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Showing metabocard for Formic acid (HMDB0000142)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:33 UTC
HMDB IDHMDB0000142
Secondary Accession Numbers
  • HMDB00142
Metabolite Identification
Common NameFormic acid
DescriptionFormic acid is the simplest carboxylic acid. Formate is an intermediate in normal metabolism. It takes part in the metabolism of one-carbon compounds and its carbon may appear in methyl groups undergoing transmethylation. It is eventually oxidized to carbon dioxide. Formate is typically produced as a byproduct in the production of acetate. It is responsible for both metabolic acidosis and disrupting mitochondrial electron transport and energy production by inhibiting cytochrome oxidase activity, the terminal electron acceptor of the electron transport chain. Cell death from cytochrome oxidase inhibition by formate is believed to result partly from depletion of ATP, reducing energy concentrations so that essential cell functions cannot be maintained. Furthermore, inhibition of cytochrome oxidase by formate may also cause cell death by increased production of cytotoxic reactive oxygen species (ROS) secondary to the blockade of the electron transport chain. In nature, formic acid is found in the stings and bites of many insects of the order Hymenoptera, including bees and ants. The principal use of formic acid is as a preservative and antibacterial agent in livestock feed. When sprayed on fresh hay or other silage, it arrests certain decay processes and causes the feed to retain its nutritive value longer. Urinary formate is produced by Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumonia, Enterobacter, Acinetobacter, Proteus mirabilis, Citrobacter frundii, Enterococcus faecalis, Streptococcus group B, Staphylococcus saprophyticus (PMID: 22292465 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000142 (Formic acid)

  Mrv1652309032023542D          

  3  2  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 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 O   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
M  END
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3D MOL for HMDB0000142 (Formic acid)

HMDB0000142
     RDKit          3D
Formic acid
  5  4  0  0  0  0  0  0  0  0999 V2000
   -0.9559    1.0159   -0.2031 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4389   -0.0656    0.1172 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9177   -0.1380    0.3190 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0350   -0.9402    0.2379 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5121    0.1280   -0.4710 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
  3  5  1  0
M  END
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3D SDF for HMDB0000142 (Formic acid)

  Mrv1652309032023542D          

  3  2  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 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 O   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
M  END
> <DATABASE_ID>
HMDB0000142

> <DATABASE_NAME>
hmdb

> <SMILES>
OC=O

> <INCHI_IDENTIFIER>
InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)

> <INCHI_KEY>
BDAGIHXWWSANSR-UHFFFAOYSA-N

> <FORMULA>
CH2O2

> <MOLECULAR_WEIGHT>
46.0254

> <EXACT_MASS>
46.005479308

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
3.374057914916533

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
formic acid

> <ALOGPS_LOGP>
-0.47

> <JCHEM_LOGP>
-0.2720444223333333

> <ALOGPS_LOGS>
1.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.2691179843154865

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
8.1532

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.77e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
formic acid

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0000142 (Formic acid)

HMDB0000142
     RDKit          3D
Formic acid
  5  4  0  0  0  0  0  0  0  0999 V2000
   -0.9559    1.0159   -0.2031 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4389   -0.0656    0.1172 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9177   -0.1380    0.3190 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0350   -0.9402    0.2379 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5121    0.1280   -0.4710 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
  3  5  1  0
M  END
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PDB for HMDB0000142 (Formic acid)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0       3.644  -2.104   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       4.977  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1                                                            
CONECT    3    1                                                            
MASTER        0    0    0    0    0    0    0    0    3    0    4    0
END
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3D PDB for HMDB0000142 (Formic acid)

COMPND    HMDB0000142
HETATM    1  O1  UNL     1      -0.956   1.016  -0.203  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.439  -0.066   0.117  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.918  -0.138   0.319  1.00  0.00           O  
HETATM    4  H1  UNL     1      -1.035  -0.940   0.238  1.00  0.00           H  
HETATM    5  H2  UNL     1       1.512   0.128  -0.471  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    5
END
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SMILES for HMDB0000142 (Formic acid)

OC=O
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INCHI for HMDB0000142 (Formic acid)

InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaCH2O2
Average Molecular Weight46.0254
Monoisotopic Molecular Weight46.005479308
IUPAC Nameformic acid
Traditional Nameformic acid
CAS Registry Number64-18-6
SMILES
OC=O
InChI Identifier
InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
InChI KeyBDAGIHXWWSANSR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carboxylic acids. Carboxylic acids are compounds containing a carboxylic acid group with the formula -C(=O)OH.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassCarboxylic acids
Direct ParentCarboxylic acids
Alternative Parents
Substituents
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point8.4 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mLNot Available
LogP-0.54HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
  • Nucleus
  • Endoplasmic reticulum
Biospecimen Locations
  • Blood
  • Breast Milk
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Sweat
  • Urine
Tissue Locations
  • Brain
  • Epidermis
  • Fibroblasts
  • Kidney
  • Liver
  • Neuron
  • Pancreas
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Methanol poisoning
  1. Sejersted OM, Jacobsen D, Ovrebo S, Jansen H: Formate concentrations in plasma from patients poisoned with methanol. Acta Med Scand. 1983;213(2):105-10. [PubMed:6837328 ]
  2. Baumann K, Angerer J: Occupational chronic exposure to organic solvents. VI. Formic acid concentration in blood and urine as an indicator of methanol exposure. Int Arch Occup Environ Health. 1979 Jan 15;42(3-4):241-9. [PubMed:422265 ]
Formic acid intoxication
  1. Moore DF, Bentley AM, Dawling S, Hoare AM, Henry JA: Folinic acid and enhanced renal elimination in formic acid intoxication. J Toxicol Clin Toxicol. 1994;32(2):199-204. [PubMed:8145360 ]
Chronic pancreatitis
  1. Zhang L, Jin H, Guo X, Yang Z, Zhao L, Tang S, Mo P, Wu K, Nie Y, Pan Y, Fan D: Distinguishing pancreatic cancer from chronic pancreatitis and healthy individuals by (1)H nuclear magnetic resonance-based metabonomic profiles. Clin Biochem. 2012 Sep;45(13-14):1064-9. doi: 10.1016/j.clinbiochem.2012.05.012. Epub 2012 May 19. [PubMed:22613268 ]
Early preeclampsia
  1. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: Metabolomics and first-trimester prediction of early-onset preeclampsia. J Matern Fetal Neonatal Med. 2012 Oct;25(10):1840-7. doi: 10.3109/14767058.2012.680254. Epub 2012 Apr 28. [PubMed:22494326 ]
Pregnancy
  1. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: Metabolomics and first-trimester prediction of early-onset preeclampsia. J Matern Fetal Neonatal Med. 2012 Oct;25(10):1840-7. doi: 10.3109/14767058.2012.680254. Epub 2012 Apr 28. [PubMed:22494326 ]
  2. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol. 2013 Jan;208(1):58.e1-7. doi: 10.1016/j.ajog.2012.11.003. Epub 2012 Nov 13. [PubMed:23159745 ]
  3. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: Metabolomic analysis for first-trimester Down syndrome prediction. Am J Obstet Gynecol. 2013 May;208(5):371.e1-8. doi: 10.1016/j.ajog.2012.12.035. Epub 2013 Jan 8. [PubMed:23313728 ]
  4. Bahado-Singh RO, Akolekar R, Chelliah A, Mandal R, Dong E, Kruger M, Wishart DS, Nicolaides K: Metabolomic analysis for first-trimester trisomy 18 detection. Am J Obstet Gynecol. 2013 Jul;209(1):65.e1-9. doi: 10.1016/j.ajog.2013.03.028. Epub 2013 Mar 25. [PubMed:23535240 ]
