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Showing NP-Card for tricine (NP0168727)

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Record Information
Version1.0
Created at2022-09-03 04:34:58 UTC
Updated at2022-09-03 04:34:59 UTC
NP-MRD IDNP0168727
Secondary Accession NumbersNone
Natural Product Identification
Common Nametricine
DescriptionN-tris(hydroxymethyl)methylglycine, also known as tricine, 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). N-tris(hydroxymethyl)methylglycine is a very strong basic compound (based on its pKa). tricine is found in Arnica acaulis and Arundo donax. A Good's buffer substance, pKa = 8.15 At 20 degreeC.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0168727 (tricine)


  Mrv1533004241511192D          

 12 11  0  0  0  0            999 V2000
    1.2375    3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.9059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
Download

3D MOL for NP0168727 (tricine)

     RDKit          3D

 25 24  0  0  0  0  0  0  0  0999 V2000
    3.0961    0.9381   -0.9546 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9214    0.3644    0.1411 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9842    0.2016    0.9968 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5937   -0.1395    0.5321 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6784    0.1903   -0.5166 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6760   -0.1755   -0.3554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9817   -1.6415   -0.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3861   -2.3325    0.7412 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3799    0.2999   -1.6450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1871    1.6811   -1.7006 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3332    0.5703    0.7761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3105    1.9488    0.5741 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6753    0.9129    1.2055 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6686   -1.2298    0.7326 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3363    0.3780    1.4963 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0524    0.0173   -1.4535 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6918   -2.0855   -1.2670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0959   -1.7319   -0.2159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9656   -3.0685    1.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4386    0.0215   -1.6573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8574   -0.1744   -2.4902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5233    1.9719   -2.6049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3935    0.2776    0.9029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8374    0.3878    1.7515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9486    2.4173    1.1429 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  9  1  0
  9 10  1  0
  6 11  1  0
 11 12  1  0
  6  5  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
  9 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  0
 11 24  1  0
 12 25  1  0
  5 16  1  0
  4 14  1  0
  4 15  1  0
  3 13  1  0
M  END
Download

3D SDF for NP0168727 (tricine)


  Mrv1533004241511192D          

 12 11  0  0  0  0            999 V2000
    1.2375    3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.9059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0168727

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC(CO)(CO)NCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO5/c8-2-6(3-9,4-10)7-1-5(11)12/h7-10H,1-4H2,(H,11,12)

> <INCHI_KEY>
SEQKRHFRPICQDD-UHFFFAOYSA-N

> <FORMULA>
C6H13NO5

> <MOLECULAR_WEIGHT>
179.172

> <EXACT_MASS>
179.079372523

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
16.910450457205638

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]amino}acetic acid

> <ALOGPS_LOGP>
-2.30

> <JCHEM_LOGP>
-5.245555093234138

> <ALOGPS_LOGS>
-0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.158074481205666

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.860765823940001

> <JCHEM_PKA_STRONGEST_BASIC>
7.614997963732533

> <JCHEM_POLAR_SURFACE_AREA>
110.02

> <JCHEM_REFRACTIVITY>
39.2147

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.61e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tricine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0168727 (tricine)

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PDB for NP0168727 (tricine)
HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  O   UNK     0       2.310   6.668   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.080   5.335   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.976   4.771   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.357   4.001   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.644   3.231   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.644   1.691   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       1.540   2.667   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    6    8                                             
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    7                                                       
CONECT    7    6                                                            
CONECT    8    3    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for NP0168727 (tricine)
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SMILES for NP0168727 (tricine)
OCC(CO)(CO)NCC(O)=O
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INCHI for NP0168727 (tricine)
InChI=1S/C6H13NO5/c8-2-6(3-9,4-10)7-1-5(11)12/h7-10H,1-4H2,(H,11,12)
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Synonyms
ValueSource
N-(Tri(hydroxymethyl)methyl)glycineChEBI
TricineChEBI
Chemical FormulaC6H13NO5
Average Mass179.1720 Da
Monoisotopic Mass179.07937 Da
IUPAC Name2-{[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]amino}acetic acid
Traditional Nametricine
CAS Registry NumberNot Available
SMILES
OCC(CO)(CO)NCC(O)=O
InChI Identifier
InChI=1S/C6H13NO5/c8-2-6(3-9,4-10)7-1-5(11)12/h7-10H,1-4H2,(H,11,12)
InChI KeySEQKRHFRPICQDD-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arnica acaulisLOTUS Database
Arundo donaxLOTUS Database
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
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Secondary amine
    • 

  • Organic nitrogen compound
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • 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-2.3ALOGPS
logP-5.2ChemAxon
logS-0.5ALOGPS
pKa (Strongest Acidic)2.86ChemAxon
pKa (Strongest Basic)7.61ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area110.02 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity39.21 m³·mol⁻¹ChemAxon
Polarizability16.91 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID39063  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]