Hmdb loader

Showing metabocard for Arecaidine propargyl ester (HMDB0248570)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 01:59:40 UTC
Update Date2021-09-26 22:58:55 UTC
HMDB IDHMDB0248570
Secondary Accession NumbersNone
Metabolite Identification
Common NameArecaidine propargyl ester
DescriptionArecaidine propargyl ester belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus. Based on a literature review a significant number of articles have been published on Arecaidine propargyl ester. This compound has been identified in human blood as reported by (PMID: 31557052 ). Arecaidine propargyl ester is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Arecaidine propargyl ester 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0248570 (Arecaidine propargyl ester)

  Mrv1652309112103592D          

 13 13  0  0  0  0            999 V2000
   -1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  3  0  0  0  0
M  END
Download

3D MOL for HMDB0248570 (Arecaidine propargyl ester)

HMDB0248570
     RDKit          3D
Arecaidine propargyl ester
 26 26  0  0  0  0  0  0  0  0999 V2000
    5.2510    1.0891    0.5444 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4080    0.4422   -0.0277 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4028   -0.3528   -0.7359 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1743   -0.1419   -0.0699 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0479   -0.7861   -0.5441 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1407   -1.5248   -1.5306 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2352   -0.5912    0.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3921    0.1837    1.1727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7241    0.3462    1.8093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7728    0.4249    0.7574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5044   -0.2789   -0.4526 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1733    0.6052   -1.5556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4636   -1.2713   -0.3709 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0069    1.6545    1.0388 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2870    0.0538   -1.7830 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -1.4346   -0.7527 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4647    0.6935    1.5590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7160    1.2303    2.4767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8533   -0.5364    2.4832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7395    0.0267    1.1696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0007    1.4831    0.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0582    0.6884   -2.1947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3572    0.1814   -2.1953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8042    1.5871   -1.2138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7637   -2.1187    0.2613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2964   -1.6535   -1.3983 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13  7  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
 10 21  1  0
 12 22  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
 13 26  1  0
M  END
Download

3D SDF for HMDB0248570 (Arecaidine propargyl ester)

  Mrv1652309112103592D          

 13 13  0  0  0  0            999 V2000
   -1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0248570

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1CCC=C(C1)C(=O)OCC#C

> <INCHI_IDENTIFIER>
InChI=1S/C10H13NO2/c1-3-7-13-10(12)9-5-4-6-11(2)8-9/h1,5H,4,6-8H2,2H3

> <INCHI_KEY>
SPHRJZBOFYIKMC-UHFFFAOYSA-N

> <FORMULA>
C10H13NO2

> <MOLECULAR_WEIGHT>
179.219

> <EXACT_MASS>
179.094628663

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.761251160962882

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
prop-2-yn-1-yl 1-methyl-1,2,5,6-tetrahydropyridine-3-carboxylate

> <ALOGPS_LOGP>
1.03

> <JCHEM_LOGP>
0.8768857066666669

> <ALOGPS_LOGS>
-2.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.074329025836382

> <JCHEM_POLAR_SURFACE_AREA>
29.540000000000003

> <JCHEM_REFRACTIVITY>
51.4412

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.57e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
prop-2-yn-1-yl 1-methyl-5,6-dihydro-2H-pyridine-3-carboxylate

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0248570 (Arecaidine propargyl ester)

HMDB0248570
     RDKit          3D
Arecaidine propargyl ester
 26 26  0  0  0  0  0  0  0  0999 V2000
    5.2510    1.0891    0.5444 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4080    0.4422   -0.0277 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4028   -0.3528   -0.7359 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1743   -0.1419   -0.0699 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0479   -0.7861   -0.5441 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1407   -1.5248   -1.5306 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2352   -0.5912    0.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3921    0.1837    1.1727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7241    0.3462    1.8093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7728    0.4249    0.7574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5044   -0.2789   -0.4526 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1733    0.6052   -1.5556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4636   -1.2713   -0.3709 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0069    1.6545    1.0388 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2870    0.0538   -1.7830 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6715   -1.4346   -0.7527 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4647    0.6935    1.5590 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7160    1.2303    2.4767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8533   -0.5364    2.4832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7395    0.0267    1.1696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0007    1.4831    0.4879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0582    0.6884   -2.1947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3572    0.1814   -2.1953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8042    1.5871   -1.2138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7637   -2.1187    0.2613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2964   -1.6535   -1.3983 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13  7  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
 10 21  1  0
 12 22  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
 13 26  1  0
M  END
Download