Late-onset preeclampsia
  1. Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol. 2013 Jan;208(1):58.e1-7. doi: 10.1016/j.ajog.2012.11.003. Epub 2012 Nov 13. [PubMed:23159745 ]
Irritable bowel syndrome
  1. Hong YS, Hong KS, Park MH, Ahn YT, Lee JH, Huh CS, Lee J, Kim IK, Hwang GS, Kim JS: Metabonomic understanding of probiotic effects in humans with irritable bowel syndrome. J Clin Gastroenterol. 2011 May-Jun;45(5):415-25. doi: 10.1097/MCG.0b013e318207f76c. [PubMed:21494186 ]
Diverticular disease
  1. Tursi A, Mastromarino P, Capobianco D, Elisei W, Miccheli A, Capuani G, Tomassini A, Campagna G, Picchio M, Giorgetti G, Fabiocchi F, Brandimarte G: Assessment of Fecal Microbiota and Fecal Metabolome in Symptomatic Uncomplicated Diverticular Disease of the Colon. J Clin Gastroenterol. 2016 Oct;50 Suppl 1:S9-S12. doi: 10.1097/MCG.0000000000000626. [PubMed:27622378 ]
Rheumatoid arthritis
  1. Tie-juan ShaoZhi-xing HeZhi-jun XieHai-chang LiMei-jiao WangCheng-ping Wen. Characterization of ankylosing spondylitis and rheumatoid arthritis using 1H NMR-based metabolomics of human fecal extracts. Metabolomics. April 2016, 12:70 [Link]
Methyl formate exposure
  1. Berode M, Sethre T, Laubli T, Savolainen H: Urinary methanol and formic acid as indicators of occupational exposure to methyl formate. Int Arch Occup Environ Health. 2000 Aug;73(6):410-4. [PubMed:11007345 ]
Lung Cancer
  1. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I: HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10. doi: 10.1093/nar/gkn810. Epub 2008 Oct 25. [PubMed:18953024 ]
Diabetes mellitus type 1
  1. (). Lorena Ivona ŞTEFAN, Alina NICOLESCU, Simona POPA, Maria MOŢA, Eugenia KOVACS and Calin DELEANU. 1H-NMR URINE METABOLIC PROFILING IN TYPE 1 DIABETES MELLITUS. Rev. Roum. Chim., 2010, 55(11-12), 1033-1037 . .
Autosomal dominant polycystic kidney disease
  1. Gronwald W, Klein MS, Zeltner R, Schulze BD, Reinhold SW, Deutschmann M, Immervoll AK, Boger CA, Banas B, Eckardt KU, Oefner PJ: Detection of autosomal dominant polycystic kidney disease by NMR spectroscopic fingerprinting of urine. Kidney Int. 2011 Jun;79(11):1244-53. doi: 10.1038/ki.2011.30. Epub 2011 Mar 9. [PubMed:21389975 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
  • 1678 (Chronic pancreatitis)
  • 180300 (Rheumatoid arthritis)
  • 211980 (Lung Cancer)
  • 222100 (Diabetes mellitus type 1)
  • 601313 (Autosomal dominant polycystic kidney disease)
  • 610247 (Eosinophilic esophagitis)
DrugBank IDDB01942
Phenol Explorer Compound IDNot Available
FooDB IDFDB012804
KNApSAcK IDC00001182
Chemspider IDNot Available
KEGG Compound IDC00058
BioCyc IDFORMATE
BiGG IDNot Available
Wikipedia LinkFormic_acid
METLIN IDNot Available
PubChem Compound284
PDB IDNot Available
ChEBI ID30751
Food Biomarker OntologyNot Available
VMH IDFOR
MarkerDB IDMDB00000068
Good Scents IDNot Available
References
Synthesis Reference Finholt, Albert E.; Jacobson, Eugene C. The reduction of carbon dioxide to formic acid with lithium aluminum hydride. Journal of the American Chemical Society (1952), 74 3943-4.
Material Safety Data Sheet (MSDS)Not Available
General References

