NP-MRD: Showing NP-Card for α-berbine (NP0311117)

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Record Information

Version

2.0

Created at

2022-09-11 06:54:11 UTC

Updated at

2022-09-11 06:54:12 UTC

NP-MRD ID

NP0311117

Secondary Accession Numbers

None

Natural Product Identification

Common Name

α-berbine

Description

Alpha-berbine, also known as berbine, belongs to the class of organic compounds known as protoberberine alkaloids and derivatives. These are alkaloids with a structure based on a protoberberine moiety, which consists of a 5,6-dihydrodibenzene moiety fused to a quinolizinium and forming 5,6-Dihydrodibenzo(a,g)quinolizinium skeleton. α-berbine is found in Apis cerana and Daphnia pulex. Based on a literature review very few articles have been published on alpha-berbine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 38  0  0  0  0  0  0  0  0999 V2000
    4.1150    1.9181    0.0168 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6224    0.6412   -0.1002 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7744   -0.4580   -0.2112 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4112   -0.2671   -0.2041 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9214    0.9936   -0.0885 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7493    2.0975    0.0229 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4768    1.2054   -0.0807 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2806    0.0121    0.4301 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7094    0.2245    0.0772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1907    1.4972   -0.2536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5050    1.6907   -0.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3813    0.6161   -0.5734 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9211   -0.6438   -0.2496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6068   -0.8228    0.0680 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0300   -2.1517    0.4245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7295   -2.2317   -0.3876 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1860   -1.2359    0.0341 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5209   -1.4280   -0.3206 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8032    2.7689    0.1030 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6948    0.4878   -0.1061 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2349   -1.4249   -0.2992 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3555    3.1013    0.1149 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1230    1.4303   -1.0983 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2722    2.0509    0.6370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2595    0.0720    1.5606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5300    2.3481   -0.2612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8743    2.6849   -0.8307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4293    0.7874   -0.8317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6039   -1.4823   -0.2491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7711   -2.1832    1.4860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6731   -2.9838    0.1055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0302   -2.0088   -1.4380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2789   -3.2328   -0.3243 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9635   -2.2474    0.3184 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5800   -1.8261   -1.3636 H   0  0  0  0  0  0  0  0  0  0  0  0
 16 15  1  0
 15 14  1  0
 14 13  2  0
 13 12  1  0
 12 11  2  0
 11 10  1  0
 10  9  2  0
  9  8  1  0
  8  7  1  0
  7  5  1  0
  5  6  2  0
  6  1  1  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4 18  1  0
 18 17  1  0
 17 16  1  0
  9 14  1  0
 17  8  1  0
  4  5  1  0
 16 32  1  0
 16 33  1  0
 15 30  1  0
 15 31  1  0
 13 29  1  0
 12 28  1  0
 11 27  1  0
 10 26  1  0
  8 25  1  1
  7 23  1  0
  7 24  1  0
  6 22  1  0
  1 19  1  0
  2 20  1  0
  3 21  1  0
 18 34  1  0
 18 35  1  0
M  END


  Mrv1652309112208542D          

 18 21  0  0  1  0            999 V2000
   -0.5401   -2.6764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8101   -3.4559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2700   -4.0796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5401   -3.9236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8101   -3.1441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2700   -2.5204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6203   -2.9882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1604   -3.6118    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9705   -3.4559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2405   -2.6764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0507   -2.5204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5908   -3.1441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3207   -3.9236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5106   -4.0796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2405   -4.8591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4304   -5.0150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8903   -4.3914    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0802   -4.5473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  9 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  8 17  1  1  0  0  0
 17 18  1  0  0  0  0
  4 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0311117

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C1CC2=CC=CC=C2[C@@H]2CC3=CC=CC=C3CN12

> <INCHI_IDENTIFIER>
InChI=1S/C17H17N/c1-2-7-15-12-18-10-9-13-5-3-4-8-16(13)17(18)11-14(15)6-1/h1-8,17H,9-12H2/t17-/m0/s1

