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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 07:10:49 UTC

Update Date

2021-09-26 23:01:32 UTC

HMDB ID

HMDB0250198

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Cyclic-hpmpc

Description

Cyclic-hpmpc belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Based on a literature review a significant number of articles have been published on Cyclic-hpmpc. This compound has been identified in human blood as reported by (PMID: 31557052 ). Cyclic-hpmpc is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cyclic-hpmpc 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0250198
     RDKit          3D
Cyclic-hpmpc
 29 30  0  0  0  0  0  0  0  0999 V2000
    4.1565   -0.3310   -2.4031 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2110   -0.0851   -1.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7377   -1.0929   -0.5538 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8235   -0.8285    0.4394 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3403    0.4328    0.6702 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3760    0.5978    1.7177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0536    0.3474    1.2971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4106    1.3092    0.2240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7634    1.3208   -0.1289 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1781   -0.2636   -0.5343 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.4384   -0.7200   -1.7667 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8373   -0.4532   -0.7467 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5768   -1.2755    0.8728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2173   -0.9930    0.9609 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8158    1.3943   -0.1336 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3989    2.5657    0.0483 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7194    1.1400   -1.1176 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9810   -1.1062   -3.0649 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0254    0.2223   -2.5435 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1059   -2.1009   -0.7173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4480   -1.6351    1.0875 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6051   -0.0074    2.6205 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3928    1.6661    2.0899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6632    0.4912    2.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8095    1.1375   -0.6634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2059    2.3407    0.6477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0542   -0.8228   -1.6496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1408   -0.9161    1.7631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7881   -2.3357    0.7222 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  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  2  0
 14  7  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
 12 27  1  0
 13 28  1  0
 13 29  1  0
M  END

  Mrv1652309112109112D          

 17 18  0  0  0  0            999 V2000
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 O   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
    2.1434   -1.2375    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6131   -0.6055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6737   -0.6055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    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  2  0  0  0  0
  5  7  1  0  0  0  0
  1  7  1  0  0  0  0
  5  8  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  2  0  0  0  0
 13 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250198

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(=O)N(CC2COP(O)(=O)CO2)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C8H12N3O5P/c9-7-1-2-11(8(12)10-7)3-6-4-16-17(13,14)5-15-6/h1-2,6H,3-5H2,(H,13,14)(H2,9,10,12)

> <INCHI_KEY>
YXQUGSXUDFTPLL-UHFFFAOYSA-N

> <FORMULA>
C8H12N3O5P

> <MOLECULAR_WEIGHT>
261.174

> <EXACT_MASS>
261.051457496

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
22.39881256273987

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2-hydroxy-2-oxo-1,4,2lambda5-dioxaphosphinan-5-yl)methyl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
-1.70

> <JCHEM_LOGP>
-2.0029163682731808

> <ALOGPS_LOGS>
-1.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.212932941826384

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8246670105163343

> <JCHEM_PKA_STRONGEST_BASIC>
1.6557660372155851

> <JCHEM_POLAR_SURFACE_AREA>
114.45

> <JCHEM_REFRACTIVITY>
56.64889999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.65e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-1-[(2-hydroxy-2-oxo-1,4,2lambda5-dioxaphosphinan-5-yl)methyl]pyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0250198
     RDKit          3D
Cyclic-hpmpc
 29 30  0  0  0  0  0  0  0  0999 V2000
    4.1565   -0.3310   -2.4031 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2110   -0.0851   -1.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7377   -1.0929   -0.5538 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8235   -0.8285    0.4394 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3403    0.4328    0.6702 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3760    0.5978    1.7177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0536    0.3474    1.2971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4106    1.3092    0.2240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7634    1.3208   -0.1289 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1781   -0.2636   -0.5343 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.4384   -0.7200   -1.7667 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8373   -0.4532   -0.7467 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5768   -1.2755    0.8728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2173   -0.9930    0.9609 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8158    1.3943   -0.1336 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3989    2.5657    0.0483 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7194    1.1400   -1.1176 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9810   -1.1062   -3.0649 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0254    0.2223   -2.5435 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1059   -2.1009   -0.7173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4480   -1.6351    1.0875 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6051   -0.0074    2.6205 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3928    1.6661    2.0899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6632    0.4912    2.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8095    1.1375   -0.6634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2059    2.3407    0.6477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0542   -0.8228   -1.6496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1408   -0.9161    1.7631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7881   -2.3357    0.7222 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  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  2  0
 14  7  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
 12 27  1  0
 13 28  1  0
 13 29  1  0
M  END

