NP-MRD: Showing NP-Card for liberine (NP0318798)

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Record Information

Version

2.0

Created at

2022-09-11 19:30:23 UTC

Updated at

2022-09-11 19:30:23 UTC

NP-MRD ID

NP0318798

Secondary Accession Numbers

None

Natural Product Identification

Common Name

liberine

Description

Liberine belongs to the class of organic compounds known as 6-oxopurines. These are purines that carry a C=O group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring. Liberine is an isolate of coffee beans, tea, cola nuts, guarana, cocoa, and yerba mate. liberine is found in Camellia sinensis. Liberine is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004191520242D          

 15 16  0  0  0  0            999 V2000
    3.4990    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  3 14  1  0  0  0  0
 14 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0318798

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=NC2=C(NC(=O)N2C)C(=O)N1C

> <INCHI_IDENTIFIER>
InChI=1S/C8H10N4O3/c1-11-5-4(9-7(11)14)6(13)12(2)8(10-5)15-3/h1-3H3,(H,9,14)

> <INCHI_KEY>
IDVFNSHOEYLXJD-UHFFFAOYSA-N

> <FORMULA>
C8H10N4O3

> <MOLECULAR_WEIGHT>
210.193

> <EXACT_MASS>
210.075290198

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
19.94704058253585

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-methoxy-1,9-dimethyl-6,7,8,9-tetrahydro-1H-purine-6,8-dione

> <ALOGPS_LOGP>
-0.69

> <JCHEM_LOGP>
-0.16440928799999982

> <ALOGPS_LOGS>
-1.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.591615221105773

> <JCHEM_PKA_STRONGEST_BASIC>
-1.354243525329013

> <JCHEM_POLAR_SURFACE_AREA>
74.24

> <JCHEM_REFRACTIVITY>
60.694900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.49e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methoxy-1,9-dimethyl-7H-purine-6,8-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0       6.531   2.073   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       5.198   1.303   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.530   1.303   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.268   4.089   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.713   2.843   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      -0.268   1.597   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -0.744   0.132   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.530   5.923   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0       3.864   3.613   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       5.198   4.383   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    5   11                                                  
CONECT   11   10                                                            
CONECT   12    6   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    3   15                                                  
CONECT   15   14                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₈H₁₀N₄O₃

Average Mass

210.1930 Da

Monoisotopic Mass

210.07529 Da

IUPAC Name

2-methoxy-1,9-dimethyl-6,7,8,9-tetrahydro-1H-purine-6,8-dione

Traditional Name

2-methoxy-1,9-dimethyl-7H-purine-6,8-dione

CAS Registry Number

Not Available

SMILES

COC1=NC2=C(NC(=O)N2C)C(=O)N1C

InChI Identifier

InChI=1S/C8H10N4O3/c1-11-5-4(9-7(11)14)6(13)12(2)8(10-5)15-3/h1-3H3,(H,9,14)

InChI Key

IDVFNSHOEYLXJD-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
Camellia sinensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 6-oxopurines. These are purines that carry a C=O group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Imidazopyrimidines

Sub Class

Purines and purine derivatives

Direct Parent

6-oxopurines

Alternative Parents

Substituents

6-oxopurine
Alkyl aryl ether
Pyrimidone
N-substituted imidazole
Pyrimidine
Azole
Imidazole
Heteroaromatic compound
Vinylogous amide
Lactam
Urea
Ether
Azacycle
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

a small molecule (CPD-12507 )

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	-0.69	ALOGPS
logP	-0.16	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	7.59	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	74.24 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	60.69 m³·mol⁻¹	ChemAxon
Polarizability	19.95 Å³	ChemAxon
Number of Rings	2	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Liberine

METLIN ID

Not Available

PubChem Compound

46926249

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for liberine (NP0318798)

MOL for NP0318798 (liberine)

3D MOL for NP0318798 (liberine)

3D SDF for NP0318798 (liberine)

3D-SDF for NP0318798 (liberine)

PDB for NP0318798 (liberine)

3D PDB for NP0318798 (liberine)

SMILES for NP0318798 (liberine)

INCHI for NP0318798 (liberine)

Structure for NP0318798 (liberine)

3D Structure for NP0318798 (liberine)