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Showing metabocard for Bicine (HMDB0011727)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-03-02 17:03:43 UTC
Update Date2023-02-21 17:17:34 UTC
HMDB IDHMDB0011727
Secondary Accession Numbers
  • HMDB11727
Metabolite Identification
Common NameBicine
DescriptionBicine, also known as bicine buffer, belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Bicine has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make bicine a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on Bicine.
Structure
Data?1676999854
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011727 (Bicine)

  Mrv0541 02231217082D          

 11 10  0  0  0  0            999 V2000
    1.4289   -4.7289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -3.9039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.0164    0.0000 O   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
Download

3D MOL for HMDB0011727 (Bicine)

HMDB0011727
     RDKit          3D
Bicine
 24 23  0  0  0  0  0  0  0  0999 V2000
   -0.0834   -2.9025    0.8822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0832   -2.3499    0.3854 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2759   -3.1246    0.2724 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1766   -0.9696   -0.1082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0021   -0.2454   -0.0912 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0070    1.0925   -0.5356 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7419    2.0830    0.3411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0883    1.7980    0.5042 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1773   -0.8646    0.2852 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4188    0.0227    0.1717 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3211    1.1555    0.9757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1286   -2.6121    0.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6515   -1.0442   -1.1497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0350   -0.4872    0.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9580    1.5173   -0.8373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6236    1.0913   -1.4981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5562    3.1169   -0.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2504    2.0410    1.3470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6785    2.1845   -0.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2162   -1.2188    1.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4013   -1.7395   -0.3533 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7294    0.2040   -0.8550 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2483   -0.6016    0.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9118    1.8533    0.5869 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
 10 23  1  0
 11 24  1  0
M  END
Download

3D SDF for HMDB0011727 (Bicine)

  Mrv0541 02231217082D          

 11 10  0  0  0  0            999 V2000
    1.4289   -4.7289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -3.9039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.0164    0.0000 O   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0011727

> <DATABASE_NAME>
hmdb

> <SMILES>
OCCN(CCO)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO4/c8-3-1-7(2-4-9)5-6(10)11/h8-9H,1-5H2,(H,10,11)

> <INCHI_KEY>
FSVCELGFZIQNCK-UHFFFAOYSA-N

> <FORMULA>
C6H13NO4

> <MOLECULAR_WEIGHT>
163.1717

> <EXACT_MASS>
163.084457909

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
16.302256020934824

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[bis(2-hydroxyethyl)amino]acetic acid

> <ALOGPS_LOGP>
-1.59

> <JCHEM_LOGP>
-4.370789566354051

> <ALOGPS_LOGS>
0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.292874213693011

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.006581234167075

> <JCHEM_PKA_STRONGEST_BASIC>
7.662486357739335

> <JCHEM_POLAR_SURFACE_AREA>
81

> <JCHEM_REFRACTIVITY>
38.6573

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.82e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
bicine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0011727 (Bicine)

HMDB0011727
     RDKit          3D
Bicine
 24 23  0  0  0  0  0  0  0  0999 V2000
   -0.0834   -2.9025    0.8822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0832   -2.3499    0.3854 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2759   -3.1246    0.2724 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1766   -0.9696   -0.1082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0021   -0.2454   -0.0912 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0070    1.0925   -0.5356 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7419    2.0830    0.3411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0883    1.7980    0.5042 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1773   -0.8646    0.2852 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4188    0.0227    0.1717 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3211    1.1555    0.9757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1286   -2.6121    0.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6515   -1.0442   -1.1497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0350   -0.4872    0.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9580    1.5173   -0.8373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6236    1.0913   -1.4981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5562    3.1169   -0.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2504    2.0410    1.3470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6785    2.1845   -0.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2162   -1.2188    1.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4013   -1.7395   -0.3533 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7294    0.2040   -0.8550 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2483   -0.6016    0.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9118    1.8533    0.5869 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
 10 23  1  0
 11 24  1  0
M  END
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PDB for HMDB0011727 (Bicine)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       2.667  -8.827   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667  -7.287   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -6.517   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.334  -4.977   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.000  -4.207   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.334  -1.897   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667  -4.207   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -2.667   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334  -1.897   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001  -1.897   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    4    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0011727 (Bicine)

COMPND    HMDB0011727
HETATM    1  O1  UNL     1      -0.083  -2.902   0.882  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.083  -2.350   0.385  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.276  -3.125   0.272  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.177  -0.970  -0.108  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.002  -0.245  -0.091  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.007   1.092  -0.536  1.00  0.00           C  
HETATM    7  C4  UNL     1      -0.742   2.083   0.341  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.088   1.798   0.504  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.177  -0.865   0.285  1.00  0.00           C  
HETATM   10  C6  UNL     1       2.419   0.023   0.172  1.00  0.00           C  
HETATM   11  O4  UNL     1       2.321   1.156   0.976  1.00  0.00           O  
HETATM   12  H1  UNL     1      -3.129  -2.612   0.148  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.652  -1.044  -1.150  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.035  -0.487   0.470  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.958   1.517  -0.837  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.624   1.091  -1.498  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.556   3.117  -0.023  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.250   2.041   1.347  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.679   2.184  -0.196  1.00  0.00           H  
HETATM   20  H9  UNL     1       1.216  -1.219   1.348  1.00  0.00           H  
HETATM   21  H10 UNL     1       1.401  -1.739  -0.353  1.00  0.00           H  
HETATM   22  H11 UNL     1       2.729   0.204  -0.855  1.00  0.00           H  
HETATM   23  H12 UNL     1       3.248  -0.602   0.625  1.00  0.00           H  
HETATM   24  H13 UNL     1       2.912   1.853   0.587  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5   13   14
CONECT    5    6    9
CONECT    6    7   15   16
CONECT    7    8   17   18
CONECT    8   19
CONECT    9   10   20   21
CONECT   10   11   22   23
CONECT   11   24
END
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SMILES for HMDB0011727 (Bicine)

OCCN(CCO)CC(O)=O
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INCHI for HMDB0011727 (Bicine)

InChI=1S/C6H13NO4/c8-3-1-7(2-4-9)5-6(10)11/h8-9H,1-5H2,(H,10,11)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H13NO4
Average Molecular Weight163.1717
Monoisotopic Molecular Weight163.084457909
IUPAC Name2-[bis(2-hydroxyethyl)amino]acetic acid
Traditional Namebicine
CAS Registry Number150-25-4
SMILES
OCCN(CCO)CC(O)=O
InChI Identifier
InChI=1S/C6H13NO4/c8-3-1-7(2-4-9)5-6(10)11/h8-9H,1-5H2,(H,10,11)
InChI KeyFSVCELGFZIQNCK-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • 1,2-aminoalcohol
  • Amino acid
  • Tertiary aliphatic amine
  • Tertiary amine
  • Alkanolamine
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Amine
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility351500 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Prostate
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03709
Phenol Explorer Compound IDNot Available
FooDB IDFDB028408
KNApSAcK IDC00024831
Chemspider ID8431
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkBicine
METLIN IDNot Available
PubChem Compound8761
PDB IDBCN
ChEBI ID39066
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1223361
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]