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Showing metabocard for Squaric acid (HMDB0258453)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 20:01:03 UTC
Update Date2021-09-26 23:15:23 UTC
HMDB IDHMDB0258453
Secondary Accession NumbersNone
Metabolite Identification
Common NameSquaric acid
Descriptionsquaric acid, also known as quadratsaeure or squarate, belongs to the class of organic compounds known as vinylogous acids. These are organic compounds containing a hydroxyl group, which is indirectly attached to a carbonyl via an intervening vinyl (>C=C<) moiety. squaric acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on squaric acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Squaric acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Squaric acid 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 HMDB0258453 (Squaric acid)


  Mrv1572004221606452D          

  8  8  0  0  0  0            999 V2000
    0.9959    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.9959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.1709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1709    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8209    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    1.8209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.9959    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  4  2  0  0  0  0
M  END
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3D MOL for HMDB0258453 (Squaric acid)

HMDB0258453
     RDKit          3D
Squaric acid
 10 10  0  0  0  0  0  0  0  0999 V2000
   -0.7698   -2.5608    0.0470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5941   -1.3109    0.0205 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5033   -0.4766    0.0201 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8664   -0.6866    0.0490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2910    0.6506   -0.0205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0878    2.0446   -0.0498 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3894   -0.1828   -0.0201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6289    0.0613   -0.0476 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5589    0.0270    0.0443 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8325    2.4341   -0.0429 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
  3  5  2  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  2  1  0
  4  9  1  0
  6 10  1  0
M  END
Download

3D SDF for HMDB0258453 (Squaric acid)


  Mrv1572004221606452D          

  8  8  0  0  0  0            999 V2000
    0.9959    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.9959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.1709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1709    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8209    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    1.8209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.9959    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  4  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258453

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=C(O)C(=O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H2O4/c5-1-2(6)4(8)3(1)7/h5-6H

> <INCHI_KEY>
PWEBUXCTKOWPCW-UHFFFAOYSA-N

> <FORMULA>
C4H2O4

> <MOLECULAR_WEIGHT>
114.056

> <EXACT_MASS>
113.995308544

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
9.12356826471437

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
dihydroxycyclobut-3-ene-1,2-dione

> <ALOGPS_LOGP>
-0.90

> <JCHEM_LOGP>
-0.23603878933333328

> <ALOGPS_LOGS>
-0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.170278643627585

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.263893978094929

> <JCHEM_PKA_STRONGEST_BASIC>
-5.294162253877851

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
24.7952

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.06e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
squaric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0258453 (Squaric acid)

HMDB0258453
     RDKit          3D
Squaric acid
 10 10  0  0  0  0  0  0  0  0999 V2000
   -0.7698   -2.5608    0.0470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5941   -1.3109    0.0205 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5033   -0.4766    0.0201 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8664   -0.6866    0.0490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2910    0.6506   -0.0205 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0878    2.0446   -0.0498 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3894   -0.1828   -0.0201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6289    0.0613   -0.0476 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5589    0.0270    0.0443 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8325    2.4341   -0.0429 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
  3  5  2  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  2  1  0
  4  9  1  0
  6 10  1  0
M  END
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PDB for HMDB0258453 (Squaric acid)

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       1.859   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.770   1.859   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770  -0.319   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.319   0.770   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.399   0.770   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.770   3.399   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.770  -1.859   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.859   0.770   0.000  0.00  0.00           O+0
CONECT    1    2    3    5                                                  
CONECT    2    1    4    6                                                  
CONECT    3    1    4    7                                                  
CONECT    4    2    3    8                                                  
CONECT    5    1                                                            
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    4                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0258453 (Squaric acid)

