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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2022-09-09 20:27:42 UTC

Update Date

2022-09-22 18:34:48 UTC

HMDB ID

HMDB0341330

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Hymeglusin

Description

Hymeglusin, also known as antibiotic 1233A, belongs to the class of organic compounds known as long-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 13 and 21 carbon atoms. Based on a literature review a significant number of articles have been published on Hymeglusin.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309092223052D          

 28 28  0  0  1  0            999 V2000
    2.7399    1.1520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0255    0.7395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3110    1.1520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3110    1.9770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.7395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0255   -0.0855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3110   -0.4980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7399   -0.4980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4544   -0.0855    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7399   -1.3230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0255   -1.7355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4544   -1.7355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1689   -1.3230    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4544   -0.9105    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1689   -0.4980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8833   -1.7355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5978   -1.3230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3123   -1.7355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0268   -1.3230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7412   -1.7355    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0867   -2.2378    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5381   -1.5220    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7516   -2.3189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4661   -2.7314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9547   -2.5324    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4570   -3.1869    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5422   -3.2469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7172   -3.2469    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
  3  5  2  0  0  0  0
  2  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  6  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 20 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  6  0  0  0
 27 28  1  0  0  0  0
M  END


  Mrv1652309092223052D          

 28 28  0  0  1  0            999 V2000
    2.7399    1.1520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0255    0.7395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3110    1.1520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3110    1.9770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5965    0.7395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0255   -0.0855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3110   -0.4980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7399   -0.4980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4544   -0.0855    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7399   -1.3230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0255   -1.7355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4544   -1.7355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1689   -1.3230    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4544   -0.9105    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1689   -0.4980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8833   -1.7355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5978   -1.3230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3123   -1.7355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0268   -1.3230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7412   -1.7355    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0867   -2.2378    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5381   -1.5220    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7516   -2.3189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4661   -2.7314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9547   -2.5324    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4570   -3.1869    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5422   -3.2469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7172   -3.2469    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
  3  5  2  0  0  0  0
  2  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  6  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 20 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  6  0  0  0
 27 28  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341330

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]\C(C(O)=O)=C(\C)/C(/[H])=C(\C)C[C@]([H])(C)CCCC[C@@]1([H])OC(=O)[C@]1([H])CO

> <INCHI_IDENTIFIER>
InChI=1S/C18H28O5/c1-12(8-13(2)9-14(3)10-17(20)21)6-4-5-7-16-15(11-19)18(22)23-16/h9-10,12,15-16,19H,4-8,11H2,1-3H3,(H,20,21)/b13-9+,14-10+/t12-,15-,16-/m1/s1

> <INCHI_KEY>
ODCZJZWSXPVLAW-KXCGKLMDSA-N

> <FORMULA>
C18H28O5

> <MOLECULAR_WEIGHT>
324.417

> <EXACT_MASS>
324.193674002

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
36.983353096590065

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E,7R)-11-[(2R,3R)-3-(hydroxymethyl)-4-oxooxetan-2-yl]-3,5,7-trimethylundeca-2,4-dienoic acid