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       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  P   UNK     0       4.001  -2.310   0.000  0.00  0.00           P+0
HETATM    6  O   UNK     0       3.011  -1.130   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.991  -1.130   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.667  -7.700   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -0.000  -7.700   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0      -1.334 -10.010   0.000  0.00  0.00           N+0
CONECT    1    2    7                                                       
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5    1                                                       
CONECT    8    5                                                            
CONECT    9    2   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15                                                            
CONECT   17   13                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0250198
HETATM    1  N1  UNL     1       4.156  -0.331  -2.403  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.211  -0.085  -1.368  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.738  -1.093  -0.554  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.824  -0.828   0.439  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.340   0.433   0.670  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.376   0.598   1.718  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.054   0.347   1.297  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.411   1.309   0.224  1.00  0.00           C  
HETATM    9  O1  UNL     1      -2.763   1.321  -0.129  1.00  0.00           O  
HETATM   10  P1  UNL     1      -3.178  -0.264  -0.534  1.00  0.00           P  
HETATM   11  O2  UNL     1      -2.438  -0.720  -1.767  1.00  0.00           O  
HETATM   12  O3  UNL     1      -4.837  -0.453  -0.747  1.00  0.00           O  
HETATM   13  C7  UNL     1      -2.577  -1.276   0.873  1.00  0.00           C  
HETATM   14  O4  UNL     1      -1.217  -0.993   0.961  1.00  0.00           O  
HETATM   15  C8  UNL     1       1.816   1.394  -0.134  1.00  0.00           C  
HETATM   16  O5  UNL     1       1.399   2.566   0.048  1.00  0.00           O  
HETATM   17  N3  UNL     1       2.719   1.140  -1.118  1.00  0.00           N  
HETATM   18  H1  UNL     1       3.981  -1.106  -3.065  1.00  0.00           H  
HETATM   19  H2  UNL     1       5.025   0.222  -2.544  1.00  0.00           H  
HETATM   20  H3  UNL     1       3.106  -2.101  -0.717  1.00  0.00           H  
HETATM   21  H4  UNL     1       1.448  -1.635   1.087  1.00  0.00           H  
HETATM   22  H5  UNL     1       0.605  -0.007   2.621  1.00  0.00           H  
HETATM   23  H6  UNL     1       0.393   1.666   2.090  1.00  0.00           H  
HETATM   24  H7  UNL     1      -1.663   0.491   2.230  1.00  0.00           H  
HETATM   25  H8  UNL     1      -0.809   1.138  -0.663  1.00  0.00           H  
HETATM   26  H9  UNL     1      -1.206   2.341   0.648  1.00  0.00           H  
HETATM   27  H10 UNL     1      -5.054  -0.823  -1.650  1.00  0.00           H  
HETATM   28  H11 UNL     1      -3.141  -0.916   1.763  1.00  0.00           H  
HETATM   29  H12 UNL     1      -2.788  -2.336   0.722  1.00  0.00           H  
CONECT    1    2   18   19
CONECT    2    3   17   17
CONECT    3    4    4   20
CONECT    4    5   21
CONECT    5    6   15
CONECT    6    7   22   23
CONECT    7    8   14   24
CONECT    8    9   25   26
CONECT    9   10
CONECT   10   11   11   12   13
CONECT   12   27
CONECT   13   14   28   29
CONECT   15   16   16   17
END

HMDB0250198
     RDKit          3D
Cyclic-hpmpc
 29 30  0  0  0  0  0  0  0  0999 V2000
    4.1565   -0.3310   -2.4031 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2110   -0.0851   -1.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7377   -1.0929   -0.5538 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8235   -0.8285    0.4394 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3403    0.4328    0.6702 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3760    0.5978    1.7177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0536    0.3474    1.2971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4106    1.3092    0.2240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7634    1.3208   -0.1289 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1781   -0.2636   -0.5343 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.4384   -0.7200   -1.7667 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8373   -0.4532   -0.7467 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5768   -1.2755    0.8728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2173   -0.9930    0.9609 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8158    1.3943   -0.1336 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3989    2.5657    0.0483 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7194    1.1400   -1.1176 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9810   -1.1062   -3.0649 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0254    0.2223   -2.5435 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1059   -2.1009   -0.7173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4480   -1.6351    1.0875 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6051   -0.0074    2.6205 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3928    1.6661    2.0899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6632    0.4912    2.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8095    1.1375   -0.6634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2059    2.3407    0.6477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0542   -0.8228   -1.6496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1408   -0.9161    1.7631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7881   -2.3357    0.7222 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  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  2  0
 14  7  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  4 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
 12 27  1  0
 13 28  1  0
 13 29  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₈H₁₂N₃O₅P

