NP-MRD: Showing NP-Card for 2,3,9,10-tetrahydroxyberbine (NP0156506)

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Record Information

Version

2.0

Created at

2022-09-02 13:43:38 UTC

Updated at

2022-09-02 13:43:38 UTC

NP-MRD ID

NP0156506

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,3,9,10-tetrahydroxyberbine

Description

2,3,9,10-Tetrahydroxyberbine 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. 2,3,9,10-Tetrahydroxyberbine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. 2,3,9,10-tetrahydroxyberbine is found in Apis cerana. Based on a literature review very few articles have been published on 2,3,9,10-tetrahydroxyberbine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 42  0  0  0  0  0  0  0  0999 V2000
   -5.9105   -0.3191    0.4210 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5347   -0.0834    0.3753 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7093   -0.8796   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3459   -0.6645   -0.4502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8125    0.3800    0.2826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6548    1.1658    1.0430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0195    0.9617    1.1117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8528    1.7787    1.8952 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3505    0.5832    0.1968 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4137   -0.3512    1.1028 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8523   -0.2750    0.7805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8008   -0.7790    1.6467 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1534   -0.7344    1.3963 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5940   -0.1617    0.2286 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9464   -0.1040   -0.0473 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6934    0.3472   -0.6529 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1880    0.9218   -1.8309 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3403    0.2961   -0.3900 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4251    0.8750   -1.4059 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0497    0.4775   -1.1787 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2571   -0.7583   -1.8046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4297   -1.4911   -1.2551 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5186    0.2435    0.9663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1117   -1.6936   -0.9638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2265    1.9789    1.6114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4037    2.5266    2.4087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1235    1.6188    0.5312 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0108   -1.3621    1.1468 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3062    0.0724    2.1447 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4816   -1.2352    2.5731 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8954   -1.1303    2.0771 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3489    0.2913   -0.8652 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5700    1.3141   -2.5195 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4745    1.9805   -1.2851 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6800    0.5518   -2.4356 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6151   -1.4741   -1.8063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4269   -0.5485   -2.9019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0457   -1.9025   -2.1084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1060   -2.4176   -0.6970 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
  7  2  1  0
 20  9  1  0
 22  4  1  0
 18 11  1  0
  1 23  1  0
  3 24  1  0
  6 25  1  0
  8 26  1  0
  9 27  1  1
 10 28  1  0
 10 29  1  0
 12 30  1  0
 13 31  1  0
 15 32  1  0
 17 33  1  0
 19 34  1  0
 19 35  1  0
 21 36  1  0
 21 37  1  0
 22 38  1  0
 22 39  1  0
M  END


  Mrv1652309022215432D          

 22 25  0  0  0  0            999 V2000
   -0.1913   -2.9882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6188   -3.1441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8889   -3.9236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990   -4.0796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2391   -3.4559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690   -2.6764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589   -2.5204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8889   -1.7409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0492   -3.6118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5893   -2.9882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3994   -3.1441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9395   -2.5204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7497   -2.6764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0197   -3.4559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8298   -3.6118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4796   -4.0796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7497   -4.8591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6695   -3.9236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1294   -4.5473    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3193   -4.3914    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7792   -5.0150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9690   -4.8591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  9  1  0  0  0  0
  9 10  1  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
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
  9 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  4 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0156506

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC2=C(C=C1O)C1CC3=CC=C(O)C(O)=C3CN1CC2

> <INCHI_IDENTIFIER>
InChI=1S/C17H17NO4/c19-14-2-1-9-5-13-11-7-16(21)15(20)6-10(11)3-4-18(13)8-12(9)17(14)22/h1-2,6-7,13,19-22H,3-5,8H2

> <INCHI_KEY>
TVKAUFJQMRSZFH-UHFFFAOYSA-N

> <FORMULA>
C17H17NO4

> <MOLECULAR_WEIGHT>
299.326

> <EXACT_MASS>
299.115758031

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
31.917872265608814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7,8,12b,13-tetrahydro-5H-6-azatetraphene-3,4,10,11-tetrol

> <ALOGPS_LOGP>
1.49

> <JCHEM_LOGP>
2.564398496333333

> <ALOGPS_LOGS>
-2.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.509760114481038

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.738147313499386

> <JCHEM_PKA_STRONGEST_BASIC>
5.812361401162132

> <JCHEM_POLAR_SURFACE_AREA>
84.16

> <JCHEM_REFRACTIVITY>
83.42629999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.35e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,9,10-tetrahydroxyberbine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  O   UNK     0      -0.357  -5.578   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.155  -5.869   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.659  -7.324   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.171  -7.615   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.180  -6.451   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.676  -4.996   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.163  -4.705   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.659  -3.250   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       5.692  -6.742   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.700  -5.578   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.212  -5.869   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.220  -4.705   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.733  -4.996   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.237  -6.451   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.749  -6.742   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      10.229  -7.615   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      10.733  -9.070   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       8.716  -7.324   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.708  -8.488   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       6.196  -8.197   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       5.188  -9.361   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.676  -9.070   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   22                                                  
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
CONECT    9    5   10   20                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   11   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19    9   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21    4                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₁₇NO₄

Average Mass

299.3260 Da

Monoisotopic Mass

299.11576 Da

IUPAC Name

7,8,12b,13-tetrahydro-5H-6-azatetraphene-3,4,10,11-tetrol

Traditional Name

2,3,9,10-tetrahydroxyberbine

CAS Registry Number

Not Available

SMILES

OC1=CC2=C(C=C1O)C1CC3=CC=C(O)C(O)=C3CN1CC2

InChI Identifier

InChI=1S/C17H17NO4/c19-14-2-1-9-5-13-11-7-16(21)15(20)6-10(11)3-4-18(13)8-12(9)17(14)22/h1-2,6-7,13,19-22H,3-5,8H2

InChI Key

TVKAUFJQMRSZFH-UHFFFAOYSA-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

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

Protoberberine skeleton
Tetrahydroprotoberberine skeleton
Tetrahydroisoquinoline
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Benzenoid
Tertiary aliphatic amine
Tertiary amine
Organoheterocyclic compound
Polyol
Azacycle
Hydrocarbon derivative
Amine
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic heterotetracyclic compound (CHEBI:31071 )
berberine alkaloid (CHEBI:31071 )
polyphenol (CHEBI:31071 )

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	2.56	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	8.74	ChemAxon
pKa (Strongest Basic)	5.81	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	84.16 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	83.43 m³·mol⁻¹	ChemAxon
Polarizability	31.92 Å³	ChemAxon
Number of Rings	4	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

391870

KEGG Compound ID

C12330

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443767

PDB ID

Not Available

ChEBI ID

31071

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2,3,9,10-tetrahydroxyberbine (NP0156506)

MOL for NP0156506 (2,3,9,10-tetrahydroxyberbine)

3D MOL for NP0156506 (2,3,9,10-tetrahydroxyberbine)

3D SDF for NP0156506 (2,3,9,10-tetrahydroxyberbine)

3D-SDF for NP0156506 (2,3,9,10-tetrahydroxyberbine)

PDB for NP0156506 (2,3,9,10-tetrahydroxyberbine)

3D PDB for NP0156506 (2,3,9,10-tetrahydroxyberbine)

SMILES for NP0156506 (2,3,9,10-tetrahydroxyberbine)

INCHI for NP0156506 (2,3,9,10-tetrahydroxyberbine)

Structure for NP0156506 (2,3,9,10-tetrahydroxyberbine)

3D Structure for NP0156506 (2,3,9,10-tetrahydroxyberbine)