NP-MRD: Showing NP-Card for Alchornine (NP0051339)

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Record Information

Version

2.0

Created at

2022-04-27 22:44:01 UTC

Updated at

2022-04-27 22:44:01 UTC

NP-MRD ID

NP0051339

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Alchornine

Description

(2S)-7,7-dimethyl-2-(prop-1-en-2-yl)-2H,3H,5H,6H,7H,8H-imidazo[1,2-a]pyrimidin-5-one belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom. Alchornine is found in Alchornea javanensis. Based on a literature review very few articles have been published on (2S)-7,7-dimethyl-2-(prop-1-en-2-yl)-2H,3H,5H,6H,7H,8H-imidazo[1,2-a]pyrimidin-5-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    3.0889   -1.4412   -1.4255 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2029   -0.4935   -0.5369 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3738    0.3863   -0.5135 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1241   -0.3018    0.4719 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5148    1.0668    0.3829 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1172    0.8021    0.1990 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0127    1.6439    0.0439 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7715    2.8503   -0.2440 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3902    1.1203    0.2137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5098   -0.2786   -0.3875 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5401   -0.1191   -1.8838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8261   -0.8365    0.1146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4063   -1.0956    0.0084 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0554   -0.5974    0.1846 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0556   -1.2094    0.3357 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8690   -1.5864   -2.1617 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2498   -2.1266   -1.4987 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2045    1.3427   -1.0520 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3096   -0.1060   -0.8995 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6083    0.5953    0.5711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5665   -0.4132    1.5087 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8530    1.5875   -0.5464 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7242    1.6817    1.2843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5423    0.9849    1.3134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1436    1.7847   -0.2114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5302   -0.1105   -2.3301 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1358   -0.9389   -2.3607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0263    0.8321   -2.1833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1168   -1.7636   -0.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5866   -0.0370    0.0553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6861   -1.1058    1.1815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5824   -2.1174    0.1823 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  3
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6 14  1  0
 14 13  1  0
 13 10  1  0
 10 11  1  6
 10 12  1  0
 10  9  1  0
  9  7  1  0
  7  8  2  0
 14 15  2  0
 15  4  1  0
  7  6  1  0
  3 18  1  0
  3 19  1  0
  3 20  1  0
  1 16  1  0
  1 17  1  0
  4 21  1  1
  5 22  1  0
  5 23  1  0
 13 32  1  0
 11 26  1  0
 11 27  1  0
 11 28  1  0
 12 29  1  0
 12 30  1  0
 12 31  1  0
  9 24  1  0
  9 25  1  0
M  END


  Mrv1652304282200442D          

 15 16  0  0  1  0            999 V2000
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    0.8085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    2.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1768    1.9642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7895    2.6351    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
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  5  9  1  0  0  0  0
  8 10  1  6  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  6 13  1  0  0  0  0
  1 13  1  0  0  0  0
  1 14  1  0  0  0  0
  1 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051339

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=C)[C@H]1CN2C(NC(C)(C)CC2=O)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C11H17N3O/c1-7(2)8-6-14-9(15)5-11(3,4)13-10(14)12-8/h8H,1,5-6H2,2-4H3,(H,12,13)/t8-/m1/s1

> <INCHI_KEY>
OWOGBGTWYNGTCR-MRVPVSSYSA-N

> <FORMULA>
C11H17N3O

> <MOLECULAR_WEIGHT>
207.277

> <EXACT_MASS>
207.137162179

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.020037281289845

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-7,7-dimethyl-2-(prop-1-en-2-yl)-2H,3H,5H,6H,7H,8H-imidazo[1,2-a]pyrimidin-5-one

> <ALOGPS_LOGP>
0.81

> <JCHEM_LOGP>
0.9179108280000002

> <ALOGPS_LOGS>
-1.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
6.510569818469502

> <JCHEM_POLAR_SURFACE_AREA>
44.7

> <JCHEM_REFRACTIVITY>
57.79889999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.99e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-7,7-dimethyl-2-(prop-1-en-2-yl)-2H,3H,6H,8H-imidazo[1,2-a]pyrimidin-5-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.924  -0.237   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       3.590   2.073   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.320   2.843   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.090   1.509   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.090   4.177   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.924   4.383   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       7.797   3.667   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.074   4.919   0.000  0.00  0.00           C+0
CONECT    1    2   13   14   15                                             
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    9                                                  
CONECT    6    5    7   13                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8    5                                                       
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    6    1                                                       
CONECT   14    1                                                            
CONECT   15    1                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₇N₃O

Average Mass

207.2770 Da

Monoisotopic Mass

207.13716 Da

IUPAC Name

(2S)-7,7-dimethyl-2-(prop-1-en-2-yl)-2H,3H,5H,6H,7H,8H-imidazo[1,2-a]pyrimidin-5-one

Traditional Name

(2S)-7,7-dimethyl-2-(prop-1-en-2-yl)-2H,3H,6H,8H-imidazo[1,2-a]pyrimidin-5-one

CAS Registry Number

Not Available

SMILES

CC(=C)[C@H]1CN2C(NC(C)(C)CC2=O)=N1

InChI Identifier

InChI=1S/C11H17N3O/c1-7(2)8-6-14-9(15)5-11(3,4)13-10(14)12-8/h8H,1,5-6H2,2-4H3,(H,12,13)/t8-/m1/s1

InChI Key

OWOGBGTWYNGTCR-MRVPVSSYSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Alchornea javanensis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Beta amino acids and derivatives

Alternative Parents

Substituents

Beta amino acid or derivatives
Imidazopyrimidinone
Imidazopyrimidine
1,3-diazinane
2-imidazoline
Guanidine
Azacycle
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Organopnictogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	0.81	ALOGPS
logP	0.92	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Basic)	6.51	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	44.7 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	57.8 m³·mol⁻¹	ChemAxon
Polarizability	23.02 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

Not Available

METLIN ID

Not Available

PubChem Compound

162849048

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Alchornine (NP0051339)

MOL for NP0051339 (Alchornine)

3D MOL for NP0051339 (Alchornine)

3D SDF for NP0051339 (Alchornine)

3D-SDF for NP0051339 (Alchornine)

PDB for NP0051339 (Alchornine)

3D PDB for NP0051339 (Alchornine)

SMILES for NP0051339 (Alchornine)

INCHI for NP0051339 (Alchornine)

Structure for NP0051339 (Alchornine)

3D Structure for NP0051339 (Alchornine)