COMPND    HMDB0258453
HETATM    1  O1  UNL     1      -0.770  -2.561   0.047  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.594  -1.311   0.021  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.503  -0.477   0.020  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.866  -0.687   0.049  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.291   0.651  -0.020  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.088   2.045  -0.050  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.389  -0.183  -0.020  1.00  0.00           C  
HETATM    8  O4  UNL     1      -2.629   0.061  -0.048  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.559   0.027   0.044  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.832   2.434  -0.043  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    5    5
CONECT    4    9
CONECT    5    6    7
CONECT    6   10
CONECT    7    8    8
END
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SMILES for HMDB0258453 (Squaric acid)

OC1=C(O)C(=O)C1=O
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INCHI for HMDB0258453 (Squaric acid)

InChI=1S/C4H2O4/c5-1-2(6)4(8)3(1)7/h5-6H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,2-Diketo-3,4-dihydroxycyclobuteneChEBI
1,2-Dioxo-3,4-dihydroxycyclobut-3-eneChEBI
1,2-Dioxo-3,4-dihydroxycyclobuteneChEBI
3,4-Dihydroxy-3-cyclobutene-1,2-dioneChEBI
Quadratic acidChEBI
QuadratsaeureChEBI
QuadratateGenerator
SquarateGenerator
Squaric acidMeSH
Squaric acid, dipotassium saltMeSH
Squaric acid, disilver (+1) saltMeSH
Squaric acid, disodium saltMeSH
Squaric acid, monopotassium saltMeSH
Squaric acid, monopotassium salt monohydrateMeSH
Squaric acid, nickel (+2), (1:1) salt dihydrateMeSH
Chemical FormulaC4H2O4
Average Molecular Weight114.056
Monoisotopic Molecular Weight113.995308544
IUPAC Namedihydroxycyclobut-3-ene-1,2-dione
Traditional Namesquaric acid
CAS Registry NumberNot Available
SMILES
OC1=C(O)C(=O)C1=O
InChI Identifier
InChI=1S/C4H2O4/c5-1-2(6)4(8)3(1)7/h5-6H
InChI KeyPWEBUXCTKOWPCW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as vinylogous acids. These are organic compounds containing a hydroxyl group, which is indirectly attached to a carbonyl via an intervening vinyl (>C=C<) moiety.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassVinylogous acids
Sub ClassNot Available
Direct ParentVinylogous acids
Alternative Parents
Substituents
  • Vinylogous acid
  • Cyclic ketone
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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-0.9ALOGPS
logP-0.24ChemAxon
logS-0.03ALOGPS
pKa (Strongest Acidic)5.26ChemAxon
pKa (Strongest Basic)-5.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity24.8 m³·mol⁻¹ChemAxon
Polarizability9.12 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]+121.29630932474
DeepCCS[M-H]-118.37230932474
DeepCCS[M-2H]-155.02930932474
DeepCCS[M+Na]+129.82130932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Squaric acidOC1=C(O)C(=O)C1=O1798.5Standard polar33892256
Squaric acidOC1=C(O)C(=O)C1=O1139.0Standard non polar33892256
Squaric acidOC1=C(O)C(=O)C1=O1283.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Squaric acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-3900000000-e1d3317646b6107993092021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Squaric acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Squaric acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Squaric acid GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Squaric acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Squaric acid GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Squaric acid 10V, Positive-QTOFsplash10-014i-0900000000-3ed542e54699285aa28f2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Squaric acid 20V, Positive-QTOFsplash10-0a4i-9400000000-262ef331ab974feb631f2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Squaric acid 40V, Positive-QTOFsplash10-0a4i-9200000000-e24b2aa6569adcc8bd3b2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Squaric acid 10V, Negative-QTOFsplash10-03di-0900000000-23f4a01cfc96efe6c23c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Squaric acid 20V, Negative-QTOFsplash10-03di-0900000000-f52602d74ff027abbd752016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Squaric acid 40V, Negative-QTOFsplash10-03di-0900000000-b542627db9025e713b832016-08-03Wishart LabView Spectrum
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 ID16919
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSquaric_acid
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID52141
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 ]