MiMeDB: Showing metabocard for (3R)-3-farnesyl-6-hydroxy-2,3,5-trimethyl-4-oxocyclohexa-1,5-diene-1-carboxylic acid (MMDBc0054893)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:37:18 UTC

Update Date

2022-08-12 20:09:08 UTC

Metabolite ID

MMDBc0054893

Metabolite Identification

Common Name

(3R)-3-farnesyl-6-hydroxy-2,3,5-trimethyl-4-oxocyclohexa-1,5-diene-1-carboxylic acid

Description

CHEBI:131857 belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Based on a literature review very few articles have been published on CHEBI:131857.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221372D          

 31 31  0  0  1  0            999 V2000
    5.9395    7.2373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1876    5.8300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9984    3.9930    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8091    2.1560    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
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5627    5.5435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3734    3.7065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8449    6.3188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7502    5.4003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6556    4.4817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5610    3.5632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4663    2.6447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6573    6.4620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4681    4.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2788    2.7880    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
    1.4289    0.8250    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
    0.7145   -0.4125    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
    2.1434   -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  1  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  5  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
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.1253    5.1137    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0640    3.2767    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13  9  1  0  0  0  0
 15 14  1  0  0  0  0
 16  1  1  0  0  0  0
 16  2  1  0  0  0  0
 16 10  2  0  0  0  0
 17  3  1  0  0  0  0
 17 11  1  0  0  0  0
 17 12  2  0  0  0  0
 18  4  1  0  0  0  0
 18 13  1  0  0  0  0
 18 14  2  0  0  0  0
 19  5  1  0  0  0  0
 20  6  1  0  0  0  0
 21 20  2  0  0  0  0
 22 19  2  0  0  0  0
 22 21  1  0  0  0  0
 23 19  1  0  0  0  0
 24 21  1  0  0  0  0
 25  7  1  1  0  0  0
 25 15  1  6  0  0  0
 25 20  1  0  0  0  0
 25 23  1  0  0  0  0
 26 22  1  0  0  0  0
 27 23  2  0  0  0  0
 28 24  2  0  0  0  0
 29 24  1  0  0  0  0
 30 12  1  0  0  0  0
 31 14  1  0  0  0  0
M  CHG  2  26  -1  29  -1
M  END


  Mrv1652306172221372D          

 31 31  0  0  1  0            999 V2000
    5.9395    7.2373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1876    5.8300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9984    3.9930    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8091    2.1560    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
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5627    5.5435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3734    3.7065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8449    6.3188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7502    5.4003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6556    4.4817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5610    3.5632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4663    2.6447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1842    1.8695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6573    6.4620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4681    4.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2788    2.7880    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
    1.4289    0.8250    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
    0.7145   -0.4125    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
    2.1434   -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  1  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  5  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
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.1253    5.1137    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0640    3.2767    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13  9  1  0  0  0  0
 15 14  1  0  0  0  0
 16  1  1  0  0  0  0
 16  2  1  0  0  0  0
 16 10  2  0  0  0  0
 17  3  1  0  0  0  0
 17 11  1  0  0  0  0
 17 12  2  0  0  0  0
 18  4  1  0  0  0  0
 18 13  1  0  0  0  0
 18 14  2  0  0  0  0
 19  5  1  0  0  0  0
 20  6  1  0  0  0  0
 21 20  2  0  0  0  0
 22 19  2  0  0  0  0
 22 21  1  0  0  0  0
 23 19  1  0  0  0  0
 24 21  1  0  0  0  0
 25  7  1  1  0  0  0
 25 15  1  6  0  0  0
 25 20  1  0  0  0  0
 25 23  1  0  0  0  0
 26 22  1  0  0  0  0
 27 23  2  0  0  0  0
 28 24  2  0  0  0  0
 29 24  1  0  0  0  0
 30 12  1  0  0  0  0
 31 14  1  0  0  0  0
M  CHG  2  26  -1  29  -1
M  END
> <DATABASE_ID>
MMDBc0054893

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(CC\C(C)=C(/[H])C[C@]1(C)C(C)=C(C([O-])=O)C([O-])=C(C)C1=O)=C(\C)CCC=C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C25H36O4/c1-16(2)10-8-11-17(3)12-9-13-18(4)14-15-25(7)20(6)21(24(28)29)22(26)19(5)23(25)27/h10,12,14,26H,8-9,11,13,15H2,1-7H3,(H,28,29)/p-2/b17-12+,18-14+/t25-/m1/s1

> <INCHI_KEY>
BAJLPQKQXYOBIY-MNPZXIHOSA-L

> <FORMULA>
C25H34O4

> <MOLECULAR_WEIGHT>
398.544

> <EXACT_MASS>
398.246806735

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
45.611233575836664

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-2,3,5-trimethyl-6-oxido-4-oxo-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]cyclohexa-1,5-diene-1-carboxylate

> <JCHEM_LOGP>
6.160789570666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.925706607321048

