Showing NP-Card for Cadaverine (NP0000244)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Show more...Show more...
Record Information
Version2.0
Created at2006-05-22 14:17:48 UTC
Updated at2021-08-19 23:57:58 UTC
NP-MRD IDNP0000244
Secondary Accession NumbersNone
Natural Product Identification
Common NameCadaverine
DescriptionCadaverine is a foul-smelling diamine formed by bacterial decarboxylation of lysine that occurs during protein hydrolysis during putrefaction of animal tissue. However, this diamine is not purely associated with putrefaction. Cadaverine is a toxic diamine with the formula NH2(CH2)5NH2, which is similar to putrescine's NH2(CH2)4NH2. Cadaverine is also known by the names 1,5-pentanediamine and pentamethylenediamine. It is also produced in small quantities by mammals. In particular, it is partially responsible for the distinctive smell of urine and semen. Elevated levels of cadaverine have been found in the urine of some patients with defects in lysine metabolism. Cadaverine is toxic in large doses. In rats it had a low acute oral toxicity of more than 2000 mg/kg body weight. Cadaverine can be found in Corynebacterium (PMID: 27872963 ).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000244 (Cadaverine)

  Mrv1652309042000272D          

  7  6  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 N   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
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   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
    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  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
Download

3D MOL for NP0000244 (Cadaverine)

HMDB0002322
     RDKit          3D
Cadaverine
 21 20  0  0  0  0  0  0  0  0999 V2000
    3.6692   -0.1381   -0.4731 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4220    0.4262    0.0583 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2331   -0.4037   -0.4379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0017    0.2389    0.1492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2667   -0.4806   -0.2589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4193    0.2816    0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6962   -0.3210    0.0871 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1442   -0.7322    0.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2575    0.5883   -0.9071 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2485    1.4538   -0.3002 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5117    0.3451    1.1602 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2180   -0.4662   -1.5295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3500   -1.4056    0.0357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1226    0.2760    1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0873    1.2834   -0.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2650   -1.5453    0.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4308   -0.3530   -1.3488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2432    0.2612    1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3433    1.3221    0.0724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0705   -0.9243    0.8360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3531    0.3622   -0.3043 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
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  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
  6 19  1  0
  7 20  1  0
  7 21  1  0
M  END
Download

3D SDF for NP0000244 (Cadaverine)

  Mrv1652309042000272D          

  7  6  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 N   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
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   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
    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  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000244

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C5H14N2/c6-4-2-1-3-5-7/h1-7H2

> <INCHI_KEY>
VHRGRCVQAFMJIZ-UHFFFAOYSA-N

> <FORMULA>
C5H14N2

> <MOLECULAR_WEIGHT>
102.1781

> <EXACT_MASS>
102.115698458

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.112767429733221

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentane-1,5-diamine

> <ALOGPS_LOGP>
-0.27

> <JCHEM_LOGP>
-0.4005515990000003

> <ALOGPS_LOGS>
-0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
10.506503804690274

> <JCHEM_POLAR_SURFACE_AREA>
52.04

> <JCHEM_REFRACTIVITY>
31.979599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.91e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cadaverine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000244 (Cadaverine)

HMDB0002322
     RDKit          3D
Cadaverine
 21 20  0  0  0  0  0  0  0  0999 V2000
    3.6692   -0.1381   -0.4731 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4220    0.4262    0.0583 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2331   -0.4037   -0.4379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0017    0.2389    0.1492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2667   -0.4806   -0.2589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4193    0.2816    0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6962   -0.3210    0.0871 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1442   -0.7322    0.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2575    0.5883   -0.9071 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2485    1.4538   -0.3002 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5117    0.3451    1.1602 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2180   -0.4662   -1.5295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3500   -1.4056    0.0357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1226    0.2760    1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0873    1.2834   -0.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2650   -1.5453    0.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4308   -0.3530   -1.3488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2432    0.2612    1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3433    1.3221    0.0724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0705   -0.9243    0.8360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3531    0.3622   -0.3043 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
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  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
  6 19  1  0
  7 20  1  0
  7 21  1  0
M  END
Download

