MiMeDB: Showing metabocard for (-)-12-hydroxysydonic acid (MMDBc0017500)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 07:52:08 UTC

Update Date

2022-08-31 06:42:32 UTC

Metabolite ID

MMDBc0017500

Metabolite Identification

Common Name

(-)-12-hydroxysydonic acid

Description

(-)-12-hydroxysydonic acid belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Based on a literature review a small amount of articles have been published on (-)-12-hydroxysydonic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152109522D          

 21 21  0  0  1  0            999 V2000
   -1.4289    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    4.1250    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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    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    5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 C   0  0  1  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
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   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 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    5.7750    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
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  2  0  0  0  0
  7  3  1  0  0  0  0
 10  1  1  6  0  0  0
 10  4  1  0  0  0  0
 10  9  1  0  0  0  0
 11  5  1  0  0  0  0
 11  8  2  0  0  0  0
 12  6  1  0  0  0  0
 13  8  1  0  0  0  0
 13 12  2  0  0  0  0
 14 11  1  0  0  0  0
 15  2  1  1  0  0  0
 15  7  1  0  0  0  0
 15 12  1  0  0  0  0
 16  9  1  0  0  0  0
 17 13  1  0  0  0  0
 18 14  2  0  0  0  0
 19 14  1  0  0  0  0
 15 20  1  1  0  0  0
 10 21  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017500

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](C)(CO)CCC[C@@](C)(O)C1=C(O)C=C(C=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O5/c1-10(9-16)4-3-7-15(2,20)12-6-5-11(14(18)19)8-13(12)17/h5-6,8,10,16-17,20H,3-4,7,9H2,1-2H3,(H,18,19)/t10-,15+/m0/s1

> <INCHI_KEY>
ISHXRANDGDVGJS-ZUZCIYMTSA-N

> <FORMULA>
C15H22O5

> <MOLECULAR_WEIGHT>
282.336

> <EXACT_MASS>
282.146723808

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
30.22274245664186

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-[(2R,6S)-2,7-dihydroxy-6-methylheptan-2-yl]-3-hydroxybenzoic acid

> <ALOGPS_LOGP>
1.84

> <JCHEM_LOGP>
2.041587927666667

> <ALOGPS_LOGS>
-3.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.878914104853289

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.830814816180773

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7410269483614251

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
75.89529999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.31e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-[(2R,6S)-2,7-dihydroxy-6-methylheptan-2-yl]-3-hydroxybenzoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -2.667   7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.874   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000   6.160   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.000   7.700   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334  10.010   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.667  10.780   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -0.206   3.850   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0      -1.334   6.930   0.000  0.00  0.00           H+0
CONECT    1   10                                                            
CONECT    2   15                                                            
CONECT    3    4    7                                                       
CONECT    4    3   10                                                       
CONECT    5    6   11                                                       
CONECT    6    5   12                                                       
CONECT    7    3   15                                                       
CONECT    8   11   13                                                       
CONECT    9   10   16                                                       
CONECT   10    1    4    9   21                                             
CONECT   11    5    8   14                                                  
CONECT   12    6   13   15                                                  
CONECT   13    8   12   17                                                  
CONECT   14   11   18   19                                                  
CONECT   15    2    7   12   20                                             
CONECT   16    9                                                            
CONECT   17   13                                                            
CONECT   18   14                                                            
CONECT   19   14                                                            
CONECT   20   15                                                            
CONECT   21   10                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

Synonyms

Value	Source
(-)-12-Hydroxysydonate	Generator

Molecular Formula

C₁₅H₂₂O₅

Average Mass

282.336

Monoisotopic Mass

282.146723808

IUPAC Name

4-[(2R,6S)-2,7-dihydroxy-6-methylheptan-2-yl]-3-hydroxybenzoic acid

Traditional Name

4-[(2R,6S)-2,7-dihydroxy-6-methylheptan-2-yl]-3-hydroxybenzoic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(CO)CCC[C@@](C)(O)C1=C(O)C=C(C=C1)C(O)=O

InChI Identifier

InChI=1S/C15H22O5/c1-10(9-16)4-3-7-15(2,20)12-6-5-11(14(18)19)8-13(12)17/h5-6,8,10,16-17,20H,3-4,7,9H2,1-2H3,(H,18,19)/t10-,15+/m0/s1

InChI Key

ISHXRANDGDVGJS-ZUZCIYMTSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Bisabolane sesquiterpenoid
Sesquiterpenoid
Hydroxybenzoic acid
Benzoic acid or derivatives
Benzoic acid
Fatty alcohol
Benzoyl
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Fatty acyl
Benzenoid
Tertiary alcohol
Carboxylic acid derivative
Carboxylic acid
Alcohol
Aromatic alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Primary alcohol
Organooxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.23 g/L	ALOGPS
logP	1.84	ALOGPS
logP	2.04	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	3.83	ChemAxon
pKa (Strongest Basic)	-1.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	75.9 m³·mol⁻¹	ChemAxon
Polarizability	30.22 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

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	2	Human feces; Human sputum; Human	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78441439

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

38351305

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for (-)-12-hydroxysydonic acid (MMDBc0017500)

MOL for #<Metabolite:0x00007f92021e79b8>

3D MOL for #<Metabolite:0x00007f92021e79b8>

3D SDF for #<Metabolite:0x00007f92021e79b8>

3D-SDF for #<Metabolite:0x00007f92021e79b8>

PDB for #<Metabolite:0x00007f92021e79b8>

3D PDB for #<Metabolite:0x00007f92021e79b8>

SMILES for #<Metabolite:0x00007f92021e79b8>

INCHI for #<Metabolite:0x00007f92021e79b8>

Structure for #<Metabolite:0x00007f92021e79b8>

3D Structure for #<Metabolite:0x00007f92021e79b8>