MiMeDB: Showing metabocard for Ligerin (MMDBc0013898)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 05:05:24 UTC

Update Date

2022-08-31 06:36:52 UTC

Metabolite ID

MMDBc0013898

Metabolite Identification

Common Name

Ligerin

Description

Ligerin belongs to the class of organic compounds known as epoxy fatty acids. These are fatty acids containing an oxirane ring as part of the aliphatic chain. Ligerin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152107052D          

 32 33  0  0  1  0            999 V2000
   -3.7200   -1.9751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2087   -0.6324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1027    1.8695    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
   -2.8015   -0.8805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6582   -0.0680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    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
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1401    3.2502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5767   -1.1627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2902    0.4623    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9525    3.3935    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    2.3317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    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
   -4.1027    0.6055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6144    0.9355    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
 10  9  1  0  0  0  0
 12  1  1  0  0  0  0
 12  2  1  0  0  0  0
 12  5  2  0  0  0  0
 13  9  1  0  0  0  0
 14  6  1  1  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17 13  1  0  0  0  0
 18 17  1  0  0  0  0
 19  3  1  1  0  0  0
 19 14  1  0  0  0  0
 18 19  1  6  0  0  0
 20 10  1  0  0  0  0
 20 11  1  1  0  0  0
 20 18  1  0  0  0  0
 21 11  1  0  0  0  0
 22 15  2  0  0  0  0
 23 15  1  0  0  0  0
 24 16  2  0  0  0  0
 20 25  1  6  0  0  0
 26  4  1  0  0  0  0
 17 26  1  6  0  0  0
 13 27  1  1  0  0  0
 27 16  1  0  0  0  0
 28 14  1  0  0  0  0
 19 28  1  6  0  0  0
 13 29  1  6  0  0  0
 14 30  1  6  0  0  0
 17 31  1  6  0  0  0
 18 32  1  1  0  0  0
M  END


  Mrv1652305152107052D          

 32 33  0  0  1  0            999 V2000
   -3.7200   -1.9751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2087   -0.6324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1027    1.8695    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
   -2.8015   -0.8805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6582   -0.0680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    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
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1401    3.2502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5767   -1.1627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2902    0.4623    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9525    3.3935    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6704    2.3317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    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
   -4.1027    0.6055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6144    0.9355    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
 10  9  1  0  0  0  0
 12  1  1  0  0  0  0
 12  2  1  0  0  0  0
 12  5  2  0  0  0  0
 13  9  1  0  0  0  0
 14  6  1  1  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17 13  1  0  0  0  0
 18 17  1  0  0  0  0
 19  3  1  1  0  0  0
 19 14  1  0  0  0  0
 18 19  1  6  0  0  0
 20 10  1  0  0  0  0
 20 11  1  1  0  0  0
 20 18  1  0  0  0  0
 21 11  1  0  0  0  0
 22 15  2  0  0  0  0
 23 15  1  0  0  0  0
 24 16  2  0  0  0  0
 20 25  1  6  0  0  0
 26  4  1  0  0  0  0
 17 26  1  6  0  0  0
 13 27  1  1  0  0  0
 27 16  1  0  0  0  0
 28 14  1  0  0  0  0
 19 28  1  6  0  0  0
 13 29  1  6  0  0  0
 14 30  1  6  0  0  0
 17 31  1  6  0  0  0
 18 32  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0013898

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CC=C(C)C)O[C@]1(C)[C@@]1([H])[C@]([H])(OC)[C@@]([H])(CC[C@]1(O)CCl)OC(=O)CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H31ClO7/c1-12(2)5-6-14-19(3,28-14)18-17(26-4)13(9-10-20(18,25)11-21)27-16(24)8-7-15(22)23/h5,13-14,17-18,25H,6-11H2,1-4H3,(H,22,23)/t13-,14-,17-,18-,19+,20+/m1/s1

> <INCHI_KEY>
FKTJAQKUCINAIF-JNYDFHNISA-N

> <FORMULA>
C20H31ClO7

> <MOLECULAR_WEIGHT>
418.91

> <EXACT_MASS>
418.175831

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
43.55715273657032

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-{[(1R,2S,3S,4R)-4-(chloromethyl)-4-hydroxy-2-methoxy-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl]oxy}-4-oxobutanoic acid

> <ALOGPS_LOGP>
2.18

> <JCHEM_LOGP>
2.0689942986666674

> <ALOGPS_LOGS>
-3.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.621653168812475

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.797477484131937

> <JCHEM_PKA_STRONGEST_BASIC>
-3.401688904003051

> <JCHEM_POLAR_SURFACE_AREA>
105.59

> <JCHEM_REFRACTIVITY>
102.91009999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.08e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-{[(1R,2S,3S,4R)-4-(chloromethyl)-4-hydroxy-2-methoxy-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl]oxy}-4-oxobutanoic 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      -6.944  -3.687   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -7.856  -1.180   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -7.658   3.490   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.229  -1.644   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.962  -0.127   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.001   5.390   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.861   6.067   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.677  -2.170   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667   3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.142   0.863   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.000   3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -5.335   3.080   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   21 Cl   UNK     0      -7.378   6.335   0.000  0.00  0.00          Cl+0
HETATM   22  O   UNK     0       5.335   3.080   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       4.001   0.770   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -0.000   4.620   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -6.851   4.353   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -4.001   0.770   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -7.658   1.130   0.000  0.00  0.00           O+0
HETATM   29  H   UNK     0      -2.667   1.540   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0      -4.880   1.746   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0      -4.001   3.850   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0      -6.668   3.850   0.000  0.00  0.00           H+0
CONECT    1   12                                                            
CONECT    2   12                                                            
CONECT    3   19                                                            
CONECT    4   26                                                            
CONECT    5    6   12                                                       
CONECT    6    5   14                                                       
CONECT    7    8   15                                                       
CONECT    8    7   16                                                       
CONECT    9   10   13                                                       
CONECT   10    9   20                                                       
CONECT   11   20   21                                                       
CONECT   12    1    2    5                                                  
CONECT   13    9   17   27   29                                             
CONECT   14    6   19   28   30                                             
CONECT   15    7   22   23                                                  
CONECT   16    8   24   27                                                  
CONECT   17   13   18   26   31                                             
CONECT   18   17   19   20   32                                             
CONECT   19    3   14   18   28                                             
CONECT   20   10   11   18   25                                             
CONECT   21   11                                                            
CONECT   22   15                                                            
CONECT   23   15                                                            
CONECT   24   16                                                            
CONECT   25   20                                                            
CONECT   26    4   17                                                       
CONECT   27   13   16                                                       
CONECT   28   14   19                                                       
CONECT   29   13                                                            
CONECT   30   14                                                            
CONECT   31   17                                                            
CONECT   32   18                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END

Synonyms

Not Available

Molecular Formula

C₂₀H₃₁ClO₇

Average Mass

418.91

Monoisotopic Mass

418.175831

IUPAC Name

4-{[(1R,2S,3S,4R)-4-(chloromethyl)-4-hydroxy-2-methoxy-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl]oxy}-4-oxobutanoic acid

Traditional Name

4-{[(1R,2S,3S,4R)-4-(chloromethyl)-4-hydroxy-2-methoxy-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl]oxy}-4-oxobutanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(CC=C(C)C)O[C@]1(C)[C@@]1([H])[C@]([H])(OC)[C@@]([H])(CC[C@]1(O)CCl)OC(=O)CCC(O)=O

InChI Identifier

InChI=1S/C20H31ClO7/c1-12(2)5-6-14-19(3,28-14)18-17(26-4)13(9-10-20(18,25)11-21)27-16(24)8-7-15(22)23/h5,13-14,17-18,25H,6-11H2,1-4H3,(H,22,23)/t13-,14-,17-,18-,19+,20+/m1/s1

InChI Key

FKTJAQKUCINAIF-JNYDFHNISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as epoxy fatty acids. These are fatty acids containing an oxirane ring as part of the aliphatic chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Epoxy fatty acids

Alternative Parents

Substituents

Branched fatty acid
Cyclohexanol
Epoxy fatty acid
Hydroxy fatty acid
Halogenated fatty acid
Fatty acid ester
Cyclitol or derivatives
Dicarboxylic acid or derivatives
Cyclic alcohol
Tertiary alcohol
Carboxylic acid ester
Chlorohydrin
Halohydrin
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Dialkyl ether
Oxirane
Ether
Alkyl chloride
Hydrocarbon derivative
Alcohol
Alkyl halide
Organooxygen compound
Organic oxygen compound
Organochloride
Organic oxide
Organohalogen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.11 g/L	ALOGPS
logP	2.18	ALOGPS
logP	2.07	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	3.8	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	105.59 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	102.91 m³·mol⁻¹	ChemAxon
Polarizability	43.56 Å³	ChemAxon
Number of Rings	2	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

Not Available

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	1	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

28637720

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

66553197

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 Ligerin (MMDBc0013898)

MOL for #<Metabolite:0x00007fece00085c8>

3D MOL for #<Metabolite:0x00007fece00085c8>

3D SDF for #<Metabolite:0x00007fece00085c8>

3D-SDF for #<Metabolite:0x00007fece00085c8>

PDB for #<Metabolite:0x00007fece00085c8>

3D PDB for #<Metabolite:0x00007fece00085c8>

SMILES for #<Metabolite:0x00007fece00085c8>

INCHI for #<Metabolite:0x00007fece00085c8>

Structure for #<Metabolite:0x00007fece00085c8>

3D Structure for #<Metabolite:0x00007fece00085c8>