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Showing metabocard for Allantoin (HMDB0000462)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-05-30 20:55:56 UTC
HMDB IDHMDB0000462
Secondary Accession Numbers
  • HMDB00462
Metabolite Identification
Common NameAllantoin
DescriptionAllantoin is a diureide of glyoxylic acid with the chemical formula C4H6N4O3. It is also called 5-ureidohydantoin or glyoxyldiureide. It is a product of the oxidation of uric acid. It is also a product of purine metabolism in most mammals except for higher apes, and it is present in their urine. In humans, uric acid is excreted instead of allantoin. The presence of allantoin in the urine can be an indication of microbial overgrowth or it can be created via non-enzymatic means through high levels of reactive oxygen species. In this regard, allantoin is sometimes used as a marker of oxidative stress. Allantoin can be isolated from cow urine or as a botanical extract of the comfrey plant. It has long been used for its healing, soothing, and anti-irritating properties. Allantoin helps to heal wounds and skin irritations and stimulates the growth of healthy tissue. Allantoin can be found in anti-acne products, sun care products, and clarifying lotions because of its ability to help heal minor wounds and promote healthy skin. Allantoin is frequently present in toothpaste, mouthwash, and other oral hygiene products as well as in shampoos, lipsticks, various cosmetic lotions and creams, and other cosmetic and pharmaceutical products. It is also a metabolite of Bacillus (PMID: 18302748 ) and Streptomyces (PMID: 24292080 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000462 (Allantoin)

  Mrv1652307292023482D          

 11 11  0  0  0  0            999 V2000
   -2.1348   -0.2887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3143   -0.2025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9018    0.5120    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7623   -0.8156    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0086   -0.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7059   -0.8925    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4203   -0.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1348   -0.8925    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4203    0.3450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0948    0.3405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5182    0.8925    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  5 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
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3D MOL for HMDB0000462 (Allantoin)

HMDB0243717
     RDKit          3D
(S)-(+)-Allantoin
 17 17  0  0  0  0  0  0  0  0999 V2000
   -3.3434    0.1633   -0.0468 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0870   -0.4830   -0.1970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1015   -1.6745   -0.5935 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8810    0.2106    0.0953 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4237   -0.3822   -0.0347 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1717    0.3983   -0.9998 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5209    0.4163   -0.5511 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5316    0.7551   -1.2097 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5790   -0.0222    0.8119 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2355   -0.3060    1.1781 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8667   -0.4564    2.3698 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2002   -0.1772   -0.5076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3917    1.0124    0.5534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9159    1.2026    0.4229 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2634   -1.4320   -0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8751    0.8857   -1.8727 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4531   -0.1106    1.4085 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10  5  1  0
  1 12  1  0
  1 13  1  0
  4 14  1  0
  5 15  1  0
  6 16  1  0
  9 17  1  0
M  END
Download

3D SDF for HMDB0000462 (Allantoin)

  Mrv1652307292023482D          

 11 11  0  0  0  0            999 V2000
   -2.1348   -0.2887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3143   -0.2025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9018    0.5120    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7623   -0.8156    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0086   -0.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7059   -0.8925    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4203   -0.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1348   -0.8925    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4203    0.3450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0948    0.3405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5182    0.8925    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  5 10  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000462

> <DATABASE_NAME>
hmdb

> <SMILES>
NC(=O)NC1NC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H6N4O3/c5-3(10)6-1-2(9)8-4(11)7-1/h1H,(H3,5,6,10)(H2,7,8,9,11)

> <INCHI_KEY>
POJWUDADGALRAB-UHFFFAOYSA-N

> <FORMULA>
C4H6N4O3

> <MOLECULAR_WEIGHT>
158.1154

> <EXACT_MASS>
158.043990078

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.894797417541849

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2,5-dioxoimidazolidin-4-yl)urea

> <ALOGPS_LOGP>
-1.95

> <JCHEM_LOGP>
-2.360540882

> <ALOGPS_LOGS>
-1.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.41419987137925

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.948848806915678

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3762243606061957

> <JCHEM_POLAR_SURFACE_AREA>
113.32

> <JCHEM_REFRACTIVITY>
32.0225

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.73e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
allantoin

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000462 (Allantoin)

HMDB0243717
     RDKit          3D
(S)-(+)-Allantoin
 17 17  0  0  0  0  0  0  0  0999 V2000
   -3.3434    0.1633   -0.0468 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0870   -0.4830   -0.1970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1015   -1.6745   -0.5935 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8810    0.2106    0.0953 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4237   -0.3822   -0.0347 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1717    0.3983   -0.9998 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5209    0.4163   -0.5511 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5316    0.7551   -1.2097 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5790   -0.0222    0.8119 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2355   -0.3060    1.1781 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8667   -0.4564    2.3698 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2002   -0.1772   -0.5076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3917    1.0124    0.5534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9159    1.2026    0.4229 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2634   -1.4320   -0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8751    0.8857   -1.8727 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4531   -0.1106    1.4085 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10  5  1  0
  1 12  1  0
  1 13  1  0
  4 14  1  0
  5 15  1  0
  6 16  1  0
  9 17  1  0
M  END
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PDB for HMDB0000462 (Allantoin)

