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Showing NP-Card for Glyceollin I (NP0047781)

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Record Information
Version2.0
Created at2022-03-17 20:45:52 UTC
Updated at2022-03-17 20:45:53 UTC
NP-MRD IDNP0047781
Secondary Accession NumbersNone
Natural Product Identification
Common NameGlyceollin I
DescriptionIsopentyl mercaptan, also known as 2-methyl-4-butanethiol or fema 3858, belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain. Isopentyl mercaptan is an extremely weak basic (essentially neutral) compound (based on its pKa). Isopentyl mercaptan is a glue and onion tasting compound. Outside of the human body, Isopentyl mercaptan has been detected, but not quantified in, alcoholic beverages. Glyceollin I is found in Psoralea bituminosa , Glycine clandestina, Glycine falcata, Glycine latifolia, Glycine latrobeana, Glycine soja , Glycine tabacina, Glycine tomentella, Psoralea acaulis and Psoralea onobrychis. This could make isopentyl mercaptan a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0047781 (Glyceollin I)


  Mrv0541 05061307262D          

 25 29  0  0  0  0            999 V2000
    7.6127   -1.5969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5027   -2.6518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6080   -1.4216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3192   -3.2232    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3925   -1.1660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1398   -3.3088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7724   -1.2197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5930   -1.3053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0507   -2.7803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3108   -0.9629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4371   -2.2287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2880   -1.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9831   -2.4698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0060   -1.7176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6242   -2.6410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8351   -2.5247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4675   -1.8019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1625   -2.3841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9291   -2.0587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8264   -1.6307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3473   -2.4842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4133   -0.9166    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1313   -1.0485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5499   -2.9367    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4447   -2.7266    0.0000 O   0  0  0  0  0  0  0  0  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
 11  3  1  0  0  0  0
 11  9  2  0  0  0  0
 12  7  1  0  0  0  0
 13  4  1  0  0  0  0
 14  5  1  0  0  0  0
 15  6  1  0  0  0  0
 15 12  2  0  0  0  0
 16  9  1  0  0  0  0
 16 14  2  0  0  0  0
 17 12  1  0  0  0  0
 17 13  2  0  0  0  0
 18 13  1  0  0  0  0
 19  1  1  0  0  0  0
 19  2  1  0  0  0  0
 19  8  1  0  0  0  0
 20 10  1  0  0  0  0
 20 14  1  0  0  0  0
 20 18  1  0  0  0  0
 21 11  1  0  0  0  0
 22 20  1  0  0  0  0
 23 10  1  0  0  0  0
 23 17  1  0  0  0  0
 24 16  1  0  0  0  0
 24 18  1  0  0  0  0
 25 15  1  0  0  0  0
 25 19  1  0  0  0  0
M  END
Download

3D MOL for NP0047781 (Glyceollin I)

Download
3D SDF for NP0047781 (Glyceollin I)

  Mrv0541 05061307262D          

 25 29  0  0  0  0            999 V2000
    7.6127   -1.5969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5027   -2.6518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6080   -1.4216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3192   -3.2232    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3925   -1.1660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1398   -3.3088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7724   -1.2197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5930   -1.3053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0507   -2.7803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3108   -0.9629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4371   -2.2287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2880   -1.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9831   -2.4698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0060   -1.7176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6242   -2.6410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8351   -2.5247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4675   -1.8019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1625   -2.3841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9291   -2.0587    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8264   -1.6307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3473   -2.4842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4133   -0.9166    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1313   -1.0485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5499   -2.9367    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4447   -2.7266    0.0000 O   0  0  0  0  0  0  0  0  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
 11  3  1  0  0  0  0
 11  9  2  0  0  0  0
 12  7  1  0  0  0  0
 13  4  1  0  0  0  0
 14  5  1  0  0  0  0
 15  6  1  0  0  0  0
 15 12  2  0  0  0  0
 16  9  1  0  0  0  0
 16 14  2  0  0  0  0
 17 12  1  0  0  0  0
 17 13  2  0  0  0  0
 18 13  1  0  0  0  0
 19  1  1  0  0  0  0
 19  2  1  0  0  0  0
 19  8  1  0  0  0  0
 20 10  1  0  0  0  0
 20 14  1  0  0  0  0
 20 18  1  0  0  0  0
 21 11  1  0  0  0  0
 22 20  1  0  0  0  0
 23 10  1  0  0  0  0
 23 17  1  0  0  0  0
 24 16  1  0  0  0  0
 24 18  1  0  0  0  0
 25 15  1  0  0  0  0
 25 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0047781

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)OC2=C(C=C1)C1=C(C=C2)C2OC3=C(C=CC(O)=C3)C2(O)CO1

> <INCHI_IDENTIFIER>
InChI=1S/C20H18O5/c1-19(2)8-7-12-15(25-19)6-4-13-17(12)23-10-20(22)14-5-3-11(21)9-16(14)24-18(13)20/h3-9,18,21-22H,10H2,1-2H3

> <INCHI_KEY>
YIFYYPKWOQSCRI-UHFFFAOYSA-N

> <FORMULA>
C20H18O5

> <MOLECULAR_WEIGHT>
338.3539

> <EXACT_MASS>
338.115423686

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
35.626105401095415

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
17,17-dimethyl-3,12,18-trioxapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁴,¹⁹]henicosa-1(13),4(9),5,7,14(19),15,20-heptaene-6,10-diol

> <ALOGPS_LOGP>
3.24

> <JCHEM_LOGP>
2.9123376819999995

> <ALOGPS_LOGS>
-3.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.154507231413769

