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Showing NP-Card for Bicine (NP0091576)

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Record Information
Version1.0
Created at2022-05-11 18:41:44 UTC
Updated at2022-05-11 18:41:44 UTC
NP-MRD IDNP0091576
Secondary Accession NumbersNone
Natural Product Identification
Common NameBicine
DescriptionBicine, also known as bicine buffer or bicene, 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). A bicine that is amino acetate in which the nitrogen atom is substituted by 2 (2-hydroxyethyl)- groups. It was first documented in 2009 (PMID: 19212411). Bicine is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0091576 (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 NP0091576 (Bicine)

     RDKit          3D

 24 23  0  0  0  0  0  0  0  0999 V2000
    1.0115   -1.9853    1.7669 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6406   -1.5809    0.7867 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8307   -2.3196    0.5262 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2938   -0.4665   -0.0950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0478    0.0997    0.1829 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9435   -0.9608   -0.2749 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3927   -0.6640   -0.0448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1820   -1.7151   -0.4978 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1609    1.2819   -0.6078 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4199    2.4747    0.0735 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7491    2.4211    0.3973 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6253   -1.9078    0.1093 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0340    0.3165    0.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3287   -0.7711   -1.1739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6981   -1.8772    0.2865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7140   -1.1714   -1.3396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6448    0.2378   -0.6507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6379   -0.4994    1.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7672   -2.0341    0.2330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1679    1.5560   -0.9673 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4330    1.1404   -1.5667 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2947    3.4038   -0.5773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1812    2.7602    0.9924 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8768    2.2611    1.3857 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  8 19  1  0
  7 17  1  0
  7 18  1  0
  6 15  1  0
  6 16  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
 10 23  1  0
 11 24  1  0
  4 13  1  0
  4 14  1  0
  3 12  1  0
M  END
Download

3D SDF for NP0091576 (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>
NP0091576

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
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3D-SDF for NP0091576 (Bicine)

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PDB for NP0091576 (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 NP0091576 (Bicine)
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SMILES for NP0091576 (Bicine)
OCCN(CCO)CC(O)=O
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INCHI for NP0091576 (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 JSmol
Synonyms
ValueSource
Bicine bufferChEBI
BiceneHMDB
Bis(2-hydroxyethyl)glycineHMDB
Diethanol glycineHMDB
DiethylolglycineHMDB
DihydroxyethylglycineHMDB
N,N-(2-Dihydroxyethyl)glycineHMDB
N,N-(2-Hydroxyethyl)glycineHMDB
N,N-Bis(2-hydroxyethyl)-glycineHMDB
N,N-Bis(2-hydroxyethyl)glycineHMDB
N,N-Bis(2-hydroxyethyl)glycine]HMDB
N,N-Bis(beta-hydroxyethyl)glycineHMDB
N,N-Bis(hydroxyethyl)glycineHMDB
N,N-Di(2-hydroxyethyl)glycineHMDB
N,N-Dihydroxyethyl glycineHMDB
N,N-DihydroxyethylglycineHMDB
N,N-Bis(2-hydroxyethyl)glycine, monosodium saltHMDB
N,N-Bis(2-hydroxyethyl)glycine, sodium saltHMDB
[Bis(2-hydroxyethyl)ammonio]acetic acidHMDB
BICINEMeSH
Chemical FormulaC6H13NO4
Average Mass163.1717 Da
Monoisotopic Mass163.08446 Da
IUPAC Name2-[bis(2-hydroxyethyl)amino]acetic acid
Traditional Namebicine
CAS Registry NumberNot Available
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
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.6ALOGPS
logP-4.4ChemAxon
logS0.05ALOGPS
pKa (Strongest Acidic)3.01ChemAxon
pKa (Strongest Basic)7.66ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area81 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity38.66 m³·mol⁻¹ChemAxon
Polarizability16.3 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0011727  
DrugBank IDDB03709  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB028408  
KNApSAcK IDNot Available
Chemspider ID8431  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkBicine  
METLIN IDNot Available
PubChem Compound8761  
PDB IDBCN  
ChEBI ID39066  
Good Scents IDNot Available
References
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  ]