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Showing metabocard for Pentaerythritol mononitrate (HMDB0256252)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:35:53 UTC
Update Date2021-09-26 23:11:46 UTC
HMDB IDHMDB0256252
Secondary Accession NumbersNone
Metabolite Identification
Common NamePentaerythritol mononitrate
DescriptionPentaerythritol mononitrate belongs to the class of organic compounds known as alkyl nitrates. These are organic compounds containing a nitrate that is O-linked to an alkyl group. Based on a literature review a small amount of articles have been published on Pentaerythritol mononitrate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pentaerythritol mononitrate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pentaerythritol mononitrate 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 HMDB0256252 (Pentaerythritol mononitrate)

  Mrv1652309112118362D          

 12 11  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.0164    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    4.0145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -1.7309    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 O   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
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  1 12  1  0  0  0  0
M  CHG  2   9   1  11  -1
M  END
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3D MOL for HMDB0256252 (Pentaerythritol mononitrate)

HMDB0256252
     RDKit          3D
Pentaerythritol mononitrate
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.7486   -1.9494   -0.1192 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1951   -0.8633    0.0945 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.9405    0.2632    0.3691 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.8433   -0.7333    0.0685 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1586    0.4526   -0.2854 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3224    0.1560   -0.1803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1405    1.3715   -0.5419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8383    2.4192    0.3181 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5842   -0.3060    1.2335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9147   -0.6104    1.4570 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6279   -0.9797   -1.1332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9744   -1.2889   -1.0734 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3790    0.7912   -1.3092 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4264    1.2145    0.4917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2028    1.1627   -0.6516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7680    1.6972   -1.5573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    3.0595    0.3348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2639    0.4597    1.9707 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0421   -1.2017    1.4227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0420   -0.5902    2.4537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0234   -1.8526   -0.7931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3121   -0.6498   -2.1429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1138   -2.0220   -0.4266 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
  6 11  1  0
 11 12  1  0
  5 13  1  0
  5 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 11 22  1  0
 12 23  1  0
M  CHG  2   2   1   3  -1
M  END
Download

3D SDF for HMDB0256252 (Pentaerythritol mononitrate)

  Mrv1652309112118362D          

 12 11  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.0164    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    4.0145   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -1.7309    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 O   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
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  1 12  1  0  0  0  0
M  CHG  2   9   1  11  -1
M  END
> <DATABASE_ID>
HMDB0256252

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC(CO)(CO)CO[N+]([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO6/c7-1-5(2-8,3-9)4-12-6(10)11/h7-9H,1-4H2

> <INCHI_KEY>
RHVYBZNTBGYKKV-UHFFFAOYSA-N

> <FORMULA>
C5H11NO6

> <MOLECULAR_WEIGHT>
181.144

> <EXACT_MASS>
181.058637078

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.865756894558304

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)-2-[(nitrooxy)methyl]propane-1,3-diol

> <ALOGPS_LOGP>
-1.57

> <JCHEM_LOGP>
-2.0400718713333332

> <ALOGPS_LOGS>
-0.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.984133941279715

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.412787019501192

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8469541208557976

> <JCHEM_POLAR_SURFACE_AREA>
113.06

> <JCHEM_REFRACTIVITY>
37.4175

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.76e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(hydroxymethyl)-2-[(nitrooxy)methyl]propane-1,3-diol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0256252 (Pentaerythritol mononitrate)

HMDB0256252
     RDKit          3D
Pentaerythritol mononitrate
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.7486   -1.9494   -0.1192 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1951   -0.8633    0.0945 N   0  0  0  0  0  4  0  0  0  0  0  0
    3.9405    0.2632    0.3691 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.8433   -0.7333    0.0685 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1586    0.4526   -0.2854 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3224    0.1560   -0.1803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1405    1.3715   -0.5419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8383    2.4192    0.3181 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5842   -0.3060    1.2335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9147   -0.6104    1.4570 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6279   -0.9797   -1.1332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9744   -1.2889   -1.0734 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3790    0.7912   -1.3092 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4264    1.2145    0.4917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2028    1.1627   -0.6516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7680    1.6972   -1.5573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    3.0595    0.3348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2639    0.4597    1.9707 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0421   -1.2017    1.4227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0420   -0.5902    2.4537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0234   -1.8526   -0.7931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3121   -0.6498   -2.1429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1138   -2.0220   -0.4266 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  6  9  1  0
  9 10  1  0
  6 11  1  0
 11 12  1  0
  5 13  1  0
  5 14  1  0
  7 15  1  0
  7 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 11 22  1  0
 12 23  1  0
M  CHG  2   2   1   3  -1
M  END
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PDB for HMDB0256252 (Pentaerythritol mononitrate)

