Showing metabocard for Choline (MMDBc0000025)

Plant
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:27:37 UTC
Update Date2022-08-30 23:10:49 UTC
Metabolite IDMMDBc0000025
Metabolite Identification
Common NameCholine
DescriptionCholine is a basic constituent of lecithin that is found in many plants and animal organs. It is important as a precursor of acetylcholine, as a methyl donor in various metabolic processes, and in lipid metabolism. Choline is now considered to be an essential vitamin. While humans can synthesize small amounts (by converting phosphatidylethanolamine to phosphatidylcholine), it must be consumed in the diet to maintain health. Required levels are between 425 mg/day (female) and 550 mg/day (male). Milk, eggs, liver, and peanuts are especially rich in choline. Most choline is found in phospholipids, namely phosphatidylcholine or lecithin. Choline can be oxidized to form betaine, which is a methyl source for many reactions (i.e. conversion of homocysteine into methionine). Lack of sufficient amounts of choline in the diet can lead to a fatty liver condition and general liver damage. This arises from the lack of VLDL, which is necessary to transport fats away from the liver. Choline deficiency also leads to elevated serum levels of alanine amino transferase and is associated with increased incidence of liver cancer.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be2372758>

122
  Mrv1652309032023522D          

  7  6  0  0  0  0            999 V2000
    4.5080    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.0791    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6501   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7936    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
M  CHG  1   2   1
M  END
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3D MOL for #<Metabolite:0x0000560be2372758>

HMDB0000097
     RDKit          3D
Choline
 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.4031    0.0214    1.2788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4628    0.0424    0.1463 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.8765   -1.0353   -0.7290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6821    1.2950   -0.5260 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8453   -0.1173    0.6850 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8752   -0.5810   -0.3081 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0259    0.3013   -1.3728 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0649   -0.7542    1.9859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4254   -0.1387    0.8969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3445    1.0024    1.8098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5989   -2.0290   -0.3612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9997   -0.9770   -0.8069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5012   -0.8016   -1.7426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7890    2.1467    0.1928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6737    1.2269   -1.0404 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0518    1.5495   -1.2795 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1692    0.8249    1.1318 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7982   -0.8774    1.4915 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8586   -0.5886    0.2292 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7123   -1.6149   -0.6585 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4853    1.1048   -1.0230 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
M  CHG  1   2   1
M  END
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3D SDF for #<Metabolite:0x0000560be2372758>

122
  Mrv1652309032023522D          

  7  6  0  0  0  0            999 V2000
    4.5080    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.0791    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6501   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7936    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
M  CHG  1   2   1
M  END
> <DATABASE_ID>
MMDBc0000025

> <DATABASE_NAME>
MIME

> <SMILES>
C[N+](C)(C)CCO

> <INCHI_IDENTIFIER>
InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1

> <INCHI_KEY>
OEYIOHPDSNJKLS-UHFFFAOYSA-N

> <FORMULA>
C5H14NO

> <MOLECULAR_WEIGHT>
104.1708

> <EXACT_MASS>
104.107539075

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
12.56561305801337

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2-hydroxyethyl)trimethylazanium

> <ALOGPS_LOGP>
-3.59

> <JCHEM_LOGP>
-4.662269162805079

> <ALOGPS_LOGS>
-1.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.968714076810006

> <JCHEM_PKA_STRONGEST_BASIC>
-3.249884462803304

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
42.194

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.61e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
choline

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for #<Metabolite:0x0000560be2372758>

HMDB0000097
     RDKit          3D
Choline
 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.4031    0.0214    1.2788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4628    0.0424    0.1463 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.8765   -1.0353   -0.7290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6821    1.2950   -0.5260 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8453   -0.1173    0.6850 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8752   -0.5810   -0.3081 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0259    0.3013   -1.3728 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0649   -0.7542    1.9859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4254   -0.1387    0.8969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3445    1.0024    1.8098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5989   -2.0290   -0.3612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9997   -0.9770   -0.8069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5012   -0.8016   -1.7426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7890    2.1467    0.1928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6737    1.2269   -1.0404 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0518    1.5495   -1.2795 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1692    0.8249    1.1318 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7982   -0.8774    1.4915 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8586   -0.5886    0.2292 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7123   -1.6149   -0.6585 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4853    1.1048   -1.0230 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
M  CHG  1   2   1
M  END
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PDB for #<Metabolite:0x0000560be2372758>