Only showing the first 10 proteins. There are 35 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Lanosterol 14-alpha demethylase
General function:
Involved in monooxygenase activity
Specific function:
Catalyzes C14-demethylation of lanosterol; it transforms lanosterol into 4,4'-dimethyl cholesta-8,14,24-triene-3-beta-ol.
Gene Name:
CYP51A1
Uniprot ID:
Q16850
Molecular weight:
57277.81
Reactions
Obtusifoliol + Oxygen + NADPH → delta8,14-Sterol + Formic acid + NADP + Waterdetails
Lanosterol + Oxygen + NADPH + Hydrogen Ion → 4,4-Dimethylcholesta-8,14,24-trienol + Formic acid + NADP + Waterdetails
Obtusifoliol + Oxygen + NADPH + Hydrogen Ion → delta8,14-Sterol + Formic acid + NADP + Waterdetails
Enzyme Details
2. S-formylglutathione hydrolase
General function:
Involved in carboxylesterase activity
Specific function:
Serine hydrolase involved in the detoxification of formaldehyde.
Gene Name:
ESD
Uniprot ID:
P10768
Molecular weight:
31462.545
Reactions
S-Formylglutathione + Water → Glutathione + Formic aciddetails
Enzyme Details
3. Aspartoacylase
General function:
Involved in hydrolase activity, acting on ester bonds
Specific function:
Catalyzes the deacetylation of N-acetylaspartic acid (NAA) to produce acetate and L-aspartate. NAA occurs in high concentration in brain and its hydrolysis NAA plays a significant part in the maintenance of intact white matter. In other tissues it act as a scavenger of NAA from body fluids.
Gene Name:
ASPA
Uniprot ID:
P45381
Molecular weight:
35734.79
Reactions
N-Formyl-L-aspartate + Water → Formic acid + L-Aspartic aciddetails
Enzyme Details
4. Aspartoacylase-2
General function:
Involved in hydrolase activity, acting on ester bonds
Specific function:
Plays an important role in deacetylating mercapturic acids in kidney proximal tubules (By similarity).
Gene Name:
ACY3
Uniprot ID:
Q96HD9
Molecular weight:
Not Available
Reactions
N-Formyl-L-aspartate + Water → Formic acid + L-Aspartic aciddetails
Enzyme Details
5. C-1-tetrahydrofolate synthase, cytoplasmic
General function:
Involved in formate-tetrahydrofolate ligase activity
Specific function:
Not Available
Gene Name:
MTHFD1
Uniprot ID:
P11586
Molecular weight:
101530.36
Reactions
Adenosine triphosphate + Formic acid + Tetrahydrofolic acid → ADP + Phosphate + 10-Formyltetrahydrofolatedetails
Enzyme Details
6. GTP cyclohydrolase 1
General function:
Involved in GTP cyclohydrolase I activity
Specific function:
Positively regulates nitric oxide synthesis in umbilical vein endothelial cells (HUVECs). May be involved in dopamine synthesis. May modify pain sensitivity and persistence. Isoform GCH-1 is the functional enzyme, the potential function of the enzymatically inactive isoforms remains unknown.
Gene Name:
GCH1
Uniprot ID:
P30793
Molecular weight:
27902.855
Reactions
Guanosine triphosphate + Water → Formic acid + 2-amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)-dihydropteridine triphosphatedetails
Formamidopyrimidine nucleoside triphosphate + Water → 2,5-Diaminopyrimidine nucleoside triphosphate + Formic aciddetails
Enzyme Details
7. Cytochrome P450 3A4
General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:
CYP3A4
Uniprot ID:
P08684
Molecular weight:
57255.585
Enzyme Details
8. Cytochrome P450 2C9
General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.
Gene Name:
CYP2C9
Uniprot ID:
P11712
Molecular weight:
55627.365
Enzyme Details
9. Cytochrome P450 2C19
General function:
Involved in monooxygenase activity
Specific function:
Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.
Gene Name:
CYP2C19
Uniprot ID:
P33261
Molecular weight:
55944.565
Enzyme Details
10. Peptide deformylase, mitochondrial
General function:
Involved in iron ion binding
Specific function:
Removes the formyl group from the N-terminal Met of newly synthesized proteins (By similarity).
Gene Name:
PDF
Uniprot ID:
Q9HBH1
Molecular weight:
27013.25
Reactions
Formyl-L-methionyl peptide + Water → Formic acid + methionyl peptidedetails

Only showing the first 10 proteins. There are 35 proteins in total.

Show all enzymes and transporters