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       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.104   2.104   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.564   2.104   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.207   1.540   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.541   0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.644  -0.564   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.184  -0.564   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       5.954  -1.897   0.000  0.00  0.00           N+1
HETATM   10  O   UNK     0       7.494  -1.897   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.184  -3.231   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       0.206   0.770   0.000  0.00  0.00           O+0
CONECT    1    2   12                                                       
CONECT    2    1    3    5    7                                             
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5                                                            
CONECT    7    2    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    1                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for HMDB0256252 (Pentaerythritol mononitrate)

COMPND    HMDB0256252
HETATM    1  O1  UNL     1       3.749  -1.949  -0.119  1.00  0.00           O  
HETATM    2  N1  UNL     1       3.195  -0.863   0.095  1.00  0.00           N1+
HETATM    3  O2  UNL     1       3.940   0.263   0.369  1.00  0.00           O1-
HETATM    4  O3  UNL     1       1.843  -0.733   0.069  1.00  0.00           O  
HETATM    5  C1  UNL     1       1.159   0.453  -0.285  1.00  0.00           C  
HETATM    6  C2  UNL     1      -0.322   0.156  -0.180  1.00  0.00           C  
HETATM    7  C3  UNL     1      -1.140   1.371  -0.542  1.00  0.00           C  
HETATM    8  O4  UNL     1      -0.838   2.419   0.318  1.00  0.00           O  
HETATM    9  C4  UNL     1      -0.584  -0.306   1.233  1.00  0.00           C  
HETATM   10  O5  UNL     1      -1.915  -0.610   1.457  1.00  0.00           O  
HETATM   11  C5  UNL     1      -0.628  -0.980  -1.133  1.00  0.00           C  
HETATM   12  O6  UNL     1      -1.974  -1.289  -1.073  1.00  0.00           O  
HETATM   13  H1  UNL     1       1.379   0.791  -1.309  1.00  0.00           H  
HETATM   14  H2  UNL     1       1.426   1.214   0.492  1.00  0.00           H  
HETATM   15  H3  UNL     1      -2.203   1.163  -0.652  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.768   1.697  -1.557  1.00  0.00           H  
HETATM   17  H5  UNL     1      -1.605   3.060   0.335  1.00  0.00           H  
HETATM   18  H6  UNL     1      -0.264   0.460   1.971  1.00  0.00           H  
HETATM   19  H7  UNL     1       0.042  -1.202   1.423  1.00  0.00           H  
HETATM   20  H8  UNL     1      -2.042  -0.590   2.454  1.00  0.00           H  
HETATM   21  H9  UNL     1      -0.023  -1.853  -0.793  1.00  0.00           H  
HETATM   22  H10 UNL     1      -0.312  -0.650  -2.143  1.00  0.00           H  
HETATM   23  H11 UNL     1      -2.114  -2.022  -0.427  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5
CONECT    5    6   13   14
CONECT    6    7    9   11
CONECT    7    8   15   16
CONECT    8   17
CONECT    9   10   18   19
CONECT   10   20
CONECT   11   12   21   22
CONECT   12   23
END
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SMILES for HMDB0256252 (Pentaerythritol mononitrate)

OCC(CO)(CO)CO[N+]([O-])=O
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INCHI for HMDB0256252 (Pentaerythritol mononitrate)

InChI=1S/C5H11NO6/c7-1-5(2-8,3-9)4-12-6(10)11/h7-9H,1-4H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Pentaerythritol mononitric acidGenerator
Chemical FormulaC5H11NO6
Average Molecular Weight181.144
Monoisotopic Molecular Weight181.058637078
IUPAC Name2-(hydroxymethyl)-2-[(nitrooxy)methyl]propane-1,3-diol
Traditional Name2-(hydroxymethyl)-2-[(nitrooxy)methyl]propane-1,3-diol
CAS Registry NumberNot Available
SMILES
OCC(CO)(CO)CO[N+]([O-])=O
InChI Identifier
InChI=1S/C5H11NO6/c7-1-5(2-8,3-9)4-12-6(10)11/h7-9H,1-4H2
InChI KeyRHVYBZNTBGYKKV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkyl nitrates. These are organic compounds containing a nitrate that is O-linked to an alkyl group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic nitrates
Direct ParentAlkyl nitrates
Alternative Parents
Substituents
  • Alkyl nitrate
  • Organic nitro compound
  • Organic nitric acid or derivatives
  • Organic 1,3-dipolar compound
  • Allyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic zwitterion
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • 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 ID133030
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound150933
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 ]