Hmdb loader

Showing metabocard for 3-chlorobenzaldehyde (HMDB0304116)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:18:50 UTC
Update Date2021-09-24 07:18:50 UTC
HMDB IDHMDB0304116
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-chlorobenzaldehyde
Description3-chlorobenzaldehyde belongs to benzoyl derivatives class of compounds. Those are organic compounds containing an acyl moiety of benzoic acid with the formula (C6H5CO-). 3-chlorobenzaldehyde is practically insoluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). 3-chlorobenzaldehyde can be found in a number of food items such as calabash, black raspberry, ginger, and tartary buckwheat, which makes 3-chlorobenzaldehyde a potential biomarker for the consumption of these food products.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304116 (3-chlorobenzaldehyde)


  Mrv1533005141521392D          

  9  9  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   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
    1.4289   -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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 Cl  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
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  3  9  2  0  0  0  0
M  END
Download

3D MOL for HMDB0304116 (3-chlorobenzaldehyde)

HMDB0304116
     RDKit          3D
3-chlorobenzaldehyde
 14 14  0  0  0  0  0  0  0  0999 V2000
    3.0522   -0.8584   -0.3890 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3544    0.1669   -0.1933 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9153    0.0697   -0.0745 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2939   -1.1693   -0.1773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0767   -1.2851   -0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8873   -0.1897    0.1478 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2702    1.0394    0.2497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2850    2.4406    0.5227 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.1002    1.1596    0.1401 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8505    1.1223   -0.1156 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9114   -2.0344   -0.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5844   -2.2594   -0.1463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9621   -0.3288    0.2279 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5878    2.1265    0.2201 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9  3  1  0
  2 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  9 14  1  0
M  END
Download

3D SDF for HMDB0304116 (3-chlorobenzaldehyde)


  Mrv1533005141521392D          

  9  9  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   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
    1.4289   -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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 Cl  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
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  3  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304116

> <DATABASE_NAME>
hmdb

> <SMILES>
ClC1=CC=CC(C=O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H5ClO/c8-7-3-1-2-6(4-7)5-9/h1-5H

> <INCHI_KEY>
SRWILAKSARHZPR-UHFFFAOYSA-N

> <FORMULA>
C7H5ClO

> <MOLECULAR_WEIGHT>
140.57

> <EXACT_MASS>
140.0028925

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
13.222074796589071

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-chlorobenzaldehyde

> <ALOGPS_LOGP>
2.25

> <JCHEM_LOGP>
2.289792837

> <ALOGPS_LOGS>
-2.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.123545689557998

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
37.446799999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.75e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
M-chlorobenzaldehyde

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0304116 (3-chlorobenzaldehyde)

HMDB0304116
     RDKit          3D
3-chlorobenzaldehyde
 14 14  0  0  0  0  0  0  0  0999 V2000
    3.0522   -0.8584   -0.3890 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3544    0.1669   -0.1933 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9153    0.0697   -0.0745 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2939   -1.1693   -0.1773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0767   -1.2851   -0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8873   -0.1897    0.1478 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2702    1.0394    0.2497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2850    2.4406    0.5227 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.1002    1.1596    0.1401 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8505    1.1223   -0.1156 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9114   -2.0344   -0.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5844   -2.2594   -0.1463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9621   -0.3288    0.2279 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5878    2.1265    0.2201 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9  3  1  0
  2 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  9 14  1  0
M  END
Download

PDB for HMDB0304116 (3-chlorobenzaldehyde)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8 Cl   UNK     0      -1.334  -0.770   0.000  0.00  0.00          Cl+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    3                                                       
CONECT    2    1                                                            
CONECT    3    1    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    3                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
Download

3D PDB for HMDB0304116 (3-chlorobenzaldehyde)

