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Showing metabocard for Iodoacetic acid (HMDB0253518)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 12:10:02 UTC
Update Date2021-09-26 23:06:47 UTC
HMDB IDHMDB0253518
Secondary Accession NumbersNone
Metabolite Identification
Common NameIodoacetic acid
Descriptioniodoacetic acid, also known as 2-iodoacetate or CH2ico2h, belongs to the class of organic compounds known as alpha-halocarboxylic acids. These are carboxylic acids containing a halogen atom bonded to the alpha carbon atom. iodoacetic acid exists in all living organisms, ranging from bacteria to humans. Based on a literature review a significant number of articles have been published on iodoacetic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Iodoacetic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Iodoacetic acid 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 HMDB0253518 (Iodoacetic acid)

Structure #1
  Mrv0541 02241207322D          

  5  4  0  0  0  0            999 V2000
    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
    0.8250    1.4289    0.0000 I   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  2  0  0  0  0
  2  5  1  0  0  0  0
M  END
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3D MOL for HMDB0253518 (Iodoacetic acid)

HMDB0253518
     RDKit          3D
Iodoacetic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
    1.0003   -0.9410    1.1387 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5961   -0.2385    0.1740 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5114    0.5459   -0.5066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8265   -0.3577   -0.2067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9412    1.2746    0.6068 I   0  0  0  0  0  0  0  0  0  0  0  0
    1.8566    1.3971   -0.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9415   -0.3627   -1.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2552   -1.3178    0.1750 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  3  6  1  0
  4  7  1  0
  4  8  1  0
M  END
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3D SDF for HMDB0253518 (Iodoacetic acid)

Structure #1
  Mrv0541 02241207322D          

  5  4  0  0  0  0            999 V2000
    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
    0.8250    1.4289    0.0000 I   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  2  0  0  0  0
  2  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253518

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CI

> <INCHI_IDENTIFIER>
InChI=1S/C2H3IO2/c3-1-2(4)5/h1H2,(H,4,5)

> <INCHI_KEY>
JDNTWHVOXJZDSN-UHFFFAOYSA-N

> <FORMULA>
C2H3IO2

> <MOLECULAR_WEIGHT>
185.9485

> <EXACT_MASS>
185.91777276

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
10.273910790779361

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-iodoacetic acid

> <ALOGPS_LOGP>
1.00

> <JCHEM_LOGP>
0.7222151540000001

> <ALOGPS_LOGS>
-0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.04738443593906

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
25.7275

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.63e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
iodoacetic acid

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0253518 (Iodoacetic acid)

HMDB0253518
     RDKit          3D
Iodoacetic acid
  8  7  0  0  0  0  0  0  0  0999 V2000
    1.0003   -0.9410    1.1387 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5961   -0.2385    0.1740 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5114    0.5459   -0.5066 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8265   -0.3577   -0.2067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9412    1.2746    0.6068 I   0  0  0  0  0  0  0  0  0  0  0  0
    1.8566    1.3971   -0.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9415   -0.3627   -1.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2552   -1.3178    0.1750 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  3  6  1  0
  4  7  1  0
  4  8  1  0
M  END
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PDB for HMDB0253518 (Iodoacetic acid)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  I   UNK     0       1.540   2.667   0.000  0.00  0.00           I+0
HETATM    4  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4    5                                                  
CONECT    3    1                                                            
CONECT    4    2                                                            
CONECT    5    2                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0253518 (Iodoacetic acid)

COMPND    HMDB0253518
HETATM    1  O1  UNL     1       1.000  -0.941   1.139  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.596  -0.238   0.174  1.00  0.00           C  
HETATM    3  O2  UNL     1       1.511   0.546  -0.507  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.826  -0.358  -0.207  1.00  0.00           C  
HETATM    5  I1  UNL     1      -1.941   1.275   0.607  1.00  0.00           I  
HETATM    6  H1  UNL     1       1.857   1.397  -0.060  1.00  0.00           H  
HETATM    7  H2  UNL     1      -0.941  -0.363  -1.321  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.255  -1.318   0.175  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    6
CONECT    4    5    7    8
END
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SMILES for HMDB0253518 (Iodoacetic acid)

OC(=O)CI
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INCHI for HMDB0253518 (Iodoacetic acid)

InChI=1S/C2H3IO2/c3-1-2(4)5/h1H2,(H,4,5)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Iodoacetic acidChEBI
CH2ICO2hChEBI
CH2ICOOHChEBI
ICH2co2hChEBI
ICH2coohChEBI
Iodoethanoic acidChEBI
Monoiodoacetic acidChEBI
2-IodoacetateGenerator
IodoethanoateGenerator
MonoiodoacetateGenerator
IodoacetateGenerator
Acid, iodoaceticMeSH
Acid, monoiodoaceticMeSH
Iodoacetate, sodiumMeSH
Sodium iodoacetateMeSH
Chemical FormulaC2H3IO2
Average Molecular Weight185.9485
Monoisotopic Molecular Weight185.91777276
IUPAC Name2-iodoacetic acid
Traditional Nameiodoacetic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CI
InChI Identifier
InChI=1S/C2H3IO2/c3-1-2(4)5/h1H2,(H,4,5)
InChI KeyJDNTWHVOXJZDSN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha-halocarboxylic acids. These are carboxylic acids containing a halogen atom bonded to the alpha carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAlpha-halocarboxylic acids and derivatives
Direct ParentAlpha-halocarboxylic acids
Alternative Parents
Substituents
  • Alpha-halocarboxylic acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organoiodide
  • Organohalogen compound
  • Carbonyl group
  • Alkyl iodide
  • Alkyl halide
  • 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
logP1ALOGPS
logP0.72ChemAxon
logS-0.85ALOGPS
pKa (Strongest Acidic)3.05ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity25.73 m³·mol⁻¹ChemAxon
Polarizability10.27 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]+125.29130932474
DeepCCS[M-H]-123.13530932474
DeepCCS[M-2H]-158.74530932474
DeepCCS[M+Na]+133.55830932474
AllCCS[M+H]+142.332859911
AllCCS[M+H-H2O]+138.332859911
AllCCS[M+NH4]+146.032859911
AllCCS[M+Na]+147.132859911
AllCCS[M-H]-162.432859911
AllCCS[M+Na-2H]-168.132859911
AllCCS[M+HCOO]-174.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202210.0258 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.67 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid770.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid364.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid120.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid278.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid102.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid272.9 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 Acid316.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)391.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid585.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid99.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid775.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid243.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid312.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate700.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA296.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water325.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Iodoacetic acidOC(=O)CI1849.5Standard polar33892256
Iodoacetic acidOC(=O)CI1043.1Standard non polar33892256
Iodoacetic acidOC(=O)CI1124.4Semi 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 ID5050
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkIodoacetic_acid
METLIN IDNot Available
PubChem Compound5240
PDB IDNot Available
ChEBI ID74571
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 ]