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.396141206226131

> <JCHEM_PKA_STRONGEST_BASIC>
-4.094360765812266

> <JCHEM_POLAR_SURFACE_AREA>
68.15

> <JCHEM_REFRACTIVITY>
92.07920000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.98e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
17,17-dimethyl-3,12,18-trioxapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁴,¹⁹]henicosa-1(13),4(9),5,7,14(19),15,20-heptaene-6,10-diol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0047781 (Glyceollin I)
Download
PDB for NP0047781 (Glyceollin I)
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      14.210  -2.981   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.005  -4.950   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.135  -2.654   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.063  -6.017   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.599  -2.177   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.594  -6.176   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.775  -2.277   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.307  -2.437   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.961  -5.190   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.180  -1.797   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.816  -4.160   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.871  -3.523   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.435  -4.610   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.745  -3.206   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.499  -4.930   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.426  -4.713   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.339  -3.364   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.903  -4.450   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.934  -3.843   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.276  -3.044   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.648  -4.637   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.505  -1.711   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       7.712  -1.957   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.760  -5.482   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      12.030  -5.090   0.000  0.00  0.00           O+0
CONECT    1   19                                                            
CONECT    2   19                                                            
CONECT    3    5   11                                                       
CONECT    4    6   13                                                       
CONECT    5    3   14                                                       
CONECT    6    4   15                                                       
CONECT    7    8   12                                                       
CONECT    8    7   19                                                       
CONECT    9   11   16                                                       
CONECT   10   20   23                                                       
CONECT   11    3    9   21                                                  
CONECT   12    7   15   17                                                  
CONECT   13    4   17   18                                                  
CONECT   14    5   16   20                                                  
CONECT   15    6   12   25                                                  
CONECT   16    9   14   24                                                  
CONECT   17   12   13   23                                                  
CONECT   18   13   20   24                                                  
CONECT   19    1    2    8   25                                             
CONECT   20   10   14   18   22                                             
CONECT   21   11                                                            
CONECT   22   20                                                            
CONECT   23   10   17                                                       
CONECT   24   16   18                                                       
CONECT   25   15   19                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   58    0
END

Download
3D PDB for NP0047781 (Glyceollin I)
Download
SMILES for NP0047781 (Glyceollin I)
CC1(C)OC2=C(C=C1)C1=C(C=C2)C2OC3=C(C=CC(O)=C3)C2(O)CO1
Download
INCHI for NP0047781 (Glyceollin I)
InChI=1S/C20H18O5/c1-19(2)8-7-12-15(25-19)6-4-13-17(12)23-10-20(22)14-5-3-11(21)9-16(14)24-18(13)20/h3-9,18,21-22H,10H2,1-2H3
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View in JSmol
Synonyms
ValueSource
1-Mercapto-3-methylbutaneHMDB
2-Methyl-4-butanethiolHMDB
3-Methyl-1-butanethiolHMDB
3-Methyl-1-butylthiolHMDB
3-Methylbutane-1-thiolHMDB
3-MethylbutanethiolHMDB
FEMA 3858HMDB
Isoamyl mercaptanHMDB
Isoamyl sulfhydrateHMDB
Isoamyl thioalcoholHMDB
IsoamylthiolHMDB
IsopentanethiolHMDB
Thioisoamyl alcoholHMDB
rac-Glyceollin IChEMBL, HMDB
(-) - Glyceollin IHMDB
(-)-Glyceollin IHMDB
2,2-Dimethyl-2H,6H-benzofuro[3,2-c]pyrano[2,3-H][1]benzopyran-6a,9(11ah)-diol, 9ciHMDB
GlyceollinHMDB
Glyceollin IMeSH
Chemical FormulaC20H18O5
Average Mass338.3539 Da
Monoisotopic Mass338.11542 Da
IUPAC Name17,17-dimethyl-3,12,18-trioxapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁴,¹⁹]henicosa-1(13),4(9),5,7,14(19),15,20-heptaene-6,10-diol
Traditional Name17,17-dimethyl-3,12,18-trioxapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁴,¹⁹]henicosa-1(13),4(9),5,7,14(19),15,20-heptaene-6,10-diol
CAS Registry Number57103-57-8
SMILES
CC1(C)OC2=C(C=C1)C1=C(C=C2)C2OC3=C(C=CC(O)=C3)C2(O)CO1
InChI Identifier
InChI=1S/C20H18O5/c1-19(2)8-7-12-15(25-19)6-4-13-17(12)23-10-20(22)14-5-3-11(21)9-16(14)24-18(13)20/h3-9,18,21-22H,10H2,1-2H3
InChI KeyYIFYYPKWOQSCRI-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Bituminaria bituminosaPlant
Glycine clandestinaPlant
Glycine falcataPlant
Glycine latifoliaPlant
Glycine latrobeanaPlant
Glycine maxFooDB
Glycine sojaPlant
Glycine tabacinaPlant
Glycine tomentellaPlant
Psoralea acaulisPlant
Psoralea onobrychisPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain.
KingdomOrganic compounds  
Super ClassOrganosulfur compounds  
ClassThiols  
Sub ClassAlkylthiols  
Direct ParentAlkylthiols  
Alternative Parents
Substituents
  • Alkylthiol
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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
logP3.24ALOGPS
logP2.91ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)9.4ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area68.15 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity92.08 m³·mol⁻¹ChemAxon
Polarizability35.63 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0033902  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012097  
KNApSAcK IDNot Available
Chemspider ID10462  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10925  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available