COMPND    HMDB0304116
HETATM    1  O1  UNL     1       3.052  -0.858  -0.389  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.354   0.167  -0.193  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.915   0.070  -0.075  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.294  -1.169  -0.177  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.077  -1.285  -0.067  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.887  -0.190   0.148  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.270   1.039   0.250  1.00  0.00           C  
HETATM    8 CL1  UNL     1      -2.285   2.441   0.523  1.00  0.00          CL  
HETATM    9  C7  UNL     1       0.100   1.160   0.140  1.00  0.00           C  
HETATM   10  H1  UNL     1       2.851   1.122  -0.116  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.911  -2.034  -0.345  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.584  -2.259  -0.146  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.962  -0.329   0.228  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.588   2.127   0.220  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4    4    9
CONECT    4    5   11
CONECT    5    6    6   12
CONECT    6    7   13
CONECT    7    8    9    9
CONECT    9   14
END
Download

SMILES for HMDB0304116 (3-chlorobenzaldehyde)

ClC1=CC=CC(C=O)=C1
Download

INCHI for HMDB0304116 (3-chlorobenzaldehyde)

InChI=1S/C7H5ClO/c8-7-3-1-2-6(4-7)5-9/h1-5H
Download
View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC7H5ClO
Average Molecular Weight140.57
Monoisotopic Molecular Weight140.0028925
IUPAC Name3-chlorobenzaldehyde
Traditional NameM-chlorobenzaldehyde
CAS Registry NumberNot Available
SMILES
ClC1=CC=CC(C=O)=C1
InChI Identifier
InChI=1S/C7H5ClO/c8-7-3-1-2-6(4-7)5-9/h1-5H
InChI KeySRWILAKSARHZPR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzoyl derivatives. These are organic compounds containing an acyl moiety of benzoic acid with the formula (C6H5CO-).
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassBenzoyl derivatives
Direct ParentBenzoyl derivatives
Alternative Parents
Substituents
  • Benzoyl
  • Benzaldehyde
  • Aryl-aldehyde
  • Halobenzene
  • Chlorobenzene
  • Aryl halide
  • Aryl chloride
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organochloride
  • Organohalogen compound
  • Aldehyde
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
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
logP2.25ALOGPS
logP2.29ChemAxon
logS-2.3ALOGPS
pKa (Strongest Basic)-7.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity37.45 m³·mol⁻¹ChemAxon
Polarizability13.22 ųChemAxon
Number of Rings1ChemAxon
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]+126.41132859911
AllCCS[M+H-H2O]+121.67332859911
AllCCS[M+Na]+132.10832859911
AllCCS[M+NH4]+130.83232859911
AllCCS[M-H]-120.77132859911
AllCCS[M+Na-2H]-122.72632859911
AllCCS[M+HCOO]-124.91932859911
DeepCCS[M+H]+124.56330932474
DeepCCS[M-H]-120.74630932474
DeepCCS[M-2H]-157.7330932474
DeepCCS[M+Na]+133.12930932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202215.2451 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.05 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1777.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid614.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid235.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid429.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid271.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid580.2 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 Acid705.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)353.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1247.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid497.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1224.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid437.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid511.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate624.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA430.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water163.9 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 10V, Positive-QTOFsplash10-0006-0900000000-2fcdd29b3c91c2f519742019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 20V, Positive-QTOFsplash10-0006-0900000000-f4a34ae7ad28e12f78dd2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 40V, Positive-QTOFsplash10-08g4-9500000000-117cafa37d216fadd3b72019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 10V, Negative-QTOFsplash10-000i-0900000000-5aecf3621c0b40afe3282019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 20V, Negative-QTOFsplash10-000i-0900000000-b69ade4ae6cb69626e272019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 40V, Negative-QTOFsplash10-03e9-6900000000-133de57cffc95fb2b5262019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 10V, Positive-QTOFsplash10-0006-0900000000-f9ac5d19b1b3f99bfa3c2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 20V, Positive-QTOFsplash10-0006-1900000000-97ebae77444eab1ce4c22021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 40V, Positive-QTOFsplash10-03di-9300000000-f300b7d8b9de1d9598b12021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 10V, Negative-QTOFsplash10-000i-2900000000-478ce562f85ac791e1762021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 20V, Negative-QTOFsplash10-001i-9400000000-c26de9e1470d71974b8d2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-chlorobenzaldehyde 40V, Negative-QTOFsplash10-03e9-7900000000-4f94a1995032c0f6c92d2021-10-21Wishart 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 IDFDB030409
KNApSAcK IDNot Available
Chemspider ID21111819
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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