PDB for HMDB0248570 (Arecaidine propargyl ester)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -2.667   3.080   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -1.334   3.850   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -1.334   5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.000   6.160   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.000   3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6    2                                                       
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
Download

3D PDB for HMDB0248570 (Arecaidine propargyl ester)

COMPND    HMDB0248570
HETATM    1  C1  UNL     1       5.251   1.089   0.544  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.408   0.442  -0.028  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.403  -0.353  -0.736  1.00  0.00           C  
HETATM    4  O1  UNL     1       2.174  -0.142  -0.070  1.00  0.00           O  
HETATM    5  C4  UNL     1       1.048  -0.786  -0.544  1.00  0.00           C  
HETATM    6  O2  UNL     1       1.141  -1.525  -1.531  1.00  0.00           O  
HETATM    7  C5  UNL     1      -0.235  -0.591   0.119  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.392   0.184   1.173  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.724   0.346   1.809  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.773   0.425   0.757  1.00  0.00           C  
HETATM   11  N1  UNL     1      -2.504  -0.279  -0.453  1.00  0.00           N  
HETATM   12  C9  UNL     1      -2.173   0.605  -1.556  1.00  0.00           C  
HETATM   13  C10 UNL     1      -1.464  -1.271  -0.371  1.00  0.00           C  
HETATM   14  H1  UNL     1       6.007   1.654   1.039  1.00  0.00           H  
HETATM   15  H2  UNL     1       3.287   0.054  -1.783  1.00  0.00           H  
HETATM   16  H3  UNL     1       3.672  -1.435  -0.753  1.00  0.00           H  
HETATM   17  H4  UNL     1       0.465   0.693   1.559  1.00  0.00           H  
HETATM   18  H5  UNL     1      -1.716   1.230   2.477  1.00  0.00           H  
HETATM   19  H6  UNL     1      -1.853  -0.536   2.483  1.00  0.00           H  
HETATM   20  H7  UNL     1      -3.740   0.027   1.170  1.00  0.00           H  
HETATM   21  H8  UNL     1      -3.001   1.483   0.488  1.00  0.00           H  
HETATM   22  H9  UNL     1      -3.058   0.688  -2.195  1.00  0.00           H  
HETATM   23  H10 UNL     1      -1.357   0.181  -2.195  1.00  0.00           H  
HETATM   24  H11 UNL     1      -1.804   1.587  -1.214  1.00  0.00           H  
HETATM   25  H12 UNL     1      -1.764  -2.119   0.261  1.00  0.00           H  
HETATM   26  H13 UNL     1      -1.296  -1.653  -1.398  1.00  0.00           H  
CONECT    1    2    2    2   14
CONECT    2    3
CONECT    3    4   15   16
CONECT    4    5
CONECT    5    6    6    7
CONECT    7    8    8   13
CONECT    8    9   17
CONECT    9   10   18   19
CONECT   10   11   20   21
CONECT   11   12   13
CONECT   12   22   23   24
CONECT   13   25   26
END
Download

SMILES for HMDB0248570 (Arecaidine propargyl ester)

CN1CCC=C(C1)C(=O)OCC#C
Download

INCHI for HMDB0248570 (Arecaidine propargyl ester)

InChI=1S/C10H13NO2/c1-3-7-13-10(12)9-5-4-6-11(2)8-9/h1,5H,4,6-8H2,2H3
Download
View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC10H13NO2
Average Molecular Weight179.219
Monoisotopic Molecular Weight179.094628663
IUPAC Nameprop-2-yn-1-yl 1-methyl-1,2,5,6-tetrahydropyridine-3-carboxylate
Traditional Nameprop-2-yn-1-yl 1-methyl-5,6-dihydro-2H-pyridine-3-carboxylate
CAS Registry NumberNot Available
SMILES
CN1CCC=C(C1)C(=O)OCC#C
InChI Identifier
InChI=1S/C10H13NO2/c1-3-7-13-10(12)9-5-4-6-11(2)8-9/h1,5H,4,6-8H2,2H3
InChI KeySPHRJZBOFYIKMC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus.
KingdomOrganic compounds
Super ClassAlkaloids and derivatives
ClassNot Available
Sub ClassNot Available
Direct ParentAlkaloids and derivatives
Alternative Parents
Substituents
  • Alkaloid or derivatives
  • Hydropyridine
  • Enoate ester
  • Alpha,beta-unsaturated carboxylic ester
  • Amino acid or derivatives
  • Carboxylic acid ester
  • Tertiary amine
  • Tertiary aliphatic amine
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Acetylide
  • Azacycle
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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 ID2142
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound2229
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 ]