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.093209091502813

> <JCHEM_PKA_STRONGEST_BASIC>
-6.878882286195104

> <JCHEM_POLAR_SURFACE_AREA>
80.26

> <JCHEM_REFRACTIVITY>
144.2576

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-2,3,5-trimethyl-6-oxido-4-oxo-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]cyclohexa-1,5-diene-1-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      11.087  13.510   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.550  10.883   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.464   7.454   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.377   4.025   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.324   3.490   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.517  10.348   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.430   6.919   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.044  11.795   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.000  10.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.957   8.366   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.914   6.651   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.870   4.937   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.344   3.490   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.560  12.062   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.474   8.633   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.387   5.204   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O-1
HETATM   27  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O-1
HETATM   30  H   UNK     0       3.967   9.546   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0      -0.119   6.117   0.000  0.00  0.00           H+0
CONECT    1   16                                                            
CONECT    2   16                                                            
CONECT    3   17                                                            
CONECT    4   18                                                            
CONECT    5   19                                                            
CONECT    6   20                                                            
CONECT    7   25                                                            
CONECT    8   10   11                                                       
CONECT    9   12   13                                                       
CONECT   10    8   16                                                       
CONECT   11    8   17                                                       
CONECT   12    9   17   30                                                  
CONECT   13    9   18                                                       
CONECT   14   15   18   31                                                  
CONECT   15   14   25                                                       
CONECT   16    1    2   10                                                  
CONECT   17    3   11   12                                                  
CONECT   18    4   13   14                                                  
CONECT   19    5   22   23                                                  
CONECT   20    6   21   25                                                  
CONECT   21   20   22   24                                                  
CONECT   22   19   21   26                                                  
CONECT   23   19   25   27                                                  
CONECT   24   21   28   29                                                  
CONECT   25    7   15   20   23                                             
CONECT   26   22                                                            
CONECT   27   23                                                            
CONECT   28   24                                                            
CONECT   29   24                                                            
CONECT   30   12                                                            
CONECT   31   14                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   62    0
END

Synonyms

Value	Source
(3R)-3-Farnesyl-6-hydroxy-2,3,5-trimethyl-4-oxocyclohexa-1,5-diene-1-carboxylate	ChEBI
(3R)-3-Farnesyl-6-hydroxy-2,3,5-trimethyl-4-oxocyclohexa-1,5-diene-1-carboxylic acid	Generator

Molecular Formula

C₂₅H₃₄O₄

Average Mass

398.544

Monoisotopic Mass

398.246806735

IUPAC Name

(3R)-2,3,5-trimethyl-6-oxido-4-oxo-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]cyclohexa-1,5-diene-1-carboxylate

Traditional Name

(3R)-2,3,5-trimethyl-6-oxido-4-oxo-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]cyclohexa-1,5-diene-1-carboxylate

CAS Registry Number

Not Available

SMILES

[H]\C(CC\C(C)=C(/[H])C[C@]1(C)C(C)=C(C([O-])=O)C([O-])=C(C)C1=O)=C(\C)CCC=C(C)C

InChI Identifier

InChI=1S/C25H36O4/c1-16(2)10-8-11-17(3)12-9-13-18(4)14-15-25(7)20(6)21(24(28)29)22(26)19(5)23(25)27/h10,12,14,26H,8-9,11,13,15H2,1-7H3,(H,28,29)/p-2/b17-12+,18-14+/t25-/m1/s1

InChI Key

BAJLPQKQXYOBIY-MNPZXIHOSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Vinylogous acid
Cyclic ketone
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Organic anion
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	6.16	ChemAxon
pKa (Strongest Acidic)	4.09	ChemAxon
pKa (Strongest Basic)	-6.9	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	80.26 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	144.26 m³·mol⁻¹	ChemAxon
Polarizability	45.61 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0016473	Farnesyl pyrophosphate	(3R)-3-farnesyl-6-hydroxy-2,3,5-trimethyl-4-oxocyclohexa-1,5-diene-1-carboxylic acid	Prenytransferase adrG	Farnesylation	RHEA	34755880
MMDBr0016474	Farnesyl pyrophosphate	(3R)-3-farnesyl-6-hydroxy-2,3,5-trimethyl-4-oxocyclohexa-1,5-diene-1-carboxylic acid	Prenytransferase adrG	Farnesylation	RHEA	34755880
MMDBr0017632	(3R)-3-farnesyl-6-hydroxy-2,3,5-trimethyl-4-oxocyclohexa-1,5-diene-1-carboxylic acid	(3R)-[(10S)-11-epoxyfarnesyl]-2,3,5-trimethyl-6-oxido-4-oxocyclohexa-1,5-diene-1-carboxylic acid	FAD-dependent monooxygenase nvfK	Oxygenation	RHEA	34755880
MMDBr0017633	(3R)-3-farnesyl-6-hydroxy-2,3,5-trimethyl-4-oxocyclohexa-1,5-diene-1-carboxylic acid	(3R)-[(10S)-11-epoxyfarnesyl]-2,3,5-trimethyl-6-oxido-4-oxocyclohexa-1,5-diene-1-carboxylic acid	FAD-dependent monooxygenase nvfK	Oxygenation	RHEA	34755880

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	7	Human feces

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

76962789

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

137333726

PDB ID

Not Available

ChEBI ID

131857

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (3R)-3-farnesyl-6-hydroxy-2,3,5-trimethyl-4-oxocyclohexa-1,5-diene-1-carboxylic acid (MMDBc0054893)

MOL for #<Metabolite:0x0000564af3745178>

3D MOL for #<Metabolite:0x0000564af3745178>

3D SDF for #<Metabolite:0x0000564af3745178>

3D-SDF for #<Metabolite:0x0000564af3745178>

PDB for #<Metabolite:0x0000564af3745178>

3D PDB for #<Metabolite:0x0000564af3745178>

SMILES for #<Metabolite:0x0000564af3745178>

INCHI for #<Metabolite:0x0000564af3745178>

Structure for #<Metabolite:0x0000564af3745178>

3D Structure for #<Metabolite:0x0000564af3745178>