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Showing metabocard for 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (HMDB0244825)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:57:23 UTC
Update Date2021-09-26 22:52:50 UTC
HMDB IDHMDB0244825
Secondary Accession NumbersNone
Metabolite Identification
Common Name1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide
Description1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide, also known as carbodiimide, ethyldimethylaminopropyl or edap carbodiimide, belongs to the class of organic compounds known as trialkylamines. These are organic compounds containing a trialkylamine group, characterized by exactly three alkyl groups bonded to the amino nitrogen. Based on a literature review a significant number of articles have been published on 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0244825 (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide)

  Mrv1652309102123572D          

 11 10  0  0  0  0            999 V2000
   -3.0493    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3349    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    1.5395    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 C   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  2  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
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3D MOL for HMDB0244825 (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide)

HMDB0244825
     RDKit          3D
1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide
 28 27  0  0  0  0  0  0  0  0999 V2000
    4.9905    0.3598    0.2871 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0983   -0.3349   -0.7260 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2052    0.7062   -1.2572 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1901    0.9611   -0.5343 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1845    1.1954    0.2347 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1638    0.1420    0.2325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7615    0.4873   -0.9124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8888   -0.4617   -1.0975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7112   -0.4892    0.0983 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8094   -1.4331   -0.0389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2035    0.8375    0.4337 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7001    1.4079    0.4681 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0546    0.3712   -0.0308 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9491   -0.1561    1.2625 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7636   -0.7232   -1.5394 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5415   -1.1699   -0.3011 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6247   -0.8577    0.1202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4239    0.1473    1.1625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1806    1.5036   -0.6700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1709    0.6464   -1.8451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5363   -1.4886   -1.2801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4734   -0.1206   -1.9770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0657   -1.7708    1.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5205   -2.3173   -0.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7199   -0.9537   -0.4391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2029    1.4844   -0.4407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5381    1.2468    1.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2593    0.7799    0.8288 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 10 23  1  0
 10 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 11 28  1  0
M  END
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3D SDF for HMDB0244825 (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide)

  Mrv1652309102123572D          

 11 10  0  0  0  0            999 V2000
   -3.0493    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3349    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    1.5395    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 C   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  2  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244825

> <DATABASE_NAME>
hmdb

> <SMILES>
CCN=C=NCCCN(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C8H17N3/c1-4-9-8-10-6-5-7-11(2)3/h4-7H2,1-3H3

> <INCHI_KEY>
LMDZBCPBFSXMTL-UHFFFAOYSA-N

> <FORMULA>
C8H17N3

> <MOLECULAR_WEIGHT>
155.245

> <EXACT_MASS>
155.142247559

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
19.468388455472983

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({[3-(dimethylamino)propyl]imino}methylidene)(ethyl)amine

> <ALOGPS_LOGP>
1.28

> <JCHEM_LOGP>
0.6291302646666659

> <ALOGPS_LOGS>
-2.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.27516245341621

> <JCHEM_POLAR_SURFACE_AREA>
27.96

> <JCHEM_REFRACTIVITY>
47.9251

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.40e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
({[3-(dimethylamino)propyl]imino}methylidene)(ethyl)amine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0244825 (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide)

HMDB0244825
     RDKit          3D
1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide
 28 27  0  0  0  0  0  0  0  0999 V2000
    4.9905    0.3598    0.2871 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0983   -0.3349   -0.7260 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2052    0.7062   -1.2572 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1901    0.9611   -0.5343 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1845    1.1954    0.2347 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1638    0.1420    0.2325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7615    0.4873   -0.9124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8888   -0.4617   -1.0975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7112   -0.4892    0.0983 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8094   -1.4331   -0.0389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2035    0.8375    0.4337 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7001    1.4079    0.4681 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0546    0.3712   -0.0308 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9491   -0.1561    1.2625 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7636   -0.7232   -1.5394 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5415   -1.1699   -0.3011 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6247   -0.8577    0.1202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4239    0.1473    1.1625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1806    1.5036   -0.6700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1709    0.6464   -1.8451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5363   -1.4886   -1.2801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4734   -0.1206   -1.9770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0657   -1.7708    1.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5205   -2.3173   -0.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7199   -0.9537   -0.4391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2029    1.4844   -0.4407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5381    1.2468    1.2162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2593    0.7799    0.8288 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 10 23  1  0
 10 24  1  0
 10 25  1  0
 11 26  1  0
 11 27  1  0
 11 28  1  0
M  END
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PDB for HMDB0244825 (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide)

