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Showing metabocard for Glutarimide (HMDB0252816)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 10:54:24 UTC
Update Date2021-09-26 23:05:40 UTC
HMDB IDHMDB0252816
Secondary Accession NumbersNone
Metabolite Identification
Common NameGlutarimide
DescriptionGlutarimide belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms. Based on a literature review a significant number of articles have been published on Glutarimide. This compound has been identified in human blood as reported by (PMID: 31557052 ). Glutarimide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Glutarimide 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 HMDB0252816 (Glutarimide)


  Mrv1652309112112542D          

  8  8  0  0  0  0            999 V2000
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
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3D MOL for HMDB0252816 (Glutarimide)

HMDB0252816
     RDKit          3D
Glutarimide
 15 15  0  0  0  0  0  0  0  0999 V2000
    1.7928    1.9430   -0.5720 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1008    1.0471   -0.0734 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2748    1.2529    0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1866    0.3340   -0.2975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7414   -1.0821   -0.2682 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6320   -1.3083    0.2244 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9512   -2.3863    0.8346 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5944   -0.2851   -0.0018 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5903    2.2903    0.4326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2668    0.8557    1.5421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1799    0.7048   -1.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2177    0.4240    0.1456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7696   -1.5117   -1.3128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4462   -1.7456    0.3074 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6023   -0.5327   -0.1045 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  2  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  8 15  1  0
M  END
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3D SDF for HMDB0252816 (Glutarimide)


  Mrv1652309112112542D          

  8  8  0  0  0  0            999 V2000
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0252816

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCCC(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO2/c7-4-2-1-3-5(8)6-4/h1-3H2,(H,6,7,8)

> <INCHI_KEY>
KNCYXPMJDCCGSJ-UHFFFAOYSA-N

> <FORMULA>
C5H7NO2

> <MOLECULAR_WEIGHT>
113.116

> <EXACT_MASS>
113.047678469

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.757647496487664

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
piperidine-2,6-dione

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
-0.548902896

> <ALOGPS_LOGS>
0.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.805803979371273

> <JCHEM_PKA_STRONGEST_BASIC>
-6.577973031398058

> <JCHEM_POLAR_SURFACE_AREA>
46.17

> <JCHEM_REFRACTIVITY>
26.8824

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.47e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glutarimide

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0252816 (Glutarimide)

HMDB0252816
     RDKit          3D
Glutarimide
 15 15  0  0  0  0  0  0  0  0999 V2000
    1.7928    1.9430   -0.5720 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1008    1.0471   -0.0734 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2748    1.2529    0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1866    0.3340   -0.2975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7414   -1.0821   -0.2682 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6320   -1.3083    0.2244 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9512   -2.3863    0.8346 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5944   -0.2851   -0.0018 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5903    2.2903    0.4326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2668    0.8557    1.5421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1799    0.7048   -1.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2177    0.4240    0.1456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7696   -1.5117   -1.3128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4462   -1.7456    0.3074 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6023   -0.5327   -0.1045 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  2  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  8 15  1  0
M  END
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PDB for HMDB0252816 (Glutarimide)

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   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    1                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0252816 (Glutarimide)

COMPND    HMDB0252816
HETATM    1  O1  UNL     1       1.793   1.943  -0.572  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.101   1.047  -0.073  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.275   1.253   0.487  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.187   0.334  -0.298  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.741  -1.082  -0.268  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.632  -1.308   0.224  1.00  0.00           C  
HETATM    7  O2  UNL     1       0.951  -2.386   0.835  1.00  0.00           O  
HETATM    8  N1  UNL     1       1.594  -0.285  -0.002  1.00  0.00           N  
HETATM    9  H1  UNL     1      -0.590   2.290   0.433  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.267   0.856   1.542  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.180   0.705  -1.344  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.218   0.424   0.146  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.770  -1.512  -1.313  1.00  0.00           H  
HETATM   14  H6  UNL     1      -1.446  -1.746   0.307  1.00  0.00           H  
HETATM   15  H7  UNL     1       2.602  -0.533  -0.105  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5    6   13   14
CONECT    6    7    7    8
CONECT    8   15
END
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SMILES for HMDB0252816 (Glutarimide)

O=C1CCCC(=O)N1
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INCHI for HMDB0252816 (Glutarimide)

InChI=1S/C5H7NO2/c7-4-2-1-3-5(8)6-4/h1-3H2,(H,6,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2,6-DiketopiperidineChEBI
2,6-PiperidinedioneChEBI
Piperidine-2,6-dioneKegg
Glutarimide calcium saltHMDB
GlutarimideChEBI
Chemical FormulaC5H7NO2
Average Molecular Weight113.116
Monoisotopic Molecular Weight113.047678469
IUPAC Namepiperidine-2,6-dione
Traditional Nameglutarimide
CAS Registry NumberNot Available
SMILES
O=C1CCCC(=O)N1
InChI Identifier
InChI=1S/C5H7NO2/c7-4-2-1-3-5(8)6-4/h1-3H2,(H,6,7,8)
InChI KeyKNCYXPMJDCCGSJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHydropyridines
Direct ParentTetrahydropyridines
Alternative Parents
Substituents
  • Tetrahydropyridine
  • N-acylimine
  • Lactim
  • Carboxylic acid derivative
  • Propargyl-type 1,3-dipolar organic compound
  • Azacycle
  • Organic 1,3-dipolar compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen 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
logP-0.59ALOGPS
logP-0.55ChemAxon
logS0.11ALOGPS
pKa (Strongest Acidic)11.81ChemAxon
pKa (Strongest Basic)-6.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area46.17 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.88 m³·mol⁻¹ChemAxon
Polarizability10.76 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+127.4430932474
DeepCCS[M-H]-125.47330932474
DeepCCS[M-2H]-161.32330932474
DeepCCS[M+Na]+135.85930932474
AllCCS[M+H]+123.432859911
AllCCS[M+H-H2O]+118.432859911
AllCCS[M+NH4]+128.032859911
AllCCS[M+Na]+129.332859911
AllCCS[M-H]-120.132859911
AllCCS[M+Na-2H]-122.632859911
AllCCS[M+HCOO]-125.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.4914 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.79 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1316.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid339.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid114.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid224.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid107.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid261.6 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 Acid383.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)99.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid733.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid246.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid886.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid223.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid262.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate511.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA238.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water161.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
GlutarimideO=C1CCCC(=O)N12634.2Standard polar33892256
GlutarimideO=C1CCCC(=O)N11037.7Standard non polar33892256
GlutarimideO=C1CCCC(=O)N11142.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Glutarimide,1TMS,isomer #1C[Si](C)(C)N1C(=O)CCCC1=O1289.3Semi standard non polar33892256
Glutarimide,1TMS,isomer #1C[Si](C)(C)N1C(=O)CCCC1=O1308.7Standard non polar33892256
Glutarimide,1TMS,isomer #1C[Si](C)(C)N1C(=O)CCCC1=O1870.9Standard polar33892256
Glutarimide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(=O)CCCC1=O1536.0Semi standard non polar33892256
Glutarimide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(=O)CCCC1=O1572.0Standard non polar33892256
Glutarimide,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C(=O)CCCC1=O1951.3Standard 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 ID63891
KEGG Compound IDC07275
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGlutarimide
METLIN IDNot Available
PubChem Compound70726
PDB IDNot Available
ChEBI ID5435
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 ]