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Showing metabocard for Bucolome (HMDB0249422)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 03:56:00 UTC
Update Date2021-09-26 23:00:18 UTC
HMDB IDHMDB0249422
Secondary Accession NumbersNone
Metabolite Identification
Common NameBucolome
Description5-butyl-1-cyclohexylbarbituric acid, also known as paramidin or bucolome, 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 very few articles have been published on 5-butyl-1-cyclohexylbarbituric acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Bucolome is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Bucolome 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 HMDB0249422 (Bucolome)


  Mrv1572004221606222D          

 19 20  0  0  0  0            999 V2000
    2.8579    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    7.0125    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
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    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
    2.1434    6.1875    0.0000 C   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
    1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.1875    0.0000 C   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
   -0.0000    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    5.7750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  3  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  1  0  0  0  0
 15 12  2  0  0  0  0
 15 14  1  0  0  0  0
 16 10  1  0  0  0  0
 16 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 12  1  0  0  0  0
 18 13  2  0  0  0  0
 19 14  2  0  0  0  0
M  END
Download

3D MOL for HMDB0249422 (Bucolome)

HMDB0249422
     RDKit          3D
Bucolome
 41 42  0  0  0  0  0  0  0  0999 V2000
    4.6056    0.9252    1.2877 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7956    0.6005   -0.1591 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7573   -0.4176   -0.6517 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3810    0.0857   -0.4968 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3332   -0.8752   -1.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0090   -0.2834   -0.8400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2822    0.8734   -1.3372 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0241   -0.9277   -0.1261 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3055   -0.2557    0.0554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0157   -0.0178   -1.2542 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4416    0.4181   -0.8910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3568    1.7016   -0.1140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6090    1.4682    1.1665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1775    1.0160    0.8468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7953   -2.2255    0.4123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7043   -2.7971    1.0434 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4810   -2.7607    0.1730 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4379   -2.2032   -0.4599 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6635   -2.9168   -0.6141 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5898    1.3184    1.6666 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8821    1.7488    1.4434 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3865    0.0202    1.8568 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6935    1.5146   -0.7801 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8008    0.1603   -0.3063 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9743   -1.3200   -0.0026 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0419   -0.6958   -1.6766 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2016    1.0816   -0.9336 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1407    0.1681    0.6033 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -0.9093   -2.1713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9438   -0.9453    0.6427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5465    0.7272   -1.8941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1279   -1.0218   -1.7419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0513    0.5076   -1.8046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8288   -0.3669   -0.2077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9218    2.5346   -0.6699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4067    1.9811    0.1732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0828    0.6038    1.7046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6183    2.3886    1.7702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6390    1.8115    0.3187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7087    0.7657    1.8257 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9299   -3.4808    0.1820 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  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
  8 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 18  5  1  0
 14  9  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  9 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 14 40  1  0
 19 41  1  0
M  END
Download

3D SDF for HMDB0249422 (Bucolome)


  Mrv1572004221606222D          

 19 20  0  0  0  0            999 V2000
    2.8579    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    7.0125    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
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    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
    2.1434    6.1875    0.0000 C   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
    1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.1875    0.0000 C   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
   -0.0000    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    5.7750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  3  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  1  0  0  0  0
 15 12  2  0  0  0  0
 15 14  1  0  0  0  0
 16 10  1  0  0  0  0
 16 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 12  1  0  0  0  0
 18 13  2  0  0  0  0
 19 14  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0249422

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC1C(O)=NC(=O)N(C2CCCCC2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H22N2O3/c1-2-3-9-11-12(17)15-14(19)16(13(11)18)10-7-5-4-6-8-10/h10-11H,2-9H2,1H3,(H,15,17,19)

> <INCHI_KEY>
DVEQCIBLXRSYPH-UHFFFAOYSA-N

> <FORMULA>
C14H22N2O3

> <MOLECULAR_WEIGHT>
266.341

> <EXACT_MASS>
266.163042576

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
29.016575304495337

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-butyl-3-cyclohexyl-6-hydroxy-2,3,4,5-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
1.89

> <JCHEM_LOGP>
2.996096584999999

> <ALOGPS_LOGS>
-2.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.958691196913648

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5039743743079743

> <JCHEM_PKA_STRONGEST_BASIC>
-2.4623682676411494

> <JCHEM_POLAR_SURFACE_AREA>
69.97

> <JCHEM_REFRACTIVITY>
70.58489999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.87e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
bucolome

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0249422 (Bucolome)