Average Molecular Weight

261.174

Monoisotopic Molecular Weight

261.051457496

IUPAC Name

4-amino-1-[(2-hydroxy-2-oxo-1,4,2lambda5-dioxaphosphinan-5-yl)methyl]-1,2-dihydropyrimidin-2-one

Traditional Name

4-amino-1-[(2-hydroxy-2-oxo-1,4,2lambda5-dioxaphosphinan-5-yl)methyl]pyrimidin-2-one

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(CC2COP(O)(=O)CO2)C=C1

InChI Identifier

InChI=1S/C8H12N3O5P/c9-7-1-2-11(8(12)10-7)3-6-4-16-17(13,14)5-15-6/h1-2,6H,3-5H2,(H,13,14)(H2,9,10,12)

InChI Key

YXQUGSXUDFTPLL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidones

Alternative Parents

Substituents

Pyrimidone
Aminopyrimidine
Imidolactam
Phosphonic acid ester
Hydropyrimidine
Heteroaromatic compound
Organophosphonic acid derivative
Organophosphonic acid
Phosphacycle
Oxacycle
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-1.7	ALOGPS
logP	-2	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	0.82	ChemAxon
pKa (Strongest Basic)	1.66	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	114.45 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	56.65 m³·mol⁻¹	ChemAxon
Polarizability	22.4 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	151.941	30932474
DeepCCS	[M-H]-	149.583	30932474
DeepCCS	[M-2H]-	182.594	30932474
DeepCCS	[M+Na]+	158.034	30932474
AllCCS	[M+H]+	157.5	32859911
AllCCS	[M+H-H2O]+	153.8	32859911
AllCCS	[M+NH4]+	160.9	32859911
AllCCS	[M+Na]+	161.9	32859911
AllCCS	[M-H]-	153.4	32859911
AllCCS	[M+Na-2H]-	153.5	32859911
AllCCS	[M+HCOO]-	153.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cyclic-hpmpc	NC1=NC(=O)N(CC2COP(O)(=O)CO2)C=C1	3195.6	Standard polar	33892256
Cyclic-hpmpc	NC1=NC(=O)N(CC2COP(O)(=O)CO2)C=C1	2245.8	Standard non polar	33892256
Cyclic-hpmpc	NC1=NC(=O)N(CC2COP(O)(=O)CO2)C=C1	2701.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cyclic-hpmpc,1TMS,isomer #1	C[Si](C)(C)OP1(=O)COC(CN2C=CC(N)=NC2=O)CO1	2476.2	Semi standard non polar	33892256
Cyclic-hpmpc,1TMS,isomer #1	C[Si](C)(C)OP1(=O)COC(CN2C=CC(N)=NC2=O)CO1	2238.3	Standard non polar	33892256
Cyclic-hpmpc,1TMS,isomer #1	C[Si](C)(C)OP1(=O)COC(CN2C=CC(N)=NC2=O)CO1	3715.6	Standard polar	33892256
Cyclic-hpmpc,1TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1	2603.1	Semi standard non polar	33892256
Cyclic-hpmpc,1TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1	2331.0	Standard non polar	33892256
Cyclic-hpmpc,1TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1	3797.0	Standard polar	33892256
Cyclic-hpmpc,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O[Si](C)(C)C)CO2)C=C1	2548.8	Semi standard non polar	33892256
Cyclic-hpmpc,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O[Si](C)(C)C)CO2)C=C1	2350.8	Standard non polar	33892256
Cyclic-hpmpc,2TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O[Si](C)(C)C)CO2)C=C1	3282.5	Standard polar	33892256
Cyclic-hpmpc,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1)[Si](C)(C)C	2523.1	Semi standard non polar	33892256
Cyclic-hpmpc,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1)[Si](C)(C)C	2495.3	Standard non polar	33892256
Cyclic-hpmpc,2TMS,isomer #2	C[Si](C)(C)N(C1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1)[Si](C)(C)C	3584.2	Standard polar	33892256
Cyclic-hpmpc,3TMS,isomer #1	C[Si](C)(C)OP1(=O)COC(CN2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CO1	2495.5	Semi standard non polar	33892256
Cyclic-hpmpc,3TMS,isomer #1	C[Si](C)(C)OP1(=O)COC(CN2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CO1	2495.7	Standard non polar	33892256
Cyclic-hpmpc,3TMS,isomer #1	C[Si](C)(C)OP1(=O)COC(CN2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CO1	3012.7	Standard polar	33892256
