Np mrd loader

Showing NP-Card for Agrocybin (NP0064652)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version1.0
Created at2022-04-28 08:50:53 UTC
Updated at2022-04-28 08:50:53 UTC
NP-MRD IDNP0064652
Secondary Accession NumbersNone
Natural Product Identification
Common NameAgrocybin
DescriptionAcetamide, also known as ethanamid or acetic acid amide, belongs to the class of organic compounds known as carboximidic acids. These are organic acids with the general formula RC(=N)-OH (R=H, organic group). Acetamide is an extremely weak basic (essentially neutral) compound (based on its pKa). On 30 July 2015, scientists reported that upon the first touchdown of the Philae lander on comet 67/P's surface, measurements by the COSAC and Ptolemy instruments revealed sixteen organic compounds, four of which – acetamide, acetone, methyl isocyanate, and propionaldehyde – were seen for the first time on a comet. Acetamide is a mousy tasting compound. Outside of the human body, Acetamide has been detected, but not quantified in, red beetroots. This could make acetamide a potential biomarker for the consumption of these foods. Acetamide is formally rated as a possible carcinogen (by IARC 2B) and is also a potentially toxic compound. It is the simplest amide derived from acetic acid. The related compound N,N-dimethylacetamide (DMA) is more widely used, but it is not prepared from acetamide. In a similar fashion to some laboratory methods, acetamide is produced by dehydrating ammonium acetate or via the hydration of acetonitrile, a byproduct of the production of acrylonitrile:CH3CN + H2O → CH3C(O)NH2A precursor to thioacetamideAcetamide has been detected near the center of the Milky Way galaxy. Acetamide can be considered an intermediate between acetone, which has two methyl (CH3) groups either side of the carbonyl (CO), and urea which has two amide (NH2) groups in those locations. Yield is typically low (up to 35%), and the acetamide made this way is generated as a salt with HCl. It finds some use as a plasticizer and as an industrial solvent. Acetamide (systematic name: Ethanamide) is an organic compound with the formula CH3CONH2. Acetamide can be produced in the laboratory from ammonium acetate by dehydration:[NH4][CH3CO2] → CH3C(O)NH2 + H2OAlternatively acetamide can be obtained in excellent yield via ammonolysis of acetylacetone under conditions commonly used in reductive amination. It can also be made from anhydrous acetic acid, acetonitrile and very well dried hydrogen chloride gas, using an ice bath, alongside more valuable reagent acetyl chloride. This finding lends support to the theory that organic molecules that can lead to life (as we know it on Earth) can form in space. Agrocybin is found in Marasmius oreades . It was first documented in 1997 (PMID: 9550095). This finding is potentially significant because acetamide has an amide bond, similar to the essential bond between amino acids in proteins (PMID: 20452462) (PMID: 14965292).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0064652 (Agrocybin)


  Mrv1652303252018052D          

  4  3  0  0  0  0            999 V2000
    1.3332   -0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957   -0.6187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    0.6187    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
  2  4  2  0  0  0  0
M  END
Download

3D MOL for NP0064652 (Agrocybin)

     RDKit          3D

  9  8  0  0  0  0  0  0  0  0999 V2000
   -1.0966   -0.0812    0.2784 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1894    0.4973   -0.2299 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3728   -0.2698   -0.1991 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2139    1.6716   -0.6858 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0018   -1.1678    0.3248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9361    0.1512   -0.4023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3451    0.2967    1.2928 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0491   -0.1403    0.5649 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5544   -0.9577   -0.9440 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  0
  1  5  1  0
  1  6  1  0
  1  7  1  0
  3  8  1  0
  3  9  1  0
M  END
Download

3D SDF for NP0064652 (Agrocybin)


  Mrv1652303252018052D          

  4  3  0  0  0  0            999 V2000
    1.3332   -0.6187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957   -0.6187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    0.6187    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
  2  4  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0064652

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(N)=O

> <INCHI_IDENTIFIER>
InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)

