NP-MRD: Showing NP-Card for (S)-Nandigerine (NP0047628)

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Record Information

Version

2.0

Created at

2022-03-17 20:43:19 UTC

Updated at

2022-03-17 20:43:19 UTC

NP-MRD ID

NP0047628

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(S)-Nandigerine

Description

(S)-Nandigerine, also known as hernangerine, belongs to the class of organic compounds known as aporphines. These are quinoline alkaloids containing the dibenzo[de,g]quinoline ring system or a dehydrogenated derivative thereof (S)-Nandigerine is a very strong basic compound (based on its pKa). Outside of the human body, (S)-nandigerine has been detected, but not quantified in, a few different foods, such as herbs and spices, sweet bay, and tea. (S)-Nandigerine is found in Dehaasia triandra, Hernandia ovigera L. , Laurus nobilis, Lindera chunii, Lindera praecox, Ocotea meziana, Ocotea teleiandra, Platycapnos spicata, Platycapnos tenuiloba, Siparuna griseo-flavescens, Siparuna tonduziana and Stephania tetrandra . This could make (S)-nandigerine a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061307052D          

 23 27  0  0  0  0            999 V2000
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1354    2.1307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3149    2.0445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4710    1.3770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  5  4  1  0  0  0  0
  9  2  1  0  0  0  0
  9  6  1  0  0  0  0
 10  4  1  0  0  0  0
 10  7  2  0  0  0  0
 11  6  1  0  0  0  0
 12  3  1  0  0  0  0
 13  7  1  0  0  0  0
 14 10  1  0  0  0  0
 14 11  1  0  0  0  0
 15  9  2  0  0  0  0
 16 14  2  0  0  0  0
 16 15  1  0  0  0  0
 17 12  2  0  0  0  0
 17 15  1  0  0  0  0
 18 13  2  0  0  0  0
 18 16  1  0  0  0  0
 19  5  1  0  0  0  0
 19 11  1  0  0  0  0
 20 12  1  0  0  0  0
 21  1  1  0  0  0  0
 21 17  1  0  0  0  0
 22  8  1  0  0  0  0
 22 13  1  0  0  0  0
 23  8  1  0  0  0  0
 23 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0047628

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C=CC2=C1C1=C3C(C2)NCCC3=CC2=C1OCO2

> <INCHI_IDENTIFIER>
InChI=1S/C18H17NO4/c1-21-17-12(20)3-2-9-6-11-14-10(4-5-19-11)7-13-18(23-8-22-13)16(14)15(9)17/h2-3,7,11,19-20H,4-6,8H2,1H3

> <INCHI_KEY>
CFUKKPQRQGCLAT-UHFFFAOYSA-N

> <FORMULA>
C18H17NO4

> <MOLECULAR_WEIGHT>
311.3319

> <EXACT_MASS>
311.115758037

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
32.58469807521295

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
18-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14(19),15,17-hexaen-17-ol

> <ALOGPS_LOGP>
1.49

> <JCHEM_LOGP>
2.088857084552003

> <ALOGPS_LOGS>
-3.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.165945195306751

> <JCHEM_PKA_STRONGEST_BASIC>
9.357262952176361

> <JCHEM_POLAR_SURFACE_AREA>
59.95

> <JCHEM_REFRACTIVITY>
84.9426

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.78e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
18-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14(19),15,17-hexaen-17-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.853   3.977   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       2.667  -3.080   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0      10.669   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       8.002   1.540   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.321   3.816   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.479   2.570   0.000  0.00  0.00           O+0
CONECT    1   21                                                            
CONECT    2    3    9                                                       
CONECT    3    2   12                                                       
CONECT    4    5   10                                                       
CONECT    5    4   19                                                       
CONECT    6    9   11                                                       
CONECT    7   10   13                                                       
CONECT    8   22   23                                                       
CONECT    9    2    6   15                                                  
CONECT   10    4    7   14                                                  
CONECT   11    6   14   19                                                  
CONECT   12    3   17   20                                                  
CONECT   13    7   18   22                                                  
CONECT   14   10   11   16                                                  
CONECT   15    9   16   17                                                  
CONECT   16   14   15   18                                                  
CONECT   17   12   15   21                                                  
CONECT   18   13   16   23                                                  
CONECT   19    5   11                                                       
CONECT   20   12                                                            
CONECT   21    1   17                                                       
CONECT   22    8   13                                                       
CONECT   23    8   18                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   54    0
END