HMDB0249422
     RDKit          3D
Bucolome
 41 42  0  0  0  0  0  0  0  0999 V2000
    4.6056    0.9252    1.2877 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7956    0.6005   -0.1591 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7573   -0.4176   -0.6517 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3810    0.0857   -0.4968 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3332   -0.8752   -1.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0090   -0.2834   -0.8400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2822    0.8734   -1.3372 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0241   -0.9277   -0.1261 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3055   -0.2557    0.0554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0157   -0.0178   -1.2542 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4416    0.4181   -0.8910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3568    1.7016   -0.1140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6090    1.4682    1.1665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1775    1.0160    0.8468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7953   -2.2255    0.4123 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7043   -2.7971    1.0434 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4810   -2.7607    0.1730 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4379   -2.2032   -0.4599 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6635   -2.9168   -0.6141 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5898    1.3184    1.6666 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8821    1.7488    1.4434 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3865    0.0202    1.8568 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6935    1.5146   -0.7801 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8008    0.1603   -0.3063 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9743   -1.3200   -0.0026 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0419   -0.6958   -1.6766 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2016    1.0816   -0.9336 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1407    0.1681    0.6033 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004   -0.9093   -2.1713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9438   -0.9453    0.6427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5465    0.7272   -1.8941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1279   -1.0218   -1.7419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0513    0.5076   -1.8046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8288   -0.3669   -0.2077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9218    2.5346   -0.6699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4067    1.9811    0.1732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0828    0.6038    1.7046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6183    2.3886    1.7702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6390    1.8115    0.3187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7087    0.7657    1.8257 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9299   -3.4808    0.1820 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  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
  8 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 18  5  1  0
 14  9  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  9 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 12 36  1  0
 13 37  1  0
 13 38  1  0
 14 39  1  0
 14 40  1  0
 19 41  1  0
M  END
Download

PDB for HMDB0249422 (Bucolome)

HEADER    PROTEIN                                 22-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-APR-16         0                                  
HETATM    1  C   UNK     0       5.335  15.400   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335  13.860   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.000   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.000   6.160   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  11.550   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.000   9.240   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -0.000  10.780   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       1.334   8.470   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0       1.334  13.090   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.001   8.470   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.334   8.470   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    9                                                       
CONECT    4    5    6                                                       
CONECT    5    4    7                                                       
CONECT    6    4    8                                                       
CONECT    7    5   10                                                       
CONECT    8    6   10                                                       
CONECT    9    3   11                                                       
CONECT   10    7    8   16                                                  
CONECT   11    9   12   13                                                  
CONECT   12   11   15   17                                                  
CONECT   13   11   16   18                                                  
CONECT   14   15   16   19                                                  
CONECT   15   12   14                                                       
CONECT   16   10   13   14                                                  
CONECT   17   12                                                            
CONECT   18   13                                                            
CONECT   19   14                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END
Download

3D PDB for HMDB0249422 (Bucolome)

COMPND    HMDB0249422
HETATM    1  C1  UNL     1       4.606   0.925   1.288  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.796   0.601  -0.159  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.757  -0.418  -0.652  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.381   0.086  -0.497  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.333  -0.875  -1.036  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.009  -0.283  -0.840  1.00  0.00           C  
HETATM    7  O1  UNL     1      -0.282   0.873  -1.337  1.00  0.00           O  
HETATM    8  N1  UNL     1      -1.024  -0.928  -0.126  1.00  0.00           N  
HETATM    9  C7  UNL     1      -2.306  -0.256   0.055  1.00  0.00           C  
HETATM   10  C8  UNL     1      -3.016  -0.018  -1.254  1.00  0.00           C  
HETATM   11  C9  UNL     1      -4.442   0.418  -0.891  1.00  0.00           C  
HETATM   12  C10 UNL     1      -4.357   1.702  -0.114  1.00  0.00           C  
HETATM   13  C11 UNL     1      -3.609   1.468   1.166  1.00  0.00           C  
HETATM   14  C12 UNL     1      -2.178   1.016   0.847  1.00  0.00           C  
HETATM   15  C13 UNL     1      -0.795  -2.225   0.412  1.00  0.00           C  
HETATM   16  O2  UNL     1      -1.704  -2.797   1.043  1.00  0.00           O  
HETATM   17  N2  UNL     1       0.481  -2.761   0.173  1.00  0.00           N  
HETATM   18  C14 UNL     1       1.438  -2.203  -0.460  1.00  0.00           C  
HETATM   19  O3  UNL     1       2.663  -2.917  -0.614  1.00  0.00           O  
HETATM   20  H1  UNL     1       5.590   1.318   1.667  1.00  0.00           H  
HETATM   21  H2  UNL     1       3.882   1.749   1.443  1.00  0.00           H  
HETATM   22  H3  UNL     1       4.386   0.020   1.857  1.00  0.00           H  
HETATM   23  H4  UNL     1       4.694   1.515  -0.780  1.00  0.00           H  
HETATM   24  H5  UNL     1       5.801   0.160  -0.306  1.00  0.00           H  
HETATM   25  H6  UNL     1       3.974  -1.320  -0.003  1.00  0.00           H  
HETATM   26  H7  UNL     1       4.042  -0.696  -1.677  1.00  0.00           H  
HETATM   27  H8  UNL     1       2.202   1.082  -0.934  1.00  0.00           H  
HETATM   28  H9  UNL     1       2.141   0.168   0.603  1.00  0.00           H  
HETATM   29  H10 UNL     1       1.500  -0.909  -2.171  1.00  0.00           H  
HETATM   30  H11 UNL     1      -2.944  -0.945   0.643  1.00  0.00           H  
HETATM   31  H12 UNL     1      -2.547   0.727  -1.894  1.00  0.00           H  
HETATM   32  H13 UNL     1      -3.128  -1.022  -1.742  1.00  0.00           H  
HETATM   33  H14 UNL     1      -5.051   0.508  -1.805  1.00  0.00           H  
HETATM   34  H15 UNL     1      -4.829  -0.367  -0.208  1.00  0.00           H  
HETATM   35  H16 UNL     1      -3.922   2.535  -0.670  1.00  0.00           H  
HETATM   36  H17 UNL     1      -5.407   1.981   0.173  1.00  0.00           H  
HETATM   37  H18 UNL     1      -4.083   0.604   1.705  1.00  0.00           H  
HETATM   38  H19 UNL     1      -3.618   2.389   1.770  1.00  0.00           H  
HETATM   39  H20 UNL     1      -1.639   1.811   0.319  1.00  0.00           H  
HETATM   40  H21 UNL     1      -1.709   0.766   1.826  1.00  0.00           H  
HETATM   41  H22 UNL     1       2.930  -3.481   0.182  1.00  0.00           H  
CONECT    1    2   20   21   22
CONECT    2    3   23   24
CONECT    3    4   25   26
CONECT    4    5   27   28
CONECT    5    6   18   29
CONECT    6    7    7    8
CONECT    8    9   15
CONECT    9   10   14   30
CONECT   10   11   31   32
CONECT   11   12   33   34
CONECT   12   13   35   36
CONECT   13   14   37   38
CONECT   14   39   40
CONECT   15   16   16   17
CONECT   17   18   18
CONECT   18   19
CONECT   19   41
END
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SMILES for HMDB0249422 (Bucolome)