Cyclic-hpmpc,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP1(=O)COC(CN2C=CC(N)=NC2=O)CO1	2728.6	Semi standard non polar	33892256
Cyclic-hpmpc,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP1(=O)COC(CN2C=CC(N)=NC2=O)CO1	2454.0	Standard non polar	33892256
Cyclic-hpmpc,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP1(=O)COC(CN2C=CC(N)=NC2=O)CO1	3826.5	Standard polar	33892256
Cyclic-hpmpc,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1	2873.2	Semi standard non polar	33892256
Cyclic-hpmpc,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1	2574.1	Standard non polar	33892256
Cyclic-hpmpc,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1	3870.8	Standard polar	33892256
Cyclic-hpmpc,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O[Si](C)(C)C(C)(C)C)CO2)C=C1	2985.0	Semi standard non polar	33892256
Cyclic-hpmpc,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O[Si](C)(C)C(C)(C)C)CO2)C=C1	2752.8	Standard non polar	33892256
Cyclic-hpmpc,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(CC2COP(=O)(O[Si](C)(C)C(C)(C)C)CO2)C=C1	3424.9	Standard polar	33892256
Cyclic-hpmpc,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1)[Si](C)(C)C(C)(C)C	2981.3	Semi standard non polar	33892256
Cyclic-hpmpc,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1)[Si](C)(C)C(C)(C)C	2870.4	Standard non polar	33892256
Cyclic-hpmpc,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(CC2COP(=O)(O)CO2)C=C1)[Si](C)(C)C(C)(C)C	3658.7	Standard polar	33892256
Cyclic-hpmpc,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP1(=O)COC(CN2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CO1	3109.3	Semi standard non polar	33892256
Cyclic-hpmpc,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP1(=O)COC(CN2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CO1	3046.3	Standard non polar	33892256
Cyclic-hpmpc,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP1(=O)COC(CN2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CO1	3208.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Cyclic-hpmpc GC-MS (Non-derivatized) - 70eV, Positive	splash10-00ou-5910000000-fd8f4605772312803297	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cyclic-hpmpc GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cyclic-hpmpc 10V, Positive-QTOF	splash10-03di-0090000000-29a5a7cb586d2b20c2cb	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cyclic-hpmpc 20V, Positive-QTOF	splash10-03di-1490000000-0f202d4f2ea60e8c6cae	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cyclic-hpmpc 40V, Positive-QTOF	splash10-0159-9100000000-f0bebd4723fbc02115a9	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cyclic-hpmpc 10V, Negative-QTOF	splash10-03di-0090000000-95f1523b0e909d9e8eb8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cyclic-hpmpc 20V, Negative-QTOF	splash10-03di-3690000000-089186b6fb3494b92e0f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cyclic-hpmpc 40V, Negative-QTOF	splash10-0006-9300000000-675458219442a903ebbe	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

13950869

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

18914028

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for Cyclic-hpmpc (HMDB0250198)

MOL for HMDB0250198 (Cyclic-hpmpc)

3D MOL for HMDB0250198 (Cyclic-hpmpc)

3D SDF for HMDB0250198 (Cyclic-hpmpc)

3D-SDF for HMDB0250198 (Cyclic-hpmpc)

PDB for HMDB0250198 (Cyclic-hpmpc)

3D PDB for HMDB0250198 (Cyclic-hpmpc)

SMILES for HMDB0250198 (Cyclic-hpmpc)

INCHI for HMDB0250198 (Cyclic-hpmpc)

Structure for HMDB0250198 (Cyclic-hpmpc)

3D Structure for HMDB0250198 (Cyclic-hpmpc)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra