MiMeDB: Showing metabocard for Arohynapene B (MMDBc0014641)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 05:37:51 UTC

Update Date

2025-10-07 16:06:18 UTC

Metabolite ID

MMDBc0014641

Metabolite Identification

Common Name

Arohynapene B

Description

Arohynapene B is a metabolite belonging to the class of pentadienoic acids. It is characterized by its structure, which includes a (2E,4E)-5-(2-hydroxymethyl-6,8-dimethyl-5,6,7,8-tetrahydronaphthalene)-2,4-pentadienoic acid backbone. This compound is related to Arohynapene A, which is defined as (2E,4E)-5-(5-hydroxy-2,6,8-trimethyl-5,6,7,8-tetrahydronaphthalene)-2,4-pentadienoic acid (PMID:8119861 ). The presence of hydroxymethyl and dimethyl groups in Arohynapene B's structure suggests potential biological activities, possibly influencing its role in metabolic pathways or interactions with biological systems. Further studies may elucidate its specific functions and applications in biochemistry or pharmacology, enhancing our understanding of its significance in natural product chemistry.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152107372D          

 25 26  0  0  0  0            999 V2000
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    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
    0.7145   -1.2375    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
    0.0000   -1.6500    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
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    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
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    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
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  2  0  0  0  0
  8  7  2  0  0  0  0
 12  1  1  0  0  0  0
 12  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  2  1  0  0  0  0
 13  9  1  0  0  0  0
 14  7  1  0  0  0  0
 14 10  1  0  0  0  0
 15  8  1  0  0  0  0
 15 11  1  0  0  0  0
 16  5  1  0  0  0  0
 16 15  2  0  0  0  0
 17  6  1  0  0  0  0
 18 13  1  0  0  0  0
 18 14  2  0  0  0  0
 18 16  1  0  0  0  0
 19 11  1  0  0  0  0
 20 17  2  0  0  0  0
 21 17  1  0  0  0  0
 22  3  1  0  0  0  0
 23  4  1  0  0  0  0
 24  5  1  0  0  0  0
 25  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0014641

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(C([H])=C([H])C1=C(CO)C=CC2=C1C(C)CC(C)C2)=C(\[H])C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C18H22O3/c1-12-9-13(2)18-14(10-12)7-8-15(11-19)16(18)5-3-4-6-17(20)21/h3-8,12-13,19H,9-11H2,1-2H3,(H,20,21)/b5-3+,6-4+

> <INCHI_KEY>
XVNDJROXVPBPBY-GGWOSOGESA-N

> <FORMULA>
C18H22O3

> <MOLECULAR_WEIGHT>
286.371

> <EXACT_MASS>
286.156894568

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
32.9198767103508

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2E,4E)-5-[2-(hydroxymethyl)-6,8-dimethyl-5,6,7,8-tetrahydronaphthalen-1-yl]penta-2,4-dienoic acid

> <ALOGPS_LOGP>
4.23

> <JCHEM_LOGP>
3.9222445646666664

> <ALOGPS_LOGS>
-5.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.9903682153791

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.6815264010962885

> <JCHEM_PKA_STRONGEST_BASIC>
-2.803081081115061

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
86.7738

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.93e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2E,4E)-5-[2-(hydroxymethyl)-6,8-dimethyl-5,6,7,8-tetrahydronaphthalen-1-yl]penta-2,4-dienoic 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       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   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       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       0.000  -1.540   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       2.667  -3.080   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       4.001  -0.770   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      -1.540  -3.080   0.000  0.00  0.00           H+0
CONECT    1   12                                                            
CONECT    2   13                                                            
CONECT    3    4    5   22                                                  
CONECT    4    3    6   23                                                  
CONECT    5    3   16   24                                                  
CONECT    6    4   17   25                                                  
CONECT    7    8   14                                                       
CONECT    8    7   15                                                       
CONECT    9   12   13                                                       
CONECT   10   12   14                                                       
CONECT   11   15   19                                                       
CONECT   12    1    9   10                                                  
CONECT   13    2    9   18                                                  
CONECT   14    7   10   18                                                  
CONECT   15    8   11   16                                                  
CONECT   16    5   15   18                                                  
CONECT   17    6   20   21                                                  
CONECT   18   13   14   16                                                  
CONECT   19   11                                                            
CONECT   20   17                                                            
CONECT   21   17                                                            
CONECT   22    3                                                            
CONECT   23    4                                                            
CONECT   24    5                                                            
CONECT   25    6                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

