Bovine Metabolome Database: Showing metabocard for Berberine (BMDB0003409)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:04:22 UTC

Update Date

2020-05-11 20:49:17 UTC

BMDB ID

BMDB0003409

Secondary Accession Numbers

BMDB03409

Metabolite Identification

Common Name

Berberine

Description

Berberine 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. Based on a literature review a significant number of articles have been published on Berberine.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
7,8,13,13a-Tetradehydro-9,10-dimethoxy-2,3-[methylenebis(oxy)]berbinium	ChEBI
9,10-Dimethoxy-2,3-(methylenedioxy)-7,8,13,13a-tetradehydroberbinium	ChEBI
Berberin	ChEBI
Coptis rhizome	HMDB

Chemical Formula

C₂₀H₁₈NO₄

Average Molecular Weight

336.3612

Monoisotopic Molecular Weight

336.123583069

IUPAC Name

16,17-dimethoxy-5,7-dioxa-13lambda5-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2,4(8),9,13,15,17,19-octaen-13-ylium

Traditional Name

16,17-dimethoxy-5,7-dioxa-13lambda5-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2,4(8),9,13,15,17,19-octaen-13-ylium

CAS Registry Number

2086-83-1

SMILES

COC1=CC=C2C=C3C4=CC5=C(OCO5)C=C4CC[N+]3=CC2=C1OC

InChI Identifier

InChI=1S/C20H18NO4/c1-22-17-4-3-12-7-16-14-9-19-18(24-11-25-19)8-13(14)5-6-21(16)10-15(12)20(17)23-2/h3-4,7-10H,5-6,11H2,1-2H3/q+1

InChI Key

YBHILYKTIRIUTE-UHFFFAOYSA-N

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
Isoquinoline
Benzodioxole
Anisole
Alkyl aryl ether
Pyridine
Pyridinium
Benzenoid
Heteroaromatic compound
Acetal
Ether
Oxacycle
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Hydrocarbon derivative
Organic nitrogen compound
Organooxygen compound
Organic oxygen compound
Organopnictogen compound
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic heteropentacyclic compound (CHEBI:16118 )
berberine alkaloid (CHEBI:16118 )
alkaloid antibiotic (CHEBI:16118 )
botanical anti-fungal agent (CHEBI:16118 )
Alkaloids (C00757 )
Isoquinoline alkaloids (C00757 )
a small molecule (BERBERINE )

Ontology

Status

Expected but not Quantified

Origin

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Membrane

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	145 °C	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	-0.18	ALOGPS
logP	-1.3	ChemAxon
logS	-6	ALOGPS
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	40.8 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	93.52 m³·mol⁻¹	ChemAxon
Polarizability	36.92 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4l-0059000000-2d03f2d248021273bb66	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-000i-0009000000-19928d40d547cbbc26dc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-0029000000-42f72c3da8025ad70c4d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0103-0089000000-dbcf680bd232ed620a00	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-000i-0009000000-2993f75f22b9532dc39f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-000i-0009000000-1d4cdb20920f8c900320	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-0079-0019000000-4995338b7526764bbad3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00dl-0059000000-ab35b8a7ec73f1063bb2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-00fu-0089000000-09273e18fcd3186156f0	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-00di-0039000000-3a3f7eba3883c388e58c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-0006-0092000000-6f10979e1ecdd29611b1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive	splash10-0006-0090000000-bacf940c54361560b64b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITTOF (Shimadzu LC20A-IT-TOFMS) , Positive	splash10-000i-0009000000-3d6d1928f5797f4633e4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITTOF (LCMS-IT-TOF) , Positive	splash10-000i-0009000000-6337ae6880e36d106adf	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00dl-0039000000-5d1ff6b7636484db90d1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00dl-0059000000-131055c16d28a84b6130	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000i-0009000000-9d8986d4bd9f3b6d634d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-000i-0009000000-4459c8c8f7b607ad7b49	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-00dr-0019000000-a0c1c55261d223b09256	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-00dl-0069000000-437bdc5509b367efef25	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0009000000-41bc0e7901cbc892051c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0009000000-b2e1ddadd60e4f52d2dd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0iki-0179000000-85594d2e5f4b265077ab	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0009000000-604df9f348201c3c531e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-0009000000-34b3c7d90696ff194395	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0nnc-3095000000-2e76003cd5b376964ba8	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, experimental)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CD₃OD, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cell membrane
Membrane

Biospecimen Locations

Fibroblasts
Intestine
Prostate Tissue

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0003409

DrugBank ID

DB04115

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Berberine

METLIN ID

3471

PubChem Compound

2353

PDB ID

Not Available

ChEBI ID

16118

References

Synthesis Reference

Dominguez, Xorge A.; Garcia Delgado, Jesus; Reeves, Wylie P.; Gardner, Pete D. Photochemical formation of berberine alkaloids from protopine alkaloids. Tetrahedron Letters (1967), (26), 2493-5.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Berberine (BMDB0003409)

Structure for BMDB0003409 (Berberine)