HEADER    PROTEIN                                 10-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-21         0                                  
HETATM    1  C   UNK     0      -5.692   2.874   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.358   2.104   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -3.025   2.874   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -1.691   2.104   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.357   1.334   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       4.977   1.334   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       6.311   2.104   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.977  -0.206   0.000  0.00  0.00           C+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    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0244825 (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide)

COMPND    HMDB0244825
HETATM    1  C1  UNL     1       4.990   0.360   0.287  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.098  -0.335  -0.726  1.00  0.00           C  
HETATM    3  N1  UNL     1       3.205   0.706  -1.257  1.00  0.00           N  
HETATM    4  C3  UNL     1       2.190   0.961  -0.534  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.185   1.195   0.235  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.164   0.142   0.233  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.762   0.487  -0.912  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.889  -0.462  -1.098  1.00  0.00           C  
HETATM    9  N3  UNL     1      -2.711  -0.489   0.098  1.00  0.00           N  
HETATM   10  C7  UNL     1      -3.809  -1.433  -0.039  1.00  0.00           C  
HETATM   11  C8  UNL     1      -3.204   0.838   0.434  1.00  0.00           C  
HETATM   12  H1  UNL     1       4.700   1.408   0.468  1.00  0.00           H  
HETATM   13  H2  UNL     1       6.055   0.371  -0.031  1.00  0.00           H  
HETATM   14  H3  UNL     1       4.949  -0.156   1.262  1.00  0.00           H  
HETATM   15  H4  UNL     1       4.764  -0.723  -1.539  1.00  0.00           H  
HETATM   16  H5  UNL     1       3.541  -1.170  -0.301  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.625  -0.858   0.120  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.424   0.147   1.163  1.00  0.00           H  
HETATM   19  H8  UNL     1      -1.181   1.504  -0.670  1.00  0.00           H  
HETATM   20  H9  UNL     1      -0.171   0.646  -1.845  1.00  0.00           H  
HETATM   21  H10 UNL     1      -1.536  -1.489  -1.280  1.00  0.00           H  
HETATM   22  H11 UNL     1      -2.473  -0.121  -1.977  1.00  0.00           H  
HETATM   23  H12 UNL     1      -4.066  -1.771   1.000  1.00  0.00           H  
HETATM   24  H13 UNL     1      -3.520  -2.317  -0.610  1.00  0.00           H  
HETATM   25  H14 UNL     1      -4.720  -0.954  -0.439  1.00  0.00           H  
HETATM   26  H15 UNL     1      -3.203   1.484  -0.441  1.00  0.00           H  
HETATM   27  H16 UNL     1      -2.538   1.247   1.216  1.00  0.00           H  
HETATM   28  H17 UNL     1      -4.259   0.780   0.829  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3   15   16
CONECT    3    4    4
CONECT    4    5    5
CONECT    5    6
CONECT    6    7   17   18
CONECT    7    8   19   20
CONECT    8    9   21   22
CONECT    9   10   11
CONECT   10   23   24   25
CONECT   11   26   27   28
END
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SMILES for HMDB0244825 (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide)

CCN=C=NCCCN(C)C
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INCHI for HMDB0244825 (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide)

InChI=1S/C8H17N3/c1-4-9-8-10-6-5-7-11(2)3/h4-7H2,1-3H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-(3-Dimethylaminopropyl)-1-ethylcarbodiimideHMDB
Carbodiimide, ethyldimethylaminopropylHMDB
EDAP carbodiimideHMDB
EDAP-carbodiimideHMDB
Ethyldimethylaminopropyl carbodiimideHMDB
Chemical FormulaC8H17N3
Average Molecular Weight155.245
Monoisotopic Molecular Weight155.142247559
IUPAC Name({[3-(dimethylamino)propyl]imino}methylidene)(ethyl)amine
Traditional Name({[3-(dimethylamino)propyl]imino}methylidene)(ethyl)amine
CAS Registry NumberNot Available
SMILES
CCN=C=NCCCN(C)C
InChI Identifier
InChI=1S/C8H17N3/c1-4-9-8-10-6-5-7-11(2)3/h4-7H2,1-3H3
InChI KeyLMDZBCPBFSXMTL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as trialkylamines. These are organic compounds containing a trialkylamine group, characterized by exactly three alkyl groups bonded to the amino nitrogen.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentTrialkylamines
Alternative Parents
Substituents
  • Tertiary aliphatic amine
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carbodiimide
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID15119
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide
METLIN IDNot Available
PubChem Compound15908
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]