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Showing metabocard for 4-Chloro-1-butanol (HMDB0246381)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:24:21 UTC
Update Date2021-09-26 22:55:26 UTC
HMDB IDHMDB0246381
Secondary Accession NumbersNone
Metabolite Identification
Common Name4-Chloro-1-butanol
Description4-Chloro-1-butanol belongs to the class of organic compounds known as primary alcohols. Primary alcohols are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl). 4-Chloro-1-butanol is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on 4-Chloro-1-butanol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 4-chloro-1-butanol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 4-Chloro-1-butanol is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0246381 (4-Chloro-1-butanol)


  Mrv1652309112101242D          

  6  5  0  0  0  0            999 V2000
    1.9520    1.1270    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
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for HMDB0246381 (4-Chloro-1-butanol)

HMDB0246381
     RDKit          3D
4-Chloro-1-butanol
 15 14  0  0  0  0  0  0  0  0999 V2000
    2.4336   -0.1832   -0.0502 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5734    0.8763    0.1837 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2007    0.4452    0.5759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4734   -0.4016   -0.4794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8587   -0.8047   -0.0210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8864    0.5873    0.2842 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1938   -0.7110   -0.8468 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5534    1.5344   -0.7168 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0090    1.4740    1.0064 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2463   -0.1581    1.4948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4128    1.3400    0.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1421   -1.3131   -0.6162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5738    0.1405   -1.4199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3299   -1.4172   -0.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8175   -1.4089    0.9151 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
  4  5  1  0
  5  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
M  END
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3D SDF for HMDB0246381 (4-Chloro-1-butanol)


  Mrv1652309112101242D          

  6  5  0  0  0  0            999 V2000
    1.9520    1.1270    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
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246381

> <DATABASE_NAME>
hmdb

> <SMILES>
OCCCCCl

> <INCHI_IDENTIFIER>
InChI=1S/C4H9ClO/c5-3-1-2-4-6/h6H,1-4H2

> <INCHI_KEY>
HXHGULXINZUGJX-UHFFFAOYSA-N

> <FORMULA>
C4H9ClO

> <MOLECULAR_WEIGHT>
108.57

> <EXACT_MASS>
108.0341926

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.350235937023715

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-chlorobutan-1-ol

> <ALOGPS_LOGP>
0.97

> <JCHEM_LOGP>
0.7232351853333332

> <ALOGPS_LOGS>
-0.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.97277695630741

> <JCHEM_PKA_STRONGEST_BASIC>
-2.3733073593111387

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
27.114599999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.82e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
chlorbutol

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0246381 (4-Chloro-1-butanol)

HMDB0246381
     RDKit          3D
4-Chloro-1-butanol
 15 14  0  0  0  0  0  0  0  0999 V2000
    2.4336   -0.1832   -0.0502 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5734    0.8763    0.1837 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2007    0.4452    0.5759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4734   -0.4016   -0.4794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8587   -0.8047   -0.0210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8864    0.5873    0.2842 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1938   -0.7110   -0.8468 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5534    1.5344   -0.7168 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0090    1.4740    1.0064 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2463   -0.1581    1.4948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4128    1.3400    0.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1421   -1.3131   -0.6162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5738    0.1405   -1.4199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3299   -1.4172   -0.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8175   -1.4089    0.9151 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
  4  5  1  0
  5  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
M  END
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PDB for HMDB0246381 (4-Chloro-1-butanol)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    4 Cl   UNK     0      -0.357   1.334   0.000  0.00  0.00          Cl+0
HETATM    5  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    1    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0246381 (4-Chloro-1-butanol)

COMPND    HMDB0246381
HETATM    1  O1  UNL     1       2.434  -0.183  -0.050  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.573   0.876   0.184  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.201   0.445   0.576  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.473  -0.402  -0.479  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.859  -0.805  -0.021  1.00  0.00           C  
HETATM    6 CL1  UNL     1      -2.886   0.587   0.284  1.00  0.00          CL  
HETATM    7  H1  UNL     1       2.194  -0.711  -0.847  1.00  0.00           H  
HETATM    8  H2  UNL     1       1.553   1.534  -0.717  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.009   1.474   1.006  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.246  -0.158   1.495  1.00  0.00           H  
HETATM   11  H5  UNL     1      -0.413   1.340   0.786  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.142  -1.313  -0.616  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.574   0.141  -1.420  1.00  0.00           H  
HETATM   14  H8  UNL     1      -2.330  -1.417  -0.817  1.00  0.00           H  
HETATM   15  H9  UNL     1      -1.817  -1.409   0.915  1.00  0.00           H  
CONECT    1    2    7
CONECT    2    3    8    9
CONECT    3    4   10   11
CONECT    4    5   12   13
CONECT    5    6   14   15
END
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SMILES for HMDB0246381 (4-Chloro-1-butanol)

OCCCCCl
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INCHI for HMDB0246381 (4-Chloro-1-butanol)

InChI=1S/C4H9ClO/c5-3-1-2-4-6/h6H,1-4H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
4-Hydroxybutyl chlorideChEBI
Hydroxypropyl methyl chlorideChEBI
Tetramethylene chlorohydrinChEBI
Chemical FormulaC4H9ClO
Average Molecular Weight108.57
Monoisotopic Molecular Weight108.0341926
IUPAC Name4-chlorobutan-1-ol
Traditional Namechlorbutol
CAS Registry NumberNot Available
SMILES
OCCCCCl
InChI Identifier
InChI=1S/C4H9ClO/c5-3-1-2-4-6/h6H,1-4H2
InChI KeyHXHGULXINZUGJX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as primary alcohols. Primary alcohols are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentPrimary alcohols
Alternative Parents
Substituents
  • Hydrocarbon derivative
  • Primary alcohol
  • Organochloride
  • Organohalogen compound
  • Alkyl halide
  • Alkyl chloride
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
logP0.97ALOGPS
logP0.72ChemAxon
logS-0.45ALOGPS
pKa (Strongest Acidic)15.97ChemAxon
pKa (Strongest Basic)-2.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity27.11 m³·mol⁻¹ChemAxon
Polarizability11.35 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
DeepCCS[M+H]+125.31130932474
DeepCCS[M-H]-123.29930932474
DeepCCS[M-2H]-158.6930932474
DeepCCS[M+Na]+133.34930932474
AllCCS[M+H]+126.232859911
AllCCS[M+H-H2O]+121.932859911
AllCCS[M+NH4]+130.132859911
AllCCS[M+Na]+131.332859911
AllCCS[M-H]-136.432859911
AllCCS[M+Na-2H]-141.132859911
AllCCS[M+HCOO]-146.232859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202211.1632 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.47 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1479.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid391.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid127.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid269.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid194.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid404.1 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 Acid451.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)150.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid875.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid313.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1070.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid316.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid320.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate456.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA287.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water70.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
4-Chloro-1-butanolOCCCCCl1641.9Standard polar33892256
4-Chloro-1-butanolOCCCCCl884.8Standard non polar33892256
4-Chloro-1-butanolOCCCCCl920.7Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID12980
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkChlorobutanol
METLIN IDNot Available
PubChem Compound13569
PDB IDNot Available
ChEBI ID87310
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 References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]