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Showing metabocard for D-2-Butylisothiocyanate (HMDB0302325)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 16:55:00 UTC
Update Date2021-09-23 16:55:00 UTC
HMDB IDHMDB0302325
Secondary Accession NumbersNone
Metabolite Identification
Common NameD-2-Butylisothiocyanate
DescriptionD-2-butylisothiocyanate is a member of the class of compounds known as isothiocyanates. Isothiocyanates are organic compounds containing the isothiocyanate group, an isocyanate analogue with the general formula RN=C=S. D-2-butylisothiocyanate is practically insoluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). D-2-butylisothiocyanate can be found in horseradish, which makes D-2-butylisothiocyanate a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302325 (D-2-Butylisothiocyanate)


  Mrv1533007301516522D          

  8  7  0  0  1  0            999 V2000
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  6  0  0  0
  5  3  1  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  5  8  1  1  0  0  0
M  END
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3D MOL for HMDB0302325 (D-2-Butylisothiocyanate)

HMDB0302325
     RDKit          3D
D-2-Butylisothiocyanate
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.8063   -0.4797    0.2127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3241   -0.6993    0.4203 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4789    0.1004   -0.5718 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2044    1.5690   -0.4301 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8684   -0.1424   -0.5435 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3723   -0.7826    0.4312 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4399   -1.8541    0.9895 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0904    0.5876    0.3066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1460   -0.8500   -0.7828 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3727   -1.0418    0.9728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1127   -1.7673    0.2983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1039   -0.4006    1.4719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0938   -0.1960   -1.5904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6514    1.9055   -1.0526 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0835    2.1777   -0.7797 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0663    1.8737    0.6476 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  6
  4 14  1  0
  4 15  1  0
  4 16  1  0
M  END
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3D SDF for HMDB0302325 (D-2-Butylisothiocyanate)


  Mrv1533007301516522D          

  8  7  0  0  1  0            999 V2000
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  6  0  0  0
  5  3  1  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  5  8  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0302325

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](C)(CC)N=C=S

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NS/c1-3-5(2)6-4-7/h5H,3H2,1-2H3/t5-/m1/s1

> <INCHI_KEY>
TUFJIDJGIQOYFY-RXMQYKEDSA-N

> <FORMULA>
C5H9NS

> <MOLECULAR_WEIGHT>
115.19

> <EXACT_MASS>
115.045570468

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
13.043732057894577

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-isothiocyanatobutane

> <ALOGPS_LOGP>
2.86

> <JCHEM_LOGP>
2.3655554283333333

> <ALOGPS_LOGS>
-2.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.218964969469592

> <JCHEM_POLAR_SURFACE_AREA>
12.36

> <JCHEM_REFRACTIVITY>
35.0205

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.03e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-isothiocyanatobutane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0302325 (D-2-Butylisothiocyanate)

HMDB0302325
     RDKit          3D
D-2-Butylisothiocyanate
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.8063   -0.4797    0.2127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3241   -0.6993    0.4203 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4789    0.1004   -0.5718 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2044    1.5690   -0.4301 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8684   -0.1424   -0.5435 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3723   -0.7826    0.4312 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4399   -1.8541    0.9895 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0904    0.5876    0.3066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1460   -0.8500   -0.7828 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3727   -1.0418    0.9728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1127   -1.7673    0.2983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1039   -0.4006    1.4719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0938   -0.1960   -1.5904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6514    1.9055   -1.0526 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0835    2.1777   -0.7797 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0663    1.8737    0.6476 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  2  0
  6  7  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  6
  4 14  1  0
  4 15  1  0
  4 16  1  0
M  END
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PDB for HMDB0302325 (D-2-Butylisothiocyanate)

HEADER    PROTEIN                                 30-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-15         0                                  
HETATM    1  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  S   UNK     0       3.080   0.000   0.000  0.00  0.00           S+0
HETATM    8  H   UNK     0      -1.540  -2.667   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    5                                                            
CONECT    3    1    5                                                       
CONECT    4    6    7                                                       
CONECT    5    2    3    6    8                                             
CONECT    6    4    5                                                       
CONECT    7    4                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0302325 (D-2-Butylisothiocyanate)

