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Showing metabocard for N-Carbamoylputrescine (HMDB0033458)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:11:31 UTC
Update Date2023-02-21 17:23:20 UTC
HMDB IDHMDB0033458
Secondary Accession Numbers
  • HMDB33458
Metabolite Identification
Common NameN-Carbamoylputrescine
DescriptionN-Carbamoylputrescine belongs to the class of organic compounds known as isoureas. These are organic compounds containing the isourea group, with the general structure R1N(R2)C(=NR3)OR4, or its hydrocarbyl derivatives (R1,R2,R3,R4=H, alkyl, aryl). N-Carbamoylputrescine exists in all living organisms, ranging from bacteria to humans. N-Carbamoylputrescine has been detected, but not quantified in, several different foods, such as american cranberries (Vaccinium macrocarpon), common beans (Phaseolus vulgaris), sea-buckthornberries (Hippophae rhamnoides), horseradish trees (Moringa oleifera), and celery stalks (Apium graveolens var. dulce). This could make N-carbamoylputrescine a potential biomarker for the consumption of these foods. N-Carbamoylputrescine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on N-Carbamoylputrescine.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033458 (N-Carbamoylputrescine)

  Mrv1652305142023402D          

  9  8  0  0  0  0            999 V2000
 9991.1554 9991.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.4411 9990.9091    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9991.8691 9990.9091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.7265 9991.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5842 9991.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.0122 9990.9091    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9989.7265 9992.1455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.2993 9990.9091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.0124 9991.3205    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  4  7  2  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0033458 (N-Carbamoylputrescine)

HMDB0033458
     RDKit          3D
N-Carbamoylputrescine
 22 21  0  0  0  0  0  0  0  0999 V2000
   -2.4531    1.2310   -0.3809 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5069   -0.0260    0.3130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7467   -1.1173   -0.3667 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2819   -0.8169   -0.5252 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4046   -0.6002    0.8046 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8104   -0.3144    0.6696 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2555    0.8242   -0.0553 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6372    1.1264   -0.2036 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4416    1.6081   -0.5935 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3156    1.1316   -1.4159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7606    1.8808    0.0490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5650   -0.4009    0.4188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0850    0.1154    1.3237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9059   -2.0792    0.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1739   -1.2069   -1.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337   -1.6926   -0.9932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1351    0.0228   -1.2075 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3056   -1.4819    1.4687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0598    0.2734    1.3223 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5545   -0.9349    1.1004 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9923    1.7317   -0.9480 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3543    0.7256    0.4659 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  1  0
  7  9  2  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
  8 21  1  0
  8 22  1  0
M  END
Download

3D SDF for HMDB0033458 (N-Carbamoylputrescine)

  Mrv1652305142023402D          

  9  8  0  0  0  0            999 V2000
 9991.1554 9991.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9990.4411 9990.9091    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9991.8691 9990.9091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.7265 9991.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5842 9991.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9989.0122 9990.9091    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9989.7265 9992.1455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.2993 9990.9091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.0124 9991.3205    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  4  7  2  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033458

> <DATABASE_NAME>
hmdb

> <SMILES>
NCCCCNC(N)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H13N3O/c6-3-1-2-4-8-5(7)9/h1-4,6H2,(H3,7,8,9)

> <INCHI_KEY>
YANFYYGANIYHGI-UHFFFAOYSA-N

> <FORMULA>
C5H13N3O

> <MOLECULAR_WEIGHT>
131.1762

> <EXACT_MASS>
131.105862053

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.58631156865809

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4-aminobutyl)urea

> <ALOGPS_LOGP>
-1.22

> <JCHEM_LOGP>
-1.3598191946666665

> <ALOGPS_LOGS>
-0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.847533757470934

> <JCHEM_PKA_STRONGEST_BASIC>
9.904072076833382

> <JCHEM_POLAR_SURFACE_AREA>
81.14

> <JCHEM_REFRACTIVITY>
35.4991

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.18e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-carbamoylputrescine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0033458 (N-Carbamoylputrescine)

HMDB0033458
     RDKit          3D
N-Carbamoylputrescine
 22 21  0  0  0  0  0  0  0  0999 V2000
   -2.4531    1.2310   -0.3809 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5069   -0.0260    0.3130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7467   -1.1173   -0.3667 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2819   -0.8169   -0.5252 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4046   -0.6002    0.8046 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8104   -0.3144    0.6696 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2555    0.8242   -0.0553 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6372    1.1264   -0.2036 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4416    1.6081   -0.5935 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3156    1.1316   -1.4159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7606    1.8808    0.0490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5650   -0.4009    0.4188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0850    0.1154    1.3237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9059   -2.0792    0.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1739   -1.2069   -1.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2337   -1.6926   -0.9932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1351    0.0228   -1.2075 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3056   -1.4819    1.4687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0598    0.2734    1.3223 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5545   -0.9349    1.1004 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9923    1.7317   -0.9480 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3543    0.7256    0.4659 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  1  0
  7  9  2  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
  8 21  1  0
  8 22  1  0
M  END
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PDB for HMDB0033458 (N-Carbamoylputrescine)

