,29-32H,1,8-10H2/t14-,15+,18+,19-,21-,22+,23-,25+,26+/m1/s1

> <INCHI_KEY>
BNDDTTIRGZIQSE-ZEZHKYRDSA-N

> <FORMULA>
C26H28N2O8

> <MOLECULAR_WEIGHT>
496.516

> <EXACT_MASS>
496.18456587

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
52.11551522831769

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,18S,19R,20S)-19-ethenyl-18-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0^{2,11}.0^{4,9}.0^{15,20}]henicosa-2(11),3,5,7,9,15-hexaen-14-one

> <JCHEM_LOGP>
0.05877065000000012

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.198719032369912

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.207016194002579

> <JCHEM_PKA_STRONGEST_BASIC>
3.1125721424344617

> <JCHEM_POLAR_SURFACE_AREA>
141.81

> <JCHEM_REFRACTIVITY>
124.60610000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,18S,19R,20S)-19-ethenyl-18-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0^{2,11}.0^{4,9}.0^{15,20}]henicosa-2(11),3,5,7,9,15-hexaen-14-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      10.946  -8.921   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.439  -8.601   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.963  -7.136   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.457  -6.816   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.427  -7.960   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.920  -7.640   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.890  -8.784   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.383  -8.464   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.353  -9.609   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.153  -9.288   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.907  -7.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.401  -6.679   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.938  -5.855   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.462  -4.391   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.444  -6.175   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.475  -5.031   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       6.981  -5.351   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       8.012  -4.207   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.518  -4.527   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.548  -3.382   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      10.072  -1.918   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0      12.055  -3.703   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      13.301  -2.797   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.546  -3.703   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      16.053  -3.382   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      17.083  -4.527   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      18.590  -4.207   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      19.620  -5.351   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      19.144  -6.816   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      17.638  -7.136   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      16.607  -5.991   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      15.101  -6.312   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      14.071  -5.167   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.531  -5.167   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      11.500  -6.312   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       9.994  -5.991   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   36                                                  
CONECT    4    3    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    6   16                                                  
CONECT   16   15                                                            
CONECT   17    4   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   36                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   34                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   33                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   31                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   26   32                                                  
CONECT   32   31   33                                                       
CONECT   33   32   24   34                                                  
CONECT   34   33   22   35                                                  
CONECT   35   34   36                                                       
CONECT   36   35   19    3                                                  
MASTER        0    0    0    0    0    0    0    0   36    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈N₂O₈

Average Mass

496.5160 Da

Monoisotopic Mass

496.18457 Da

IUPAC Name

(1S,18S,19R,20S)-19-ethenyl-18-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0^{2,11}.0^{4,9}.0^{15,20}]henicosa-2(11),3,5,7,9,15-hexaen-14-one

Traditional Name

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@H]2OC=C3[C@@H](C[C@@H]4N(CC5=C4N=C4C=CC=CC4=C5)C3=O)[C@H]2C=C)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C26H28N2O8/c1-2-14-15-8-18-20-13(7-12-5-3-4-6-17(12)27-20)9-28(18)24(33)16(15)11-34-25(14)36-26-23(32)22(31)21(30)19(10-29)35-26/h2-7,11,14-15,18-19,21-23,25-26,29-32H,1,8-10H2/t14-,15+,18+,19-,21-,22+,23-,25+,26+/m1/s1

InChI Key

BNDDTTIRGZIQSE-ZEZHKYRDSA-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
Mostuea brunonis	LOTUS Database	35616633
Ophiorrhiza pumila	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Hexose monosaccharide
O-glycosyl compound
Quinoline
Delta-lactam
Piperidinone
Monosaccharide
Oxane
Piperidine
Pyridine
Benzenoid
Heteroaromatic compound
Vinylogous ester
Tertiary carboxylic acid amide
Secondary alcohol
Carboxamide group
Lactam
Organoheterocyclic compound
Carboxylic acid derivative
Polyol
Acetal
Oxacycle
Azacycle
Alcohol
Organopnictogen compound
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Carbonyl group
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

glycoside (CHEBI:80685 )

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	0.059	ChemAxon
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	3.11	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	141.81 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	124.61 m³·mol⁻¹	ChemAxon
Polarizability	52.12 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

Not Available

KNApSAcK ID

C00029323

Chemspider ID

30791757

KEGG Compound ID

C16725

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46173817

PDB ID

Not Available

ChEBI ID

80685

Good Scents ID

Not Available

References

General References

Sun Y, Zhang N, Wang C, Wei Y, Liu J: Distribution of camptothecin biosynthetic intermediates and identification the rate-limiting step of camptothecin biosynthesis. Nat Prod Res. 2021 Jul;35(13):2170-2177. doi: 10.1080/14786419.2019.1665252. Epub 2019 Sep 19. [PubMed:31537116 ]
Liu H, Liao W, Fan L, Zheng Z, Liu D, Zhang QW, Yang A, Liu F: Ethanol extract of Ophiorrhiza pumila suppresses liver cancer cell proliferation and migration. Chin Med. 2020 Jan 31;15:11. doi: 10.1186/s13020-020-0291-4. eCollection 2020. [PubMed:32021647 ]
Jin Z, Wan R, Yan R, Su Y, Huang H, Zi L, Yu F: Microwave-Assisted Extraction of Multiple Trace Levels of Intermediate Metabolites for Camptothecin Biosynthesis in Camptotheca acuminata and Their Simultaneous Determination by HPLC-LTQ-Orbitrap-MS/MS and HPLC-TSQ-MS. Molecules. 2019 Feb 25;24(4):815. doi: 10.3390/molecules24040815. [PubMed:30823523 ]
Suma HK, Kumar V, Senthilkumar U, Kumara PM, Ravikanth G, Santhoshkumar TR, Shaanker RU: Pyrenacantha volubilis Wight, (Icacinaceae) a rich source of camptothecine and its derivatives, from the Coromandel Coast forests of India. Fitoterapia. 2014 Sep;97:105-10. doi: 10.1016/j.fitote.2014.05.017. Epub 2014 May 29. [PubMed:24882065 ]
Asano T, Kobayashi K, Kashihara E, Sudo H, Sasaki R, Iijima Y, Aoki K, Shibata D, Saito K, Yamazaki M: Suppression of camptothecin biosynthetic genes results in metabolic modification of secondary products in hairy roots of Ophiorrhiza pumila. Phytochemistry. 2013 Jul;91:128-39. doi: 10.1016/j.phytochem.2012.04.019. Epub 2012 May 30. [PubMed:22652243 ]
LOTUS database [Link]

Showing NP-Card for deoxypumiloside (NP0286731)

MOL for NP0286731 (deoxypumiloside)

3D MOL for NP0286731 (deoxypumiloside)

3D SDF for NP0286731 (deoxypumiloside)

3D-SDF for NP0286731 (deoxypumiloside)

PDB for NP0286731 (deoxypumiloside)

3D PDB for NP0286731 (deoxypumiloside)

SMILES for NP0286731 (deoxypumiloside)

INCHI for NP0286731 (deoxypumiloside)

Structure for NP0286731 (deoxypumiloside)

3D Structure for NP0286731 (deoxypumiloside)