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Showing NP-Card for 3-Amino-2-piperidone (NP0083862)

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Record Information
Version2.0
Created at2022-04-29 04:46:22 UTC
Updated at2022-04-29 04:46:22 UTC
NP-MRD IDNP0083862
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Amino-2-piperidone
Description3-Amino-2-piperidone, also known as cyclo-ornithine or 3-aminopiperidine-2-one, belongs to the class of organic compounds known as alpha amino acid amides. These are amide derivatives of alpha amino acids. 3-Amino-2-piperidone is a very strong basic compound (based on its pKa). A delta-lactam that is 2-piperidone substituted at position 3 by an amino group. 3-Amino-2-piperidone is found in Arabidopsis thaliana and Phoma medicaginis. 3-Amino-2-piperidone was first documented in 1978 (PMID: 679477). 3-Amino-2-piperidone exists in all living organisms, ranging from bacteria to humans (PMID: 6188612) (PMID: 491962).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0083862 (3-Amino-2-piperidone)


  Mrv0541 02231218272D          

  8  8  0  0  0  0            999 V2000
   10.4095  -10.7760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8385  -10.7760    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.4095   -9.1260    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.8385   -9.1260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1240   -9.5385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5530   -9.5385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5530  -10.3635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1240  -10.3635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  2  0  0  0  0
  2  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  5  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
Download

3D MOL for NP0083862 (3-Amino-2-piperidone)

     RDKit          3D

 18 18  0  0  0  0  0  0  0  0999 V2000
   -2.3833    0.1991    0.1604 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0657   -0.0511    0.6890 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3476   -1.0382   -0.2309 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1146   -0.9820    0.1793 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6907    0.2081   -0.6024 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8625    1.3516   -0.2182 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2433    1.1991    0.6612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5233    2.1456    1.4265 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2775    0.9153   -0.5933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7248   -0.7297   -0.2242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0902   -0.5115    1.6826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4884   -0.6642   -1.2660 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7718   -2.0374   -0.1649 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2156   -0.6973    1.2568 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6644   -1.9004   -0.0671 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4872   -0.0433   -1.6739 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7489    0.3633   -0.3893 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1321    2.2731   -0.6258 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  2  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  1
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
Download

3D SDF for NP0083862 (3-Amino-2-piperidone)


  Mrv0541 02231218272D          

  8  8  0  0  0  0            999 V2000
   10.4095  -10.7760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8385  -10.7760    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.4095   -9.1260    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.8385   -9.1260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1240   -9.5385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5530   -9.5385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5530  -10.3635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1240  -10.3635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  2  0  0  0  0
  2  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  5  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0083862

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1CCCNC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10N2O/c6-4-2-1-3-7-5(4)8/h4H,1-3,6H2,(H,7,8)

> <INCHI_KEY>
YCCMTCQQDULIFE-UHFFFAOYSA-N

> <FORMULA>
C5H10N2O

> <MOLECULAR_WEIGHT>
114.1457

> <EXACT_MASS>
114.079312952

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
11.833530425102632

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-aminopiperidin-2-one

> <ALOGPS_LOGP>
-1.34

> <JCHEM_LOGP>
-1.1129883506666665

> <ALOGPS_LOGS>
0.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.551320100513177

> <JCHEM_PKA_STRONGEST_BASIC>
8.438548999200513

> <JCHEM_POLAR_SURFACE_AREA>
55.120000000000005

> <JCHEM_REFRACTIVITY>
30.008599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.44e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-amino-2-piperidone

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0083862 (3-Amino-2-piperidone)

Download
PDB for NP0083862 (3-Amino-2-piperidone)
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      19.431 -20.115   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0      22.099 -20.115   0.000  0.00  0.00           N+0
HETATM    3  N   UNK     0      19.431 -17.035   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      22.099 -17.035   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      20.765 -17.805   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      23.432 -17.805   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      23.432 -19.345   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      20.765 -19.345   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    7    8                                                       
CONECT    3    5                                                            
CONECT    4    5    6                                                       
CONECT    5    3    4    8                                                  
CONECT    6    4    7                                                       
CONECT    7    2    6                                                       
CONECT    8    1    2    5                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

Download
3D PDB for NP0083862 (3-Amino-2-piperidone)
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SMILES for NP0083862 (3-Amino-2-piperidone)
NC1CCCNC1=O
Download
INCHI for NP0083862 (3-Amino-2-piperidone)
InChI=1S/C5H10N2O/c6-4-2-1-3-7-5(4)8/h4H,1-3,6H2,(H,7,8)
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View in JSmol
Synonyms
ValueSource
Cyclo-ornithineChEBI
(+)-3-Aminopiperidin-2-oneHMDB
(R)-(+)-3-Amino-2-piperidinonHMDB
(S)-(-)-3-Amino-2-piperidinonHMDB
(S)-3-Amino-2-piperidinonHMDB
3-Amino-2-piperidinoneHMDB
Ornithine N5-lactamHMDB
3-Aminopiperidine-2-oneHMDB
3-Amino-2-piperidoneChEBI
Chemical FormulaC5H10N2O
Average Mass114.1457 Da
Monoisotopic Mass114.07931 Da
IUPAC Name3-aminopiperidin-2-one
Traditional Name3-amino-2-piperidone
CAS Registry NumberNot Available
SMILES
NC1CCCNC1=O
InChI Identifier
InChI=1S/C5H10N2O/c6-4-2-1-3-7-5(4)8/h4H,1-3,6H2,(H,7,8)
InChI KeyYCCMTCQQDULIFE-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
Arabidopsis thalianaLOTUS Database
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
Phoma medicaginisFungi
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acid amides. These are amide derivatives of alpha amino acids.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acid amides  
Alternative Parents
Substituents
  • Alpha-amino acid amide
    • 

  • 3-aminopiperidine
    • 

  • Delta-lactam
    • 

  • Piperidinone
    • 

  • Piperidine
    • 

  • Carboxamide group
    • 

  • Lactam
    • 

  • Secondary carboxylic acid amide
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • Primary amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-1.3ALOGPS
logP-1.1ChemAxon
logS0.59ALOGPS
pKa (Strongest Acidic)14.55ChemAxon
pKa (Strongest Basic)8.44ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area55.12 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.01 m³·mol⁻¹ChemAxon
Polarizability11.83 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000323  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021949  
KNApSAcK IDNot Available
Chemspider ID4371576  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5312  
PubChem Compound5200225  
PDB IDNot Available
ChEBI ID76341  
Good Scents IDNot Available
References
General References
  1. Gadow A, Vater J, Schlumbohm W, Palacz Z, Salnikow J, Kleinkauf H: Gramicidin S synthetase. Stability of reactive thioester intermediates and formation of 3-amino-2-piperidone. Eur J Biochem. 1983 May 2;132(2):229-34. doi: 10.1111/j.1432-1033.1983.tb07352.x. [PubMed:6188612  ] 
  2. Oberholzer VG, Briddon A: 3-Amino-2-piperidone in the urine of patients with hyperornithinemia. Clin Chim Acta. 1978 Aug 1;87(3):411-5. doi: 10.1016/0009-8981(78)90186-9. [PubMed:679477  ] 
  3. Arshinoff SA, McCulloch JC, Matuk Y, Phillips MJ, Gordon BA, Marliss EB: Amino-acid metabolism and liver ultrastructure in hyperornithinemia with gyrate atrophy of the choroid and retina. Metabolism. 1979 Oct;28(10):979-88. doi: 10.1016/0026-0495(79)90001-5. [PubMed:491962  ]