> <JCHEM_LOGP>
3.1527223346666675

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.148942167715305

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.091636668535739

> <JCHEM_PKA_STRONGEST_BASIC>
-2.733652695857973

> <JCHEM_POLAR_SURFACE_AREA>
83.83

> <JCHEM_REFRACTIVITY>
89.24199999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2E,4E,7R)-11-[(2R,3R)-3-(hydroxymethyl)-4-oxooxetan-2-yl]-3,5,7-trimethylundeca-2,4-dienoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  H   UNK     0       5.115   2.150   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       3.781   1.380   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.447   2.150   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.447   3.690   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       1.113   1.380   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.781  -0.160   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.447  -0.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.115  -0.930   0.000  0.00  0.00           C+0
HETATM    9  H   UNK     0       6.448  -0.160   0.000  0.00  0.00           H+0
HETATM   10  C   UNK     0       5.115  -2.470   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.781  -3.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.448  -3.240   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.782  -2.470   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0       6.448  -1.700   0.000  0.00  0.00           H+0
HETATM   15  C   UNK     0       7.782  -0.930   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.116  -3.240   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.449  -2.470   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.783  -3.240   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.117  -2.470   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      14.450  -3.240   0.000  0.00  0.00           C+0
HETATM   21  H   UNK     0      13.229  -4.177   0.000  0.00  0.00           H+0
HETATM   22  O   UNK     0      15.938  -2.841   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      16.336  -4.329   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      17.670  -5.099   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      14.849  -4.727   0.000  0.00  0.00           C+0
HETATM   26  H   UNK     0      15.786  -5.949   0.000  0.00  0.00           H+0
HETATM   27  C   UNK     0      14.079  -6.061   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      12.539  -6.061   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22   25                                             
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   20   26   27                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   56    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Antibiotic 1233a sodium	MeSH
11-(3-(Hydroxymethyl)-4-oxo-2-oxytanyl)-3,5,7-trimethyl-2,4-undecadienenoic acid	MeSH
3,5,7-Trimethyl-12-hydroxy-13-hydroxymethyl-2,4-tetradecadiendioic acid 12,14-lactone	MeSH
Antibiotic 1233a	MeSH
Antibiotic 1233a calcium	MeSH
11-(3'-(Hydroxymethyl)-4'-oxo-2'-oxetanyl)-3,5,7-trimethyl-2,4-undecadienoic acid	MeSH
Antibiotic 1233a potassium	MeSH

Chemical Formula

C₁₈H₂₈O₅

Average Molecular Weight

324.417

Monoisotopic Molecular Weight

324.193674002

IUPAC Name

(2E,4E,7R)-11-[(2R,3R)-3-(hydroxymethyl)-4-oxooxetan-2-yl]-3,5,7-trimethylundeca-2,4-dienoic acid

Traditional Name

(2E,4E,7R)-11-[(2R,3R)-3-(hydroxymethyl)-4-oxooxetan-2-yl]-3,5,7-trimethylundeca-2,4-dienoic acid

CAS Registry Number

Not Available

SMILES

[H]\C(C(O)=O)=C(\C)/C(/[H])=C(\C)C[C@]([H])(C)CCCC[C@@]1([H])OC(=O)[C@]1([H])CO

InChI Identifier

InChI=1S/C18H28O5/c1-12(8-13(2)9-14(3)10-17(20)21)6-4-5-7-16-15(11-19)18(22)23-16/h9-10,12,15-16,19H,4-8,11H2,1-3H3,(H,20,21)/b13-9+,14-10+/t12-,15-,16-/m1/s1

InChI Key

ODCZJZWSXPVLAW-KXCGKLMDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as long-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 13 and 21 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Long-chain fatty acids

Alternative Parents

Substituents

Long-chain fatty acid
Branched fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Methyl-branched fatty acid
Dicarboxylic acid or derivatives
Unsaturated fatty acid
Beta_propiolactone
Carboxylic acid ester
Lactone
Oxetane
Organoheterocyclic compound
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxide
Primary alcohol
Organooxygen compound
Organic oxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.15	ChemAxon
pKa (Strongest Acidic)	5.09	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.83 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	89.24 m³·mol⁻¹	ChemAxon
Polarizability	36.98 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Kovats Retention Indices

Not Available

Spectra

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4945132

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6440895

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920 ]

Showing metabocard for Hymeglusin (HMDB0341330)

MOL for HMDB0341330 (Hymeglusin)

3D MOL for HMDB0341330 (Hymeglusin)

3D SDF for HMDB0341330 (Hymeglusin)

3D-SDF for HMDB0341330 (Hymeglusin)

PDB for HMDB0341330 (Hymeglusin)

3D PDB for HMDB0341330 (Hymeglusin)

SMILES for HMDB0341330 (Hymeglusin)

INCHI for HMDB0341330 (Hymeglusin)

Structure for HMDB0341330 (Hymeglusin)

3D Structure for HMDB0341330 (Hymeglusin)

Predicted Kovats Retention Indices