CCCCC1C(O)=NC(=O)N(C2CCCCC2)C1=O
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INCHI for HMDB0249422 (Bucolome)

InChI=1S/C14H22N2O3/c1-2-3-9-11-12(17)15-14(19)16(13(11)18)10-7-5-4-6-8-10/h10-11H,2-9H2,1H3,(H,15,17,19)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
5-Butyl-1-cyclohexyl-2,4,6(1H,3H,5H)-pyrimidinetrioneChEBI
BucolomeChEBI
ParamidinKegg
5-Butyl-1-cyclohexylbarbitateGenerator
5-Butyl-1-cyclohexylbarbitic acidGenerator
1-Cyclohexyl-5-butylbarbituric acidMeSH
ParamidineMeSH
Chemical FormulaC14H22N2O3
Average Molecular Weight266.341
Monoisotopic Molecular Weight266.163042576
IUPAC Name5-butyl-3-cyclohexyl-6-hydroxy-2,3,4,5-tetrahydropyrimidine-2,4-dione
Traditional Namebucolome
CAS Registry NumberNot Available
SMILES
CCCCC1C(O)=NC(=O)N(C2CCCCC2)C1=O
InChI Identifier
InChI=1S/C14H22N2O3/c1-2-3-9-11-12(17)15-14(19)16(13(11)18)10-7-5-4-6-8-10/h10-11H,2-9H2,1H3,(H,15,17,19)
InChI KeyDVEQCIBLXRSYPH-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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • 1,2,5,6-tetrahydropyrimidine
  • Dicarboximide
  • Carbonic acid derivative
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboxylic acid derivative
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Organopnictogen compound
  • Organic oxygen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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
PropertyValueSource
logP1.89ALOGPS
logP3ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)3.5ChemAxon
pKa (Strongest Basic)-2.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area69.97 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity70.58 m³·mol⁻¹ChemAxon
Polarizability29.02 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+167.77930932474
DeepCCS[M-H]-165.42130932474
DeepCCS[M-2H]-198.30730932474
DeepCCS[M+Na]+173.87230932474
AllCCS[M+H]+163.732859911
AllCCS[M+H-H2O]+160.432859911
AllCCS[M+NH4]+166.932859911
AllCCS[M+Na]+167.832859911
AllCCS[M-H]-166.632859911
AllCCS[M+Na-2H]-166.632859911
AllCCS[M+HCOO]-166.832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202217.216 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.53 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2656.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid482.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid198.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid257.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid494.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid728.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid816.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)102.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1507.2 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid508.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1664.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid454.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid436.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate444.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA385.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water19.3 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
BucolomeCCCCC1C(O)=NC(=O)N(C2CCCCC2)C1=O3108.9Standard polar33892256
BucolomeCCCCC1C(O)=NC(=O)N(C2CCCCC2)C1=O2179.2Standard non polar33892256
BucolomeCCCCC1C(O)=NC(=O)N(C2CCCCC2)C1=O2060.6Semi standard non polar33892256
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 ID2367
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound2461
PDB IDNot Available
ChEBI ID31314
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 ]