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 122                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  O   UNK     0       8.415   0.770   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0       4.414   0.000   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0       5.748   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.080  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.184  -1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.081   0.000   0.000  0.00  0.00           C+0
CONECT    1    7                                                            
CONECT    2    3    4    5    6                                             
CONECT    3    2    7                                                       
CONECT    4    2                                                            
CONECT    5    2                                                            
CONECT    6    2                                                            
CONECT    7    1    3                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for #<Metabolite:0x0000560be2372758>

COMPND    HMDB0000097
HETATM    1  C1  UNL     1      -1.403   0.021   1.279  1.00  0.00           C  
HETATM    2  N1  UNL     1      -0.463   0.042   0.146  1.00  0.00           N1+
HETATM    3  C2  UNL     1      -0.876  -1.035  -0.729  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.682   1.295  -0.526  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.845  -0.117   0.685  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.875  -0.581  -0.308  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.026   0.301  -1.373  1.00  0.00           O  
HETATM    8  H1  UNL     1      -1.065  -0.754   1.986  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.425  -0.139   0.897  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.345   1.002   1.810  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.599  -2.029  -0.361  1.00  0.00           H  
HETATM   12  H5  UNL     1      -2.000  -0.977  -0.807  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.501  -0.802  -1.743  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.789   2.147   0.193  1.00  0.00           H  
HETATM   15  H8  UNL     1      -1.674   1.227  -1.040  1.00  0.00           H  
HETATM   16  H9  UNL     1       0.052   1.549  -1.280  1.00  0.00           H  
HETATM   17  H10 UNL     1       1.169   0.825   1.132  1.00  0.00           H  
HETATM   18  H11 UNL     1       0.798  -0.877   1.492  1.00  0.00           H  
HETATM   19  H12 UNL     1       2.859  -0.589   0.229  1.00  0.00           H  
HETATM   20  H13 UNL     1       1.712  -1.615  -0.659  1.00  0.00           H  
HETATM   21  H14 UNL     1       2.485   1.105  -1.023  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    4    5
CONECT    3   11   12   13
CONECT    4   14   15   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7   21
END
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SMILES for #<Metabolite:0x0000560be2372758>

C[N+](C)(C)CCO
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INCHI for #<Metabolite:0x0000560be2372758>

InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1
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Synonyms
ValueSource
BilineurineChEBI
CHOLINE ionChEBI
N,N,N-Trimethylethanol-ammoniumChEBI
N-TrimethylethanolamineChEBI
TrimethylethanolamineChEBI
Choline cationKegg
(2-Hydroxyethyl)trimethyl ammoniumHMDB
(2-Hydroxyethyl)trimethylammoniumHMDB
(beta-Hydroxyethyl)trimethylammoniumHMDB
2-Hydroxy-N,N,N-trimethyl-ethanaminiumHMDB
2-Hydroxy-N,N,N-trimethylethanaminiumHMDB
BiocolinaHMDB
BiocolineHMDB
CholinumHMDB
HepacholineHMDB
HormoclineHMDB
LipotrilHMDB
N,N,N-TrimethylethanolammoniumHMDB
NeocolinaHMDB
ParesanHMDB
Choline O-sulfateHMDB
Citrate, cholineHMDB
FagineHMDB
Hydroxide, cholineHMDB
VidineHMDB
BursineHMDB
Chloride, cholineHMDB
Choline chlorideHMDB
Choline citrateHMDB
Bitartrate, cholineHMDB
Choline bitartrateHMDB
Choline hydroxideHMDB
Choline O sulfateHMDB
O-Sulfate, cholineHMDB
Molecular FormulaC5H14NO
Average Mass104.1708
Monoisotopic Mass104.107539075
IUPAC Name(2-hydroxyethyl)trimethylazanium
Traditional Namecholine
CAS Registry Number62-49-7
SMILES
C[N+](C)(C)CCO
InChI Identifier
InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1
InChI KeyOEYIOHPDSNJKLS-UHFFFAOYSA-N