> <INCHI_KEY>
DLFVBJFMPXGRIB-UHFFFAOYSA-N

> <FORMULA>
C2H5NO

> <MOLECULAR_WEIGHT>
59.0672

> <EXACT_MASS>
59.037113787

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
5.756158253961428

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
acetamide

> <ALOGPS_LOGP>
-1.10

> <JCHEM_LOGP>
-1.030288328

> <ALOGPS_LOGS>
0.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.74512898335727

> <JCHEM_PKA_STRONGEST_BASIC>
-1.4048213434597656

> <JCHEM_POLAR_SURFACE_AREA>
43.09

> <JCHEM_REFRACTIVITY>
14.4659

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.69e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
acetamide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0064652 (Agrocybin)

Download
PDB for NP0064652 (Agrocybin)
HEADER    PROTEIN                                 25-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAR-20         0                                  
HETATM    1  C   UNK     0       2.489  -1.155   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.155  -0.385   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.179  -1.155   0.000  0.00  0.00           N+0
HETATM    4  O   UNK     0       1.155   1.155   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END

Download
3D PDB for NP0064652 (Agrocybin)
Download
SMILES for NP0064652 (Agrocybin)
CC(N)=O
Download
INCHI for NP0064652 (Agrocybin)
InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)
Download
View in JSmol
Synonyms
ValueSource
AcetamidChEBI
Acetic acid amideChEBI
AzetamidChEBI
CH3CONH2ChEBI
EssigsaeureamidChEBI
EthanamidChEBI
EthanamideChEBI
MethanecarboxamideChEBI
Acetate amideGenerator
Acetimidic acidHMDB
ACMHMDB
Amid kyseliny octoveHMDB
Acetamide, monosodium saltHMDB
Chemical FormulaC2H5NO
Average Mass59.0672 Da
Monoisotopic Mass59.03711 Da
IUPAC Nameacetamide
Traditional Nameacetamide
CAS Registry NumberNot Available
SMILES
CC(N)=O
InChI Identifier
InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)
InChI KeyDLFVBJFMPXGRIB-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 90 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50.18 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
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
Marasmius oreadesFungi
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carboximidic acids. These are organic acids with the general formula RC(=N)-OH (R=H, organic group).
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboximidic acids and derivatives  
Sub ClassCarboximidic acids  
Direct ParentCarboximidic acids  
Alternative Parents
Substituents
  • Carboximidic acid
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • 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-1.1ALOGPS
logP-1ChemAxon
logS0.8ALOGPS
pKa (Strongest Acidic)16.75ChemAxon
pKa (Strongest Basic)-1.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area43.09 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity14.47 m³·mol⁻¹ChemAxon
Polarizability5.76 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0031645  
DrugBank IDDB02736  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB008298  
KNApSAcK IDNot Available
Chemspider ID173  
KEGG Compound IDC06244  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAcetamide  
METLIN IDNot Available
PubChem Compound178  
PDB IDNot Available
ChEBI ID27856  
Good Scents IDNot Available
References
General References
  1. Yalcin I, Kaymakcioglu BK, Oren I, Sener E, Temiz O, Akin A, Altanlar N: Synthesis and microbiological activity of some novel N-(2-hydroxyl-5-substitutedphenyl)benzacetamides, phenoxyacetamides and thiophenoxyacetamides as the possible metabolites of antimicrobial active benzoxazoles. Farmaco. 1997 Nov;52(11):685-9. [PubMed:9550095  ] 
  2. Jawed H, Shah SU, Jamall S, Simjee SU: N-(2-hydroxy phenyl) acetamide inhibits inflammation-related cytokines and ROS in adjuvant-induced arthritic (AIA) rats. Int Immunopharmacol. 2010 Aug;10(8):900-5. doi: 10.1016/j.intimp.2010.04.028. Epub 2010 May 7. [PubMed:20452462  ] 
  3. Muri EM, Williamson JS: Anti-Helicobacter pylori agents. An update. Mini Rev Med Chem. 2004 Feb;4(2):201-6. [PubMed:14965292  ]