HEADER    PROTEIN                                 14-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-20         0                                  
HETATM    1  C   UNK     0    8650.1578650.465   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0    8648.8238649.697   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0    8651.4898649.697   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8647.4898650.465   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8652.8248650.465   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    8646.1568649.697   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0    8647.4898652.005   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8654.1598649.697   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0    8655.4908650.465   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6    7                                                  
CONECT    5    3    8                                                       
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    5    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0033458 (N-Carbamoylputrescine)

COMPND    HMDB0033458
HETATM    1  N1  UNL     1      -2.453   1.231  -0.381  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.507  -0.026   0.313  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.747  -1.117  -0.367  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.282  -0.817  -0.525  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.405  -0.600   0.805  1.00  0.00           C  
HETATM    6  N2  UNL     1       1.810  -0.314   0.670  1.00  0.00           N  
HETATM    7  C5  UNL     1       2.256   0.824  -0.055  1.00  0.00           C  
HETATM    8  N3  UNL     1       3.637   1.126  -0.204  1.00  0.00           N  
HETATM    9  O1  UNL     1       1.442   1.608  -0.594  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.316   1.132  -1.416  1.00  0.00           H  
HETATM   11  H2  UNL     1      -1.761   1.881   0.049  1.00  0.00           H  
HETATM   12  H3  UNL     1      -3.565  -0.401   0.419  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.085   0.115   1.324  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.906  -2.079   0.161  1.00  0.00           H  
HETATM   15  H6  UNL     1      -2.174  -1.207  -1.407  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.234  -1.693  -0.993  1.00  0.00           H  
HETATM   17  H8  UNL     1      -0.135   0.023  -1.208  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.306  -1.482   1.469  1.00  0.00           H  
HETATM   19  H10 UNL     1      -0.060   0.273   1.322  1.00  0.00           H  
HETATM   20  H11 UNL     1       2.555  -0.935   1.100  1.00  0.00           H  
HETATM   21  H12 UNL     1       3.992   1.732  -0.948  1.00  0.00           H  
HETATM   22  H13 UNL     1       4.354   0.726   0.466  1.00  0.00           H  
CONECT    1    2   10   11
CONECT    2    3   12   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7   20
CONECT    7    8    9    9
CONECT    8   21   22
END
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SMILES for HMDB0033458 (N-Carbamoylputrescine)

NCCCCNC(N)=O
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INCHI for HMDB0033458 (N-Carbamoylputrescine)

InChI=1S/C5H13N3O/c6-3-1-2-4-8-5(7)9/h1-4,6H2,(H3,7,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(4-Aminobutyl)-ureaHMDB
1-(4-Aminobutyl)ureaHMDB
(4-Aminobutyl)ureaHMDB
1-Amino-4-ureidobutaneHMDB
N-(4-Aminobutyl)ureaHMDB
N-CarbamoylputrescineHMDB
N-CarbamylputrescineHMDB
Chemical FormulaC5H13N3O
Average Molecular Weight131.1762
Monoisotopic Molecular Weight131.105862053
IUPAC Name(4-aminobutyl)urea
Traditional NameN-carbamoylputrescine
CAS Registry Number6851-51-0
SMILES
NCCCCNC(N)=O
InChI Identifier
InChI=1S/C5H13N3O/c6-3-1-2-4-8-5(7)9/h1-4,6H2,(H3,7,8,9)
InChI KeyYANFYYGANIYHGI-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as isoureas. These are organic compounds containing the isourea group, with the general structure R1N(R2)C(=NR3)OR4, or its hydrocarbyl derivatives (R1,R2,R3,R4=H, alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboximidic acids and derivatives
Sub ClassCarboximidic acids
Direct ParentIsoureas
Alternative Parents
Substituents
  • Isourea
  • Carboximidamide
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Imine
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility37780 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB011499
KNApSAcK IDC00001404
Chemspider ID488
KEGG Compound IDC00436
BioCyc IDCPD-597
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound502
PDB IDNot Available
ChEBI ID17902
Food Biomarker OntologyNot Available
VMH IDNCPTRC
MarkerDB IDNot Available
Good Scents IDrw1835801
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .