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Showing metabocard for Monomethyl succinate (HMDB0246492)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:30:37 UTC
Update Date2021-09-26 22:55:37 UTC
HMDB IDHMDB0246492
Secondary Accession NumbersNone
Metabolite Identification
Common NameMonomethyl succinate
Descriptionmonomethyl succinate belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group. Based on a literature review a significant number of articles have been published on monomethyl succinate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Monomethyl succinate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Monomethyl succinate 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 HMDB0246492 (Monomethyl succinate)


  Mrv0541 05041407572D          

  9  8  0  0  0  0            999 V2000
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    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
    3.5724    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  8  5  2  0  0  0  0
  9  1  1  0  0  0  0
  9  5  1  0  0  0  0
M  END
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3D MOL for HMDB0246492 (Monomethyl succinate)

HMDB0246492
     RDKit          3D
Monomethyl succinate
 17 16  0  0  0  0  0  0  0  0999 V2000
    2.6991    1.3009   -0.1126 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6792    0.4405   -0.5604 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9485   -0.4093    0.2343 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2042   -0.4274    1.4797 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1126   -1.2984   -0.2865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4977   -0.9564    0.1602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9035    0.4070   -0.2422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1361    1.3825   -0.0391 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1240    0.6238   -0.8459 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6081    2.2951   -0.5618 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6717    0.8007   -0.3273 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6137    1.3001    1.0112 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0687   -2.3827    0.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0605   -1.3290   -1.3988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5505   -1.0619    1.2800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1740   -1.7390   -0.2469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344    1.0536   -0.4671 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
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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3D SDF for HMDB0246492 (Monomethyl succinate)


  Mrv0541 05041407572D          

  9  8  0  0  0  0            999 V2000
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    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
    3.5724    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  8  5  2  0  0  0  0
  9  1  1  0  0  0  0
  9  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246492

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O4/c1-9-5(8)3-2-4(6)7/h2-3H2,1H3,(H,6,7)

> <INCHI_KEY>
JDRMYOQETPMYQX-UHFFFAOYSA-N

> <FORMULA>
C5H8O4

> <MOLECULAR_WEIGHT>
132.1146

> <EXACT_MASS>
132.042258744

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
12.159632050161846

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-methoxy-4-oxobutanoic acid

> <ALOGPS_LOGP>
-0.13

> <JCHEM_LOGP>
-0.2525889113333334

> <ALOGPS_LOGS>
0.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.053937854380926

> <JCHEM_PKA_STRONGEST_BASIC>
-7.029745225080873

> <JCHEM_POLAR_SURFACE_AREA>
63.599999999999994

> <JCHEM_REFRACTIVITY>
28.3061

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.84e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-methoxy-4-oxobutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0246492 (Monomethyl succinate)

HMDB0246492
     RDKit          3D
Monomethyl succinate
 17 16  0  0  0  0  0  0  0  0999 V2000
    2.6991    1.3009   -0.1126 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6792    0.4405   -0.5604 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9485   -0.4093    0.2343 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2042   -0.4274    1.4797 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1126   -1.2984   -0.2865 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4977   -0.9564    0.1602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9035    0.4070   -0.2422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1361    1.3825   -0.0391 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1240    0.6238   -0.8459 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6081    2.2951   -0.5618 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6717    0.8007   -0.3273 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6137    1.3001    1.0112 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0687   -2.3827    0.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0605   -1.3290   -1.3988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5505   -1.0619    1.2800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1740   -1.7390   -0.2469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9344    1.0536   -0.4671 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
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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PDB for HMDB0246492 (Monomethyl succinate)

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6    7                                                  
CONECT    5    3    8    9                                                  
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9    1    5                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0246492 (Monomethyl succinate)

COMPND    HMDB0246492
HETATM    1  C1  UNL     1       2.699   1.301  -0.113  1.00  0.00           C  
HETATM    2  O1  UNL     1       1.679   0.440  -0.560  1.00  0.00           O  
HETATM    3  C2  UNL     1       0.948  -0.409   0.234  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.204  -0.427   1.480  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.113  -1.298  -0.287  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.498  -0.956   0.160  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.904   0.407  -0.242  1.00  0.00           C  
HETATM    8  O3  UNL     1      -1.136   1.382  -0.039  1.00  0.00           O  
HETATM    9  O4  UNL     1      -3.124   0.624  -0.846  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.608   2.295  -0.562  1.00  0.00           H  
HETATM   11  H2  UNL     1       3.672   0.801  -0.327  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.614   1.300   1.011  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.069  -2.383   0.001  1.00  0.00           H  
HETATM   14  H5  UNL     1      -0.060  -1.329  -1.399  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.550  -1.062   1.280  1.00  0.00           H  
HETATM   16  H7  UNL     1      -2.174  -1.739  -0.247  1.00  0.00           H  
HETATM   17  H8  UNL     1      -3.934   1.054  -0.467  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3
CONECT    3    4    4    5
CONECT    5    6   13   14
CONECT    6    7   15   16
CONECT    7    8    8    9
CONECT    9   17
END
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SMILES for HMDB0246492 (Monomethyl succinate)

COC(=O)CCC(O)=O
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INCHI for HMDB0246492 (Monomethyl succinate)

InChI=1S/C5H8O4/c1-9-5(8)3-2-4(6)7/h2-3H2,1H3,(H,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-Carbomethoxypropanoic acidChEBI
Butanedioic acid 1-methyl esterChEBI
Butanedioic acid monomethyl esterChEBI
Butanedioic acid, 1-methyl esterChEBI
Methyl hydrogen succinateChEBI
Succinic acid 4-methyl esterChEBI
Succinic acid monomethyl esterChEBI
Succinic acid, monomethyl esterChEBI
3-CarbomethoxypropanoateGenerator
Butanedioate 1-methyl esterGenerator
Butanedioate monomethyl esterGenerator
Butanedioate, 1-methyl esterGenerator
Methyl hydrogen succinic acidGenerator
Succinate 4-methyl esterGenerator
Succinate monomethyl esterGenerator
Succinate, monomethyl esterGenerator
Monomethyl succinic acidGenerator
3H-MethylsuccinateMeSH, HMDB
DL-MethylsuccinateMeSH, HMDB
Monomethyl succinate sodium saltMeSH, HMDB
Methyl succinateMeSH, HMDB
(S)-MethylbutanethioateGenerator
Monomethyl succinateMeSH
Chemical FormulaC5H8O4
Average Molecular Weight132.1146
Monoisotopic Molecular Weight132.042258744
IUPAC Name4-methoxy-4-oxobutanoic acid
Traditional Name4-methoxy-4-oxobutanoic acid
CAS Registry NumberNot Available
SMILES
COC(=O)CCC(O)=O
InChI Identifier
InChI=1S/C5H8O4/c1-9-5(8)3-2-4(6)7/h2-3H2,1H3,(H,6,7)
InChI KeyJDRMYOQETPMYQX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acid esters
Direct ParentFatty acid methyl esters
Alternative Parents
Substituents
  • Fatty acid methyl ester
  • Dicarboxylic acid or derivatives
  • Methyl ester
  • Carboxylic acid ester
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-0.13ALOGPS
logP-0.25ChemAxon
logS0.14ALOGPS
pKa (Strongest Acidic)4.05ChemAxon
pKa (Strongest Basic)-7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area63.6 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity28.31 m³·mol⁻¹ChemAxon
Polarizability12.16 ųChemAxon
Number of Rings0ChemAxon
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]+126.99630932474
DeepCCS[M-H]-124.16130932474
DeepCCS[M-2H]-160.56830932474
DeepCCS[M+Na]+135.50530932474
AllCCS[M+H]+131.432859911
AllCCS[M+H-H2O]+127.332859911
AllCCS[M+NH4]+135.232859911
AllCCS[M+Na]+136.332859911
AllCCS[M-H]-127.232859911
AllCCS[M+Na-2H]-129.932859911
AllCCS[M+HCOO]-132.932859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.2961 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.61 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1219.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid320.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid96.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid202.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid60.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid254.8 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 Acid322.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)114.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid674.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid234.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid863.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid209.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid239.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate616.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA206.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water315.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Monomethyl succinateCOC(=O)CCC(O)=O2129.6Standard polar33892256
Monomethyl succinateCOC(=O)CCC(O)=O998.8Standard non polar33892256
Monomethyl succinateCOC(=O)CCC(O)=O1154.5Semi 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 IDC00032250
Chemspider ID69896
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID75146
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1261591
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 ]