COMPND    HMDB0302325
HETATM    1  C1  UNL     1      -1.806  -0.480   0.213  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.324  -0.699   0.420  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.479   0.100  -0.572  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.204   1.569  -0.430  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.868  -0.142  -0.544  1.00  0.00           N  
HETATM    6  C5  UNL     1       2.372  -0.783   0.431  1.00  0.00           C  
HETATM    7  S1  UNL     1       3.440  -1.854   0.990  1.00  0.00           S  
HETATM    8  H1  UNL     1      -2.090   0.588   0.307  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.146  -0.850  -0.783  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.373  -1.042   0.973  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.113  -1.767   0.298  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.104  -0.401   1.472  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.094  -0.196  -1.590  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.651   1.906  -1.053  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.084   2.178  -0.780  1.00  0.00           H  
HETATM   16  H9  UNL     1       0.066   1.874   0.648  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4    5   13
CONECT    4   14   15   16
CONECT    5    6    6
CONECT    6    7    7
END
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SMILES for HMDB0302325 (D-2-Butylisothiocyanate)

[H][C@@](C)(CC)N=C=S
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INCHI for HMDB0302325 (D-2-Butylisothiocyanate)

InChI=1S/C5H9NS/c1-3-5(2)6-4-7/h5H,3H2,1-2H3/t5-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
D-2-Butylisothiocyanic acidGenerator
Chemical FormulaC5H9NS
Average Molecular Weight115.19
Monoisotopic Molecular Weight115.045570468
IUPAC Name(2R)-2-isothiocyanatobutane
Traditional Name(2R)-2-isothiocyanatobutane
CAS Registry NumberNot Available
SMILES
[H][C@@](C)(CC)N=C=S
InChI Identifier
InChI=1S/C5H9NS/c1-3-5(2)6-4-7/h5H,3H2,1-2H3/t5-/m1/s1
InChI KeyTUFJIDJGIQOYFY-RXMQYKEDSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as isothiocyanates. These are organic compounds containing the isothiocyanate group, an isocyanate analogue with the general formula RN=C=S.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassIsothiocyanates
Sub ClassNot Available
Direct ParentIsothiocyanates
Alternative Parents
Substituents
  • Isothiocyanate
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP2.86ALOGPS
logP2.37ChemAxon
logS-2.5ALOGPS
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.36 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity35.02 m³·mol⁻¹ChemAxon
Polarizability13.04 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+128.35832859911
AllCCS[M+H-H2O]+124.12532859911
AllCCS[M+Na]+133.44532859911
AllCCS[M+NH4]+132.30632859911
AllCCS[M-H]-132.62932859911
AllCCS[M+Na-2H]-136.59732859911
AllCCS[M+HCOO]-140.97732859911
DeepCCS[M+H]+127.58430932474
DeepCCS[M-H]-125.29730932474
DeepCCS[M-2H]-160.84930932474
DeepCCS[M+Na]+134.84230932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202212.1788 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.62 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1495.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid498.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid182.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid328.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid167.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid417.6 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid640.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)232.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid995.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid362.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1034.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid315.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid332.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate513.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA373.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water98.1 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 10V, Positive-QTOFsplash10-014i-3900000000-4a9cbee0fe0897af46a82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 20V, Positive-QTOFsplash10-066r-9400000000-d89fd734393c1de11dc22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 40V, Positive-QTOFsplash10-0a4i-9000000000-64da0d24f8dbf27a2a302016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 10V, Negative-QTOFsplash10-03di-3900000000-4527d9e46b4cc57482242016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 20V, Negative-QTOFsplash10-03di-8900000000-a2b4bc6406648bcf59fb2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 40V, Negative-QTOFsplash10-0a4i-9000000000-bcefd5e57889c60f95ca2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 10V, Positive-QTOFsplash10-066r-7900000000-f0d0f608c57cc746ca532021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 20V, Positive-QTOFsplash10-0a59-9000000000-b6072335f4afde487cee2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 40V, Positive-QTOFsplash10-0a4i-9000000000-55ddc5ebd5ee5efe7df22021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 10V, Negative-QTOFsplash10-0bt9-9500000000-c021715b107eba94e19b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 20V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-2-Butylisothiocyanate 40V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB004143
KNApSAcK IDNot Available
Chemspider ID4541774
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5399110
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available