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Showing NP-Card for Glycylsarcosine (NP0333401)

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Record Information
Version2.0
Created at2024-06-10 18:45:10 UTC
Updated at2024-09-03 04:22:15 UTC
NP-MRD IDNP0333401
Natural Product DOIhttps://doi.org/10.57994/2793
Secondary Accession NumbersNone
Natural Product Identification
Common NameGlycylsarcosine
DescriptionGlycylsarcosine zwitterion, also known as glycyl-sarcosine, belongs to the class of organic compounds known as peptoid-peptide hybrids. Peptoid-peptide hybrids are compounds containing a peptoid-peptide backbone, which consists alternating amino acid and n-substituted amino acids linked to each other by a peptide bond. Glycylsarcosine was first documented in 1996 (PMID: 8843163). Glycylsarcosine zwitterion is a very strong basic compound (based on its pKa) (PMID: 9190878).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0333401 (Glycylsarcosine)


  Mrv1652310282019322D          

 10  9  0  0  0  0            999 V2000
    3.9039    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   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  2  0  0  0  0
  4  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
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3D MOL for NP0333401 (Glycylsarcosine)

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3D SDF for NP0333401 (Glycylsarcosine)

  Mrv1652310282019322D          

 10  9  0  0  0  0            999 V2000
    3.9039    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   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  2  0  0  0  0
  4  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333401

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN(CC(O)=O)C(=O)CN

> <INCHI_IDENTIFIER>
InChI=1S/C5H10N2O3/c1-7(3-5(9)10)4(8)2-6/h2-3,6H2,1H3,(H,9,10)

> <INCHI_KEY>
VYAMLSCELQQRAE-UHFFFAOYSA-N

> <FORMULA>
C5H10N2O3

> <MOLECULAR_WEIGHT>
146.146

> <EXACT_MASS>
146.06914219

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.802116211039422

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(2-amino-N-methylacetamido)acetic acid

> <ALOGPS_LOGP>
-2.85

> <JCHEM_LOGP>
-4.293664374749857

> <ALOGPS_LOGS>
0.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6557534509717686

> <JCHEM_PKA_STRONGEST_BASIC>
8.133035571866637

> <JCHEM_POLAR_SURFACE_AREA>
83.63000000000001

> <JCHEM_REFRACTIVITY>
33.7036

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.14e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2-amino-N-methylacetamido)acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0333401 (Glycylsarcosine)
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PDB for NP0333401 (Glycylsarcosine)
HEADER    PROTEIN                                 28-OCT-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-OCT-20         0                                  
HETATM    1  C   UNK     0       7.287   1.127   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       7.287   2.667   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      11.288   3.437   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0333401 (Glycylsarcosine)
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SMILES for NP0333401 (Glycylsarcosine)
CN(CC(O)=O)C(=O)CN
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INCHI for NP0333401 (Glycylsarcosine)
InChI=1S/C5H10N2O3/c1-7(3-5(9)10)4(8)2-6/h2-3,6H2,1H3,(H,9,10)
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View in JSmol
Synonyms
ValueSource
Gly-sar zwitterionChEBI
Glycyl-N-methylglycine zwitterionChEBI
Glycyl-sarcosineChEBI
Glycyl-sarcosine zwitterionChEBI
N-Glycyl-N-methylglycine zwitterionChEBI
N-Glycylsarcosine zwitterionChEBI
Gly-sarMeSH
Chemical FormulaC5H10N2O3
Average Mass146.1460 Da
Monoisotopic Mass146.06914 Da
IUPAC Name2-(2-amino-N-methylacetamido)acetic acid
Traditional Name(2-amino-N-methylacetamido)acetic acid
CAS Registry NumberNot Available
SMILES
CN(CC(O)=O)C(=O)CN
InChI Identifier
InChI=1S/C5H10N2O3/c1-7(3-5(9)10)4(8)2-6/h2-3,6H2,1H3,(H,9,10)
InChI KeyVYAMLSCELQQRAE-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-10View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-10View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-10View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-10View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-10View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as peptoid-peptide hybrids. Peptoid-peptide hybrids are compounds containing a peptoid-peptide backbone, which consists alternating amino acid and n-substituted amino acids linked to each other by a peptide bond.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassPeptidomimetics  
Sub ClassPeptoid-peptide hybrids  
Direct ParentPeptoid-peptide hybrids  
Alternative Parents
Substituents
  • Peptoid/peptide hybrid
    • 

  • Alpha-dipeptide
    • 

  • N-acyl-alpha-amino acid
    • 

  • N-acyl-alpha amino acid or derivatives
    • 

  • Alpha-amino acid amide
    • 

  • Alpha-amino acid or derivatives
    • 

  • Tertiary carboxylic acid amide
    • 

  • Amino acid or derivatives
    • 

  • Carboxamide group
    • 

  • Amino acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Organic oxygen compound
    • 

  • Primary amine
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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-2.8ALOGPS
logP-4.3ChemAxon
logS0.16ALOGPS
pKa (Strongest Acidic)3.66ChemAxon
pKa (Strongest Basic)8.13ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area83.63 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity33.7 m³·mol⁻¹ChemAxon
Polarizability13.8 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 ID84077  
KEGG Compound IDNot Available
BioCyc IDCPD0-1914  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound93131  
PDB IDNot Available
ChEBI ID155838  
Good Scents IDNot Available
References
General References
  1. Terada T, Saito H, Mukai M, Inui K: Characterization of stably transfected kidney epithelial cell line expressing rat H+/peptide cotransporter PEPT1: localization of PEPT1 and transport of beta-lactam antibiotics. J Pharmacol Exp Ther. 1997 Jun;281(3):1415-21. [PubMed:9190878  ] 
  2. Terada T, Saito H, Mukai M, Inui KI: Identification of the histidine residues involved in substrate recognition by a rat H+/peptide cotransporter, PEPT1. FEBS Lett. 1996 Sep 30;394(2):196-200. doi: 10.1016/0014-5793(96)00952-0. [PubMed:8843163  ]