Np mrd loader

Showing NP-Card for Vinylacetylglycine (NP0000917)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:19:21 UTC
NP-MRD IDNP0000917
Secondary Accession NumbersNone
Natural Product Identification
Common NameVinylacetylglycine
DescriptionVinylacetylglycine is an acyl glycine. Acyl glycines are normally minor metabolites of fatty acids. However, the excretion of certain acyl glycines is increased in several inborn errors of metabolism. In certain cases the measurement of these metabolites in body fluids can be used to diagnose disorders associated with mitochondrial fatty acid beta-oxidation. Acyl glycines are produced through the action of glycine N-acyltransferase (EC 2.3.1.13) Which is an enzyme that catalyzes the chemical reaction:. Acyl-CoA + glycine < -- > CoA + N-acylglycine. Vinylacetylglycine is a human metabolite that had been identified in a GC/MS urine screen. Increased amounts of this metabolite in the urine has been linked to a metabolomic disorder termed Isovaleric acidemia. (Gas-Chromatographic Method of Analysis for Urinary Organic Acids. I. Retention indices of 155 metaboically Important Compounds; Kay Tanaka, David G. Hine, Agnes West-Dull, and Theodore B. Lynn.).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000917 (Vinylacetylglycine)


  Mrv1652305271900322D          

 10  9  0  0  0  0            999 V2000
   11.8201   -7.4041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.4076   -6.6896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8201   -5.9752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5826   -6.6896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1701   -5.9752    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.3451   -5.9752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9326   -5.2607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9326   -6.6896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1076   -6.6896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6951   -7.4042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
M  END
Download

3D MOL for NP0000917 (Vinylacetylglycine)

HMDB0000894
     RDKit          3D
Vinylacetylglycine
 19 18  0  0  0  0  0  0  0  0999 V2000
   -3.8109   -0.4124   -0.3141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6955   -1.1103   -0.1496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5705   -0.4999    0.6097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3494   -0.3842   -0.2051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3583   -0.7800   -1.3830 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8168    0.1722    0.3532 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0260    0.2916   -0.4394 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1315    0.8967    0.3230 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9378    1.2301    1.5066 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3588    1.0900   -0.2653 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9185    0.5854    0.0902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6324   -0.8316   -0.8567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5456   -2.1026   -0.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8205    0.4942    1.0162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3373   -1.1648    1.4834 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8358    0.5074    1.3399 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8349    0.8029   -1.4012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3126   -0.7631   -0.7094 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7847    1.9784   -0.4650 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
 10 19  1  0
M  END
Download

3D SDF for NP0000917 (Vinylacetylglycine)


  Mrv1652305271900322D          

 10  9  0  0  0  0            999 V2000
   11.8201   -7.4041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.4076   -6.6896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8201   -5.9752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5826   -6.6896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1701   -5.9752    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.3451   -5.9752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9326   -5.2607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9326   -6.6896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1076   -6.6896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6951   -7.4042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0000917

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CNC(=O)CC=C

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO3/c1-2-3-5(8)7-4-6(9)10/h2H,1,3-4H2,(H,7,8)(H,9,10)

> <INCHI_KEY>
UKISAGFGRDHYFO-UHFFFAOYSA-N

> <FORMULA>
C6H9NO3

> <MOLECULAR_WEIGHT>
143.1406

> <EXACT_MASS>
143.058243159

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
13.804168011765078

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(but-3-enamido)acetic acid

> <ALOGPS_LOGP>
-0.48

> <JCHEM_LOGP>
-0.4875124283333333

> <ALOGPS_LOGS>
-0.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.659456232820723

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9791898794746783

> <JCHEM_PKA_STRONGEST_BASIC>
-2.4457501550632674

> <JCHEM_POLAR_SURFACE_AREA>
66.4

> <JCHEM_REFRACTIVITY>
34.7192

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.53e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
but-3-enamidoacetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000917 (Vinylacetylglycine)

HMDB0000894
     RDKit          3D
Vinylacetylglycine
 19 18  0  0  0  0  0  0  0  0999 V2000
   -3.8109   -0.4124   -0.3141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6955   -1.1103   -0.1496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5705   -0.4999    0.6097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3494   -0.3842   -0.2051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3583   -0.7800   -1.3830 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8168    0.1722    0.3532 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0260    0.2916   -0.4394 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1315    0.8967    0.3230 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9378    1.2301    1.5066 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3588    1.0900   -0.2653 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9185    0.5854    0.0902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6324   -0.8316   -0.8567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5456   -2.1026   -0.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8205    0.4942    1.0162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3373   -1.1648    1.4834 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8358    0.5074    1.3399 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8349    0.8029   -1.4012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3126   -0.7631   -0.7094 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7847    1.9784   -0.4650 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
 10 19  1  0
M  END
Download