Synonyms

Value	Source
5-(2-Hydroxymethyl-6,8-dimethyl-5,6,7,8-tetrahydronaphthalene)-2,4-pentadienoic acid	MeSH

Molecular Formula

C₁₈H₂₂O₃

Average Mass

286.371

Monoisotopic Mass

286.156894568

IUPAC Name

(2E,4E)-5-[2-(hydroxymethyl)-6,8-dimethyl-5,6,7,8-tetrahydronaphthalen-1-yl]penta-2,4-dienoic acid

Traditional Name

(2E,4E)-5-[2-(hydroxymethyl)-6,8-dimethyl-5,6,7,8-tetrahydronaphthalen-1-yl]penta-2,4-dienoic acid

CAS Registry Number

Not Available

SMILES

[H]\C(C([H])=C([H])C1=C(CO)C=CC2=C1C(C)CC(C)C2)=C(\[H])C(O)=O

InChI Identifier

InChI=1S/C18H22O3/c1-12-9-13(2)18-14(10-12)7-8-15(11-19)16(18)5-3-4-6-17(20)21/h3-8,12-13,19H,9-11H2,1-2H3,(H,20,21)/b5-3+,6-4+

InChI Key

XVNDJROXVPBPBY-GGWOSOGESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetralins. These are polycyclic aromatic compounds containing a tetralin moiety, which consists of a benzene fused to a cyclohexane.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Tetralins

Sub Class

Not Available

Direct Parent

Tetralins

Alternative Parents

Substituents

Tetralin
Styrene
Medium-chain fatty acid
Hydroxy fatty acid
Fatty acyl
Fatty acid
Unsaturated fatty acid
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Aromatic alcohol
Organic oxygen compound
Alcohol
Primary alcohol
Organooxygen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0019 g/L	ALOGPS
logP	4.23	ALOGPS
logP	3.92	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Acidic)	4.68	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	86.77 m³·mol⁻¹	ChemAxon
Polarizability	32.92 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

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	532.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	28.8
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	617.2
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	766.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	835.0
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	494.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	2554.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	85.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	532.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	629.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	418.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	268.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	196.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-23	8.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	335.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	346.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	457.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1830.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1644.6

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Arohynapene B_TMS_1	CC1CC2=CC=C(CO[Si](C)(C)C)C(C=C/C=C/C(=O)O)=C2C(C)C1	standard non polar	2025-10-23	2217.45
Gas Chromatography	Arohynapene B_TMS_2	CC1CC2=CC=C(CO)C(C=C/C=C/C(=O)O[Si](C)(C)C)=C2C(C)C1	standard non polar	2025-10-23	2457.19
Gas Chromatography	Arohynapene B_TMS_3	CC1CC2=CC=C(CO[Si](C)(C)C)C(C=C/C=C/C(=O)O[Si](C)(C)C)=C2C(C)C1	standard non polar	2025-10-23	1467.03
Gas Chromatography	Arohynapene B_TMS_1	CC1CC2=CC=C(CO[Si](C)(C)C)C(C=C/C=C/C(=O)O)=C2C(C)C1	standard polar	2025-10-23	2064.38
Gas Chromatography	Arohynapene B_TMS_2	CC1CC2=CC=C(CO)C(C=C/C=C/C(=O)O[Si](C)(C)C)=C2C(C)C1	standard polar	2025-10-23	1798.54
Gas Chromatography	Arohynapene B_TMS_3	CC1CC2=CC=C(CO[Si](C)(C)C)C(C=C/C=C/C(=O)O[Si](C)(C)C)=C2C(C)C1	standard polar	2025-10-23	1626.67

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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 sputum; Human ; Human feces	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

C00016930

Chemspider ID

4947681

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6443712

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 Arohynapene B (MMDBc0014641)

MOL for #<Metabolite:0x00007fc93bcf3d00>

3D MOL for #<Metabolite:0x00007fc93bcf3d00>

3D SDF for #<Metabolite:0x00007fc93bcf3d00>

3D-SDF for #<Metabolite:0x00007fc93bcf3d00>

PDB for #<Metabolite:0x00007fc93bcf3d00>

3D PDB for #<Metabolite:0x00007fc93bcf3d00>

SMILES for #<Metabolite:0x00007fc93bcf3d00>

INCHI for #<Metabolite:0x00007fc93bcf3d00>

Structure for #<Metabolite:0x00007fc93bcf3d00>

3D Structure for #<Metabolite:0x00007fc93bcf3d00>