MiMeDB: Showing metabocard for 1-deoxypentalenate (MMDBc0055103)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:43:32 UTC

Update Date

2022-08-12 20:09:14 UTC

Metabolite ID

MMDBc0055103

Metabolite Identification

Common Name

1-deoxypentalenate

Description

1-deoxypentalenate belongs to the class of organic compounds known as angular triquinanes. These are triquinane with a structure based on a [6.3.0.0^1,5] undecane carbon skeleton. Based on a literature review very few articles have been published on 1-deoxypentalenate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221432D          

 20 22  0  0  1  0            999 V2000
    2.3838    2.3151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0408    1.8192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1476    2.4682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0739    1.6477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8190    0.8631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5663   -0.4065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4887    0.8631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4088    1.6477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8989    1.6477    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8213    0.3782    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7413   -0.4065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4864    0.3782    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2564   -1.0739    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2338    1.6477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1538    0.8631    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5920   -1.8276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4359   -0.9877    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.5244    2.3828    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4887   -0.1068    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8190   -0.1068    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0  0  0  0
  9  1  1  1  0  0  0
  9  4  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 11  6  2  0  0  0  0
 12  5  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  1  0  0  0  0
 14  2  1  0  0  0  0
 14  3  1  0  0  0  0
 14  7  1  0  0  0  0
 14  8  1  0  0  0  0
 15  8  1  1  0  0  0
 15  9  1  0  0  0  0
 15 10  1  0  0  0  0
 15 12  1  0  0  0  0
 16 13  2  0  0  0  0
 17 13  1  0  0  0  0
  9 18  1  6  0  0  0
 10 19  1  6  0  0  0
 12 20  1  1  0  0  0
M  CHG  1  17  -1
M  END
> <DATABASE_ID>
MMDBc0055103

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(C)CC[C@@]2([H])C(=C[C@]3([H])CC(C)(C)C[C@]123)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O2/c1-9-4-5-12-11(13(16)17)6-10-7-14(2,3)8-15(9,10)12/h6,9-10,12H,4-5,7-8H2,1-3H3,(H,16,17)/p-1/t9-,10-,12+,15-/m1/s1

> <INCHI_KEY>
DCFDRCCHOOORSB-DSKWVYQCSA-M

> <FORMULA>
C15H21O2

> <MOLECULAR_WEIGHT>
233.332

> <EXACT_MASS>
233.154703496

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
26.456844467508194

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,5R,8S)-2,10,10-trimethyltricyclo[6.3.0.0^{1,5}]undec-6-ene-6-carboxylate

> <JCHEM_LOGP>
3.292850785333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.940756821335709

> <JCHEM_POLAR_SURFACE_AREA>
40.129999999999995

> <JCHEM_REFRACTIVITY>
78.2487

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5R,8S)-2,10,10-trimethyltricyclo[6.3.0.0^{1,5}]undec-6-ene-6-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       4.450   4.322   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.543   3.396   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.875   4.607   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.005   3.076   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.529   1.611   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.791  -0.759   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.512   1.611   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.496   3.076   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.545   3.076   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.266   0.706   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.251  -0.759   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.775   0.706   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.345  -2.005   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.036   3.076   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.021   1.611   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.972  -3.411   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.814  -1.844   0.000  0.00  0.00           O-1
HETATM   18  H   UNK     0       2.845   4.448   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       6.512  -0.199   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       1.529  -0.199   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2   14                                                            
CONECT    3   14                                                            
CONECT    4    5    9                                                       
CONECT    5    4   12                                                       
CONECT    6   10   11                                                       
CONECT    7   10   14                                                       
CONECT    8   14   15                                                       
CONECT    9    1    4   15   18                                             
CONECT   10    6    7   15   19                                             
CONECT   11    6   12   13                                                  
CONECT   12    5   11   15   20                                             
CONECT   13   11   16   17                                                  
CONECT   14    2    3    7    8                                             
CONECT   15    8    9   10   12                                             
CONECT   16   13                                                            
CONECT   17   13                                                            
CONECT   18    9                                                            
CONECT   19   10                                                            
CONECT   20   12                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

Synonyms

Value	Source
1-Deoxypentalenic acid	Generator

Molecular Formula

C₁₅H₂₁O₂

Average Mass

233.332

Monoisotopic Mass

233.154703496

IUPAC Name

(1R,2R,5R,8S)-2,10,10-trimethyltricyclo[6.3.0.0^{1,5}]undec-6-ene-6-carboxylate

Traditional Name

(1R,2R,5R,8S)-2,10,10-trimethyltricyclo[6.3.0.0^{1,5}]undec-6-ene-6-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C)CC[C@@]2([H])C(=C[C@]3([H])CC(C)(C)C[C@]123)C([O-])=O

InChI Identifier

InChI=1S/C15H22O2/c1-9-4-5-12-11(13(16)17)6-10-7-14(2,3)8-15(9,10)12/h6,9-10,12H,4-5,7-8H2,1-3H3,(H,16,17)/p-1/t9-,10-,12+,15-/m1/s1

InChI Key

DCFDRCCHOOORSB-DSKWVYQCSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as angular triquinanes. These are triquinane with a structure based on a [6.3.0.0^1,5] Undecane carbon skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Angular triquinanes

Alternative Parents

Substituents

Angular triquinane sesquiterpenoid
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Organic anion
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

monocarboxylic acid anion (CHEBI:68650 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	3.29	ChemAxon
pKa (Strongest Acidic)	4.94	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	40.13 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	78.25 m³·mol⁻¹	ChemAxon
Polarizability	26.46 Å³	ChemAxon
Number of Rings	3	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0015366	1-deoxypentalenate	1-deoxy-11beta-hydroxypentalenate	1-deoxypentalenic acid 11-beta-hydroxylase	Hydroxylation	RHEA	34755880
MMDBr0024928	Hydrogen Ion	Water	Pentalenic acid synthase	Synthesis	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
Bacteria	Actinobacteria	3

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

28533248

KEGG Compound ID

Not Available

BioCyc ID

CPD-13618

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70678894

PDB ID

Not Available

ChEBI ID

68650

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 1-deoxypentalenate (MMDBc0055103)

MOL for #<Metabolite:0x00007fe2862205b8>

3D MOL for #<Metabolite:0x00007fe2862205b8>

3D SDF for #<Metabolite:0x00007fe2862205b8>

3D-SDF for #<Metabolite:0x00007fe2862205b8>

PDB for #<Metabolite:0x00007fe2862205b8>

3D PDB for #<Metabolite:0x00007fe2862205b8>

SMILES for #<Metabolite:0x00007fe2862205b8>

INCHI for #<Metabolite:0x00007fe2862205b8>

Structure for #<Metabolite:0x00007fe2862205b8>

3D Structure for #<Metabolite:0x00007fe2862205b8>