PDB for NP0000917 (Vinylacetylglycine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      22.064 -13.821   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      21.294 -12.487   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      22.064 -11.154   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      19.754 -12.487   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      18.984 -11.154   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      17.444 -11.154   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      16.674  -9.820   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      16.674 -12.487   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      15.134 -12.487   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.364 -13.821   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
Download

3D PDB for NP0000917 (Vinylacetylglycine)

COMPND    HMDB0000894
HETATM    1  C1  UNL     1      -3.811  -0.412  -0.314  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.695  -1.110  -0.150  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.571  -0.500   0.610  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.349  -0.384  -0.205  1.00  0.00           C  
HETATM    5  O1  UNL     1      -0.358  -0.780  -1.383  1.00  0.00           O  
HETATM    6  N1  UNL     1       0.817   0.172   0.353  1.00  0.00           N  
HETATM    7  C5  UNL     1       2.026   0.292  -0.439  1.00  0.00           C  
HETATM    8  C6  UNL     1       3.131   0.897   0.323  1.00  0.00           C  
HETATM    9  O2  UNL     1       2.938   1.230   1.507  1.00  0.00           O  
HETATM   10  O3  UNL     1       4.359   1.090  -0.265  1.00  0.00           O  
HETATM   11  H1  UNL     1      -3.919   0.585   0.090  1.00  0.00           H  
HETATM   12  H2  UNL     1      -4.632  -0.832  -0.857  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.546  -2.103  -0.533  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.821   0.494   1.016  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.337  -1.165   1.483  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.836   0.507   1.340  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.835   0.803  -1.401  1.00  0.00           H  
HETATM   18  H8  UNL     1       2.313  -0.763  -0.709  1.00  0.00           H  
HETATM   19  H9  UNL     1       4.785   1.978  -0.465  1.00  0.00           H  
CONECT    1    2    2   11   12
CONECT    2    3   13
CONECT    3    4   14   15
CONECT    4    5    5    6
CONECT    6    7   16
CONECT    7    8   17   18
CONECT    8    9    9   10
CONECT   10   19
END
Download

SMILES for NP0000917 (Vinylacetylglycine)

OC(=O)CNC(=O)CC=C
Download

INCHI for NP0000917 (Vinylacetylglycine)

InChI=1S/C6H9NO3/c1-2-3-5(8)7-4-6(9)10/h2H,1,3-4H2,(H,7,8)(H,9,10)
Download
View in JSmol
Synonyms
ValueSource
2-(But-3-enamido)acetic acidChEBI
2-(But-3-enamido)acetateGenerator
Chemical FormulaC6H9NO3
Average Mass143.1406 Da
Monoisotopic Mass143.05824 Da
IUPAC Name2-(but-3-enamido)acetic acid
Traditional Namebut-3-enamidoacetic acid
CAS Registry Number73122-61-9
SMILES
OC(=O)CNC(=O)CC=C
InChI Identifier
InChI=1S/C6H9NO3/c1-2-3-5(8)7-4-6(9)10/h2H,1,3-4H2,(H,7,8)(H,9,10)
InChI KeyUKISAGFGRDHYFO-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
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
Trypanosoma bruceiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as n-acyl-alpha amino acids. N-acyl-alpha amino acids are compounds containing an alpha amino acid which bears an acyl group at its terminal nitrogen atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentN-acyl-alpha amino acids
Alternative Parents
Substituents
  • N-acyl-alpha-amino acid
  • N-acyl-amine
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility55.3 g/LALOGPS
logP-0.48ALOGPS
logP-0.49ChemAxon
logS-0.41ALOGPS
pKa (Strongest Acidic)3.98ChemAxon
pKa (Strongest Basic)-2.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.4 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity34.72 m³·mol⁻¹ChemAxon
Polarizability13.8 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000894
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022303
KNApSAcK IDNot Available
Chemspider ID27976741
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5851
PubChem Compound53477718
PDB IDNot Available
ChEBI ID74435
Good Scents IDNot Available
References
General References
  1. Bao W, Cao C, Li S, Bo L, Zhang M, Zhao X, Liu Y, Sun C: Metabonomic analysis of quercetin against the toxicity of acrylamide in rat urine. Food Funct. 2017 Mar 22;8(3):1204-1214. doi: 10.1039/c6fo01553k. [PubMed:28224155 ]
  2. Shi H, Hu L, Chen S, Bao W, Yang S, Zhao X, Sun C: Metabolomics analysis of urine from rats administered with long-term, low-dose acrylamide by ultra-performance liquid chromatography-mass spectrometry. Xenobiotica. 2017 May;47(5):439-449. doi: 10.1080/00498254.2016.1196509. Epub 2016 Jun 27. [PubMed:27347750 ]