PDB for NP0000244 (Cadaverine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       3.286   3.437   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      11.288   3.437   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
Download

3D PDB for NP0000244 (Cadaverine)

COMPND    HMDB0002322
HETATM    1  N1  UNL     1       3.669  -0.138  -0.473  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.422   0.426   0.058  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.233  -0.404  -0.438  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.002   0.239   0.149  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.267  -0.481  -0.259  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.419   0.282   0.408  1.00  0.00           C  
HETATM    7  N2  UNL     1      -3.696  -0.321   0.087  1.00  0.00           N  
HETATM    8  H1  UNL     1       4.144  -0.732   0.218  1.00  0.00           H  
HETATM    9  H2  UNL     1       4.258   0.588  -0.907  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.249   1.454  -0.300  1.00  0.00           H  
HETATM   11  H4  UNL     1       2.512   0.345   1.160  1.00  0.00           H  
HETATM   12  H5  UNL     1       1.218  -0.466  -1.530  1.00  0.00           H  
HETATM   13  H6  UNL     1       1.350  -1.406   0.036  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.123   0.276   1.249  1.00  0.00           H  
HETATM   15  H8  UNL     1      -0.087   1.283  -0.234  1.00  0.00           H  
HETATM   16  H9  UNL     1      -1.265  -1.545   0.027  1.00  0.00           H  
HETATM   17  H10 UNL     1      -1.431  -0.353  -1.349  1.00  0.00           H  
HETATM   18  H11 UNL     1      -2.243   0.261   1.492  1.00  0.00           H  
HETATM   19  H12 UNL     1      -2.343   1.322   0.072  1.00  0.00           H  
HETATM   20  H13 UNL     1      -4.071  -0.924   0.836  1.00  0.00           H  
HETATM   21  H14 UNL     1      -4.353   0.362  -0.304  1.00  0.00           H  
CONECT    1    2    8    9
CONECT    2    3   10   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5    6   16   17
CONECT    6    7   18   19
CONECT    7   20   21
END
Download

SMILES for NP0000244 (Cadaverine)

NCCCCCN
Download

INCHI for NP0000244 (Cadaverine)

InChI=1S/C5H14N2/c6-4-2-1-3-5-7/h1-7H2
Download
View in JSmol
Synonyms
ValueSource
1,5-DiaminopentaneChEBI
1,5-PentamethylenediamineChEBI
1,5-PentanediamineChEBI
DAPEChEBI
PentamethylenediamineChEBI
PENTANE-1,5-diamineChEBI
1,5-Diaminopentane dihydrochlorideHMDB
CadaverinHMDB
Cadaverine dihydrochlorideHMDB
Pentamethylenediamine dihydrochlorideHMDB
BioDex 1HMDB
1,5 PentanediamineHMDB
Chemical FormulaC5H14N2
Average Mass102.1781 Da
Monoisotopic Mass102.11570 Da
IUPAC Namepentane-1,5-diamine
Traditional Namecadaverine
CAS Registry Number462-94-2
SMILES
NCCCCCN
InChI Identifier
InChI=1S/C5H14N2/c6-4-2-1-3-5-7/h1-7H2
InChI KeyVHRGRCVQAFMJIZ-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)Varshavi.d262021-08-05View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monoalkylamines. These are organic compounds containing an primary aliphatic amine group.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentMonoalkylamines
Alternative Parents
Substituents
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point9 °CNot Available
Boiling Point179.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.490 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility89.1 g/LALOGPS
logP-0.27ALOGPS
logP-0.4ChemAxon
logS-0.06ALOGPS
pKa (Strongest Basic)10.51ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area52.04 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.98 m³·mol⁻¹ChemAxon
Polarizability13.11 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002322
DrugBank IDDB03854
Phenol Explorer Compound IDNot Available
FoodDB IDFDB001493
KNApSAcK IDC00001403
Chemspider ID13866593
KEGG Compound IDC01672
BioCyc IDCADAVERINE
BiGG IDNot Available
Wikipedia LinkCadaverine
METLIN ID3236
PubChem Compound273
PDB IDNot Available
ChEBI ID18127
Good Scents IDrw1149431
References
General References