View in JSmol

Synonyms

Value	Source
(+)-Nandigerine	HMDB
Hernangerine	HMDB
Nandigerine	HMDB

Chemical Formula

C₁₈H₁₇NO₄

Average Mass

311.3319 Da

Monoisotopic Mass

311.11576 Da

IUPAC Name

18-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14(19),15,17-hexaen-17-ol

Traditional Name

18-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0²,⁶.0⁸,²⁰.0¹⁴,¹⁹]icosa-1(20),2(6),7,14(19),15,17-hexaen-17-ol

CAS Registry Number

31520-97-5

SMILES

COC1=C(O)C=CC2=C1C1=C3C(C2)NCCC3=CC2=C1OCO2

InChI Identifier

InChI=1S/C18H17NO4/c1-21-17-12(20)3-2-9-6-11-14-10(4-5-19-11)7-13-18(23-8-22-13)16(14)15(9)17/h2-3,7,11,19-20H,4-6,8H2,1H3

InChI Key

CFUKKPQRQGCLAT-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Dehaasia triandra	Plant	KNApSAcK
Hernandia ovigera	Plant	KNApSAcK
Laurus nobilis	LOTUS Database	35616633
Laurus nobilis L.	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Lindera chunii	Plant	KNApSAcK
Lindera praecox	LOTUS Database	35616633
Ocotea meziana	Plant	KNApSAcK
Ocotea teleiandra	Plant	KNApSAcK
Platycapnos spicata	Plant	KNApSAcK
Platycapnos tenuiloba	Plant	KNApSAcK
Siparuna griseo-flavescens	Plant	KNApSAcK
Siparuna tonduziana	Plant	KNApSAcK
Stephania tetrandra	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aporphines. These are quinoline alkaloids containing the dibenzo[de,g]quinoline ring system or a dehydrogenated derivative thereof.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Aporphines

Sub Class

Not Available

Direct Parent

Aporphines

Alternative Parents

Substituents

Aporphine
Benzoquinoline
Phenanthrene
2-naphthol
Naphthalene
Tetrahydroisoquinoline
Quinoline
Benzodioxole
Anisole
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Alkyl aryl ether
Benzenoid
Organoheterocyclic compound
Azacycle
Ether
Secondary aliphatic amine
Acetal
Oxacycle
Secondary amine
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Amine
Organic oxygen compound
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	1.49	ALOGPS
logP	2.09	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	10.17	ChemAxon
pKa (Strongest Basic)	9.36	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	59.95 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	84.94 m³·mol⁻¹	ChemAxon
Polarizability	32.58 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0033362

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB011390

KNApSAcK ID

C00027566

Chemspider ID

374109

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

422682

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (S)-Nandigerine (NP0047628)

MOL for NP0047628 ((S)-Nandigerine)

3D MOL for NP0047628 ((S)-Nandigerine)

3D SDF for NP0047628 ((S)-Nandigerine)

3D-SDF for NP0047628 ((S)-Nandigerine)

PDB for NP0047628 ((S)-Nandigerine)

3D PDB for NP0047628 ((S)-Nandigerine)

SMILES for NP0047628 ((S)-Nandigerine)

INCHI for NP0047628 ((S)-Nandigerine)

Structure for NP0047628 ((S)-Nandigerine)

3D Structure for NP0047628 ((S)-Nandigerine)