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Showing NP-Card for Geosmin (NP0048515)

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Record Information
Version2.0
Created at2022-03-17 20:57:40 UTC
Updated at2022-03-17 20:57:40 UTC
NP-MRD IDNP0048515
Secondary Accession NumbersNone
Natural Product Identification
Common NameGeosmin
DescriptionGeosmin belongs to the class of organic compounds known as tertiary alcohols. Tertiary alcohols are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ). Geosmin is an extremely weak basic (essentially neutral) compound (based on its pKa). Geosmin is a beet, earthy, and fresh tasting compound. Outside of the human body, Geosmin is found, on average, in the highest concentration within corns. Geosmin has also been detected, but not quantified in, common beets. This could make geosmin a potential biomarker for the consumption of these foods. Under acidic conditions, geosmin decomposes into odorless substances. Besides the production of volatile geosmin, it also produces many other complex molecules of pharmacological interest; its genome sequence is available at the Sanger Institute. Geosmin is also an issue for saltwater fish grown in recirculating aquaculture systems, such as Atlantic salmon. These systems rely on biological filtration using cultured microbial communities to process the nitrogenous waste from the fish (ammonia) into less harmful compounds (nitrite and nitrate) that can be tolerated at higher concentrations. The human nose is extremely sensitive to geosmin and is able to detect it at concentrations as low as 5 parts per trillion. Geosmin is produced by the gram-positive bacteria Streptomyces and various cyanobacteria, and released when these microorganisms die. Geosmin is an organic compound with a distinct earthy flavor and aroma produced by certain bacteria, and is responsible for the earthy taste of beetroots and a contributor to the strong scent (petrichor) that occurs in the air when rain falls after a dry spell of weather or when soil is disturbed. Geosmin is found in Basella alba, Beta vulgaris, Coffea arabica, Cystoderma carcharias, Kitasatospora aureofaciens, Oscillatoria brevis, Phaseolus vulgaris, Physarum polycephalum, Streptomyces albidoflavus, Streptomyces alboflavus, Streptomyces avermitilis, Streptomyces coelicolor, Streptomyces fradiae, Streptomyces odorifer, Streptomyces rimosus, Streptomyces spp., Streptomyces tendae, Streptomyces thermocarboxydus, Symphyogyna brongniartii and Zea mays. Geosmin breaks down in acid conditions; hence, vinegar and other acidic ingredients are used in fish recipes to reduce the muddy flavor.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0048515 (Geosmin)


  Mrv0541 05061309092D          

 13 14  0  0  0  0            999 V2000
    2.8579    3.3000    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  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
    3.5724    2.0625    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
    2.8579    0.8250    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
    2.8579    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
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  1  0  0  0  0
  9  4  1  0  0  0  0
 10  1  1  0  0  0  0
 10  6  1  0  0  0  0
 11  2  1  0  0  0  0
 11  7  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 12 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
M  END
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3D MOL for NP0048515 (Geosmin)

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3D SDF for NP0048515 (Geosmin)

  Mrv0541 05061309092D          

 13 14  0  0  0  0            999 V2000
    2.8579    3.3000    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  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
    3.5724    2.0625    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
    2.8579    0.8250    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
    2.8579    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
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  1  0  0  0  0
  9  4  1  0  0  0  0
 10  1  1  0  0  0  0
 10  6  1  0  0  0  0
 11  2  1  0  0  0  0
 11  7  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 12 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048515

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1CCCC2(C)CCCCC12O

> <INCHI_IDENTIFIER>
InChI=1S/C12H22O/c1-10-6-5-8-11(2)7-3-4-9-12(10,11)13/h10,13H,3-9H2,1-2H3

> <INCHI_KEY>
JLPUXFOGCDVKGO-UHFFFAOYSA-N

> <FORMULA>
C12H22O

> <MOLECULAR_WEIGHT>
182.3025

> <EXACT_MASS>
182.167065326

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
22.187172402164265

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4,8a-dimethyl-decahydronaphthalen-4a-ol

> <ALOGPS_LOGP>
3.66

> <JCHEM_LOGP>
3.172581791333333

> <ALOGPS_LOGS>
-3.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-0.004709431003981135

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
54.577799999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.12e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
geosmin

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0048515 (Geosmin)
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PDB for NP0048515 (Geosmin)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   1.540   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       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.001   5.390   0.000  0.00  0.00           O+0
CONECT    1   10                                                            
CONECT    2   11                                                            
CONECT    3    4    7                                                       
CONECT    4    3    9                                                       
CONECT    5    6    8                                                       
CONECT    6    5   10                                                       
CONECT    7    3   11                                                       
CONECT    8    5   11                                                       
CONECT    9    4   12                                                       
CONECT   10    1    6   12                                                  
CONECT   11    2    7    8   12                                             
CONECT   12    9   10   11   13                                             
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

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3D PDB for NP0048515 (Geosmin)
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SMILES for NP0048515 (Geosmin)
CC1CCCC2(C)CCCCC12O
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INCHI for NP0048515 (Geosmin)
InChI=1S/C12H22O/c1-10-6-5-8-11(2)7-3-4-9-12(10,11)13/h10,13H,3-9H2,1-2H3
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Synonyms
ValueSource
1,10-Dimethyl-9-decalolHMDB
11,12,13-Trinor-5-eudesmanolHMDB
4,8a-Dimethyloctahydro-4a(2H)-naphthalenolHMDB
4,8alpha-Dimethyl-octahydro-naphthalen-4alpha-olHMDB
Octahydro-4,8a-dimethyl-4a(2H)-naphthalenol, 9ciHMDB
Chemical FormulaC12H22O
Average Mass182.3025 Da
Monoisotopic Mass182.16707 Da
IUPAC Name4,8a-dimethyl-decahydronaphthalen-4a-ol
Traditional Namegeosmin
CAS Registry Number19700-21-1
SMILES
CC1CCCC2(C)CCCCC12O
InChI Identifier
InChI=1S/C12H22O/c1-10-6-5-8-11(2)7-3-4-9-12(10,11)13/h10,13H,3-9H2,1-2H3
InChI KeyJLPUXFOGCDVKGO-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Basella albaLOTUS Database
Beta vulgarisLOTUS Database
Coffea arabicaLOTUS Database
Cystoderma carchariasLOTUS Database
Kitasatospora aureofaciensLOTUS Database
Oscillatoria brevisLOTUS Database
Phaseolus vulgarisLOTUS Database
Physarum polycephalumLOTUS Database
Streptomyces albidoflavusLOTUS Database
Streptomyces alboflavusLOTUS Database
Streptomyces avermitilisLOTUS Database
Streptomyces coelicolorLOTUS Database
Streptomyces fradiaeLOTUS Database
Streptomyces odoriferLOTUS Database
Streptomyces rimosusLOTUS Database
Streptomyces spp.Bacteria
Streptomyces tendaeLOTUS Database
Streptomyces thermocarboxydusLOTUS Database
Symphyogyna brongniartiiLOTUS Database
Zea maysLOTUS Database
Zea mays L.FooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tertiary alcohols. Tertiary alcohols are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ).
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassAlcohols and polyols  
Direct ParentTertiary alcohols  
Alternative Parents
Substituents
  • Tertiary alcohol
    • 

  • Cyclic alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP3.66ALOGPS
logP3.17ChemAxon
logS-3.6ALOGPS
pKa (Strongest Basic)-0.0047ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity54.58 m³·mol⁻¹ChemAxon
Polarizability22.19 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0036461  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB015352  
KNApSAcK IDC00013224  
Chemspider ID1176  
KEGG Compound IDC16286  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGeosmin  
METLIN IDNot Available
PubChem Compound1213  
PDB IDNot Available
ChEBI ID46702  
Good Scents IDNot Available
References
General ReferencesNot Available