> <INCHI_KEY>
BRLDZKPJJNASGG-KRWDZBQOSA-N

> <FORMULA>
C17H17N

> <MOLECULAR_WEIGHT>
235.33

> <EXACT_MASS>
235.136099551

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
26.990600744857193

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(12bS)-7,8,12b,13-tetrahydro-5H-6-azatetraphene

> <JCHEM_LOGP>
3.7786597829999993

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
7.1260110624122825

> <JCHEM_POLAR_SURFACE_AREA>
3.24

> <JCHEM_REFRACTIVITY>
75.5027

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
α-berbine

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.008  -4.996   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.512  -6.451   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.504  -7.615   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.008  -7.324   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.512  -5.869   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.504  -4.705   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.024  -5.578   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.033  -6.742   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.545  -6.451   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.049  -4.996   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.561  -4.705   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.569  -5.869   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.065  -7.324   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.553  -7.615   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.049  -9.070   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.537  -9.361   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       3.529  -8.197   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       2.016  -8.488   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   18                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   17                                                  
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    9   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    8   18                                                  
CONECT   18   17    4                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   42    0
END

View in JSmol

Synonyms

Value	Source
(S)-5,8,13,13a-Tetrahydro-6H-dibenzo[a,g]quinolizine	ChEBI
(S)-7,8,13,14-Tetrahydroprotoberberine	ChEBI
(S)-Tetrahydroprotoberberine	ChEBI
Berbine	ChEBI
a-Berbine	Generator
Α-berbine	Generator
Tetrahydroprotoberberine	MeSH

Chemical Formula

C₁₇H₁₇N

Average Mass

235.3300 Da

Monoisotopic Mass

235.13610 Da

IUPAC Name

(12bS)-7,8,12b,13-tetrahydro-5H-6-azatetraphene

Traditional Name

α-berbine

CAS Registry Number

Not Available

SMILES

C1CC2=CC=CC=C2[C@@H]2CC3=CC=CC=C3CN12

InChI Identifier

InChI=1S/C17H17N/c1-2-7-15-12-18-10-9-13-5-3-4-8-16(13)17(18)11-14(15)6-1/h1-8,17H,9-12H2/t17-/m0/s1

InChI Key

BRLDZKPJJNASGG-KRWDZBQOSA-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
Apis cerana	LOTUS Database	35616633
Daphnia pulex	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as protoberberine alkaloids and derivatives. These are alkaloids with a structure based on a protoberberine moiety, which consists of a 5,6-dihydrodibenzene moiety fused to a quinolizinium and forming 5,6-Dihydrodibenzo(a,g)quinolizinium skeleton.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Protoberberine alkaloids and derivatives

Sub Class

Not Available

Direct Parent

Protoberberine alkaloids and derivatives

Alternative Parents

Substituents

Tetrahydroprotoberberine skeleton
Protoberberine skeleton
Tetrahydroisoquinoline
Aralkylamine
Benzenoid
Tertiary aliphatic amine
Tertiary amine
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

berbine (CHEBI:50400 )
Isoquinoline alkaloids (C05204 )

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	3.78	ChemAxon
pKa (Strongest Basic)	7.13	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	3.24 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	75.5 m³·mol⁻¹	ChemAxon
Polarizability	26.99 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

Not Available

Chemspider ID

144245

KEGG Compound ID

C05204

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

164543

PDB ID

Not Available

ChEBI ID

50400

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for α-berbine (NP0311117)

MOL for NP0311117 (α-berbine)

3D MOL for NP0311117 (α-berbine)

3D SDF for NP0311117 (α-berbine)

3D-SDF for NP0311117 (α-berbine)

PDB for NP0311117 (α-berbine)

3D PDB for NP0311117 (α-berbine)

SMILES for NP0311117 (α-berbine)

INCHI for NP0311117 (α-berbine)

Structure for NP0311117 (α-berbine)

3D Structure for NP0311117 (α-berbine)