HEADER    PROTEIN                                 29-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUL-20         0                                  
HETATM    1  O   UNK     0      -3.985  -0.539   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.453  -0.378   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -1.683   0.956   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      -1.423  -1.522   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -0.016  -0.896   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.318  -1.666   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       2.651  -0.896   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       3.985  -1.666   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0       2.651   0.644   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.177   0.636   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.967   1.666   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2   10                                                       
CONECT    4    2    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    5    3   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for HMDB0000462 (Allantoin)

COMPND    HMDB0000462
HETATM    1  N1  UNL     1       3.091  -0.068   0.934  1.00  0.00           N  
HETATM    2  C1  UNL     1       1.747   0.258   1.218  1.00  0.00           C  
HETATM    3  O1  UNL     1       1.430   0.840   2.277  1.00  0.00           O  
HETATM    4  N2  UNL     1       0.745  -0.079   0.289  1.00  0.00           N  
HETATM    5  C2  UNL     1      -0.662   0.208   0.479  1.00  0.00           C  
HETATM    6  N3  UNL     1      -1.481  -0.952   0.342  1.00  0.00           N  
HETATM    7  C3  UNL     1      -2.009  -0.958  -0.976  1.00  0.00           C  
HETATM    8  O2  UNL     1      -2.553  -1.934  -1.560  1.00  0.00           O  
HETATM    9  N4  UNL     1      -1.819   0.349  -1.542  1.00  0.00           N  
HETATM   10  C4  UNL     1      -1.174   1.134  -0.551  1.00  0.00           C  
HETATM   11  O3  UNL     1      -1.053   2.402  -0.542  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.522  -0.984   1.190  1.00  0.00           H  
HETATM   13  H2  UNL     1       3.745   0.602   0.441  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.007  -0.562  -0.589  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.780   0.727   1.467  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.664  -1.667   1.066  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.093   0.685  -2.495  1.00  0.00           H  
CONECT    1    2   12   13
CONECT    2    3    3    4
CONECT    4    5   14
CONECT    5    6   10   15
CONECT    6    7   16
CONECT    7    8    8    9
CONECT    9   10   17
CONECT   10   11   11
END
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SMILES for HMDB0000462 (Allantoin)

NC(=O)NC1NC(=O)NC1=O
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INCHI for HMDB0000462 (Allantoin)

InChI=1S/C4H6N4O3/c5-3(10)6-1-2(9)8-4(11)7-1/h1H,(H3,5,6,10)(H2,7,8,9,11)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC4H6N4O3
Average Molecular Weight158.1154
Monoisotopic Molecular Weight158.043990078
IUPAC Name(2,5-dioxoimidazolidin-4-yl)urea
Traditional Nameallantoin
CAS Registry Number97-59-6
SMILES
NC(=O)NC1NC(=O)NC1=O
InChI Identifier
InChI=1S/C4H6N4O3/c5-3(10)6-1-2(9)8-4(11)7-1/h1H,(H3,5,6,10)(H2,7,8,9,11)
InChI KeyPOJWUDADGALRAB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as imidazoles. Imidazoles are compounds containing an imidazole ring, which is an aromatic five-member ring with two nitrogen atoms at positions 1 and 3, and three carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzoles
Sub ClassImidazoles
Direct ParentImidazoles
Alternative Parents
Substituents
  • Imidazole
  • Isourea
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidamide
  • Carboximidic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point239 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility5.26 mg/mLNot Available
LogP-1.523 (est)The Good Scents Company Information System
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Astarita_neg127.730932474
[M-H]-Baker128.38630932474
[M-H]-Not Available126.8http://allccs.zhulab.cn/database/detail?ID=AllCCS00001789
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Chronic renal failure
  1. Kand'ar R, Zakova P: Allantoin as a marker of oxidative stress in human erythrocytes. Clin Chem Lab Med. 2008;46(9):1270-4. doi: 10.1515/CCLM.2008.244. [PubMed:18636793 ]
Schizophrenia
  1. Xuan J, Pan G, Qiu Y, Yang L, Su M, Liu Y, Chen J, Feng G, Fang Y, Jia W, Xing Q, He L: Metabolomic profiling to identify potential serum biomarkers for schizophrenia and risperidone action. J Proteome Res. 2011 Dec 2;10(12):5433-43. doi: 10.1021/pr2006796. Epub 2011 Nov 8. [PubMed:22007635 ]
Meningitis
  1. Kastenbauer S, Koedel U, Becker BF, Pfister HW: Oxidative stress in bacterial meningitis in humans. Neurology. 2002 Jan 22;58(2):186-91. [PubMed:11805243 ]
Crohn's disease
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Ulcerative colitis
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Colorectal cancer
  1. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
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
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB001613
KNApSAcK IDC00007468
Chemspider ID199
KEGG Compound IDC01551
BioCyc IDALLANTOIN
BiGG IDNot Available
Wikipedia LinkAllantoin
METLIN ID89
PubChem Compound204
PDB IDNot Available
ChEBI ID15676
Food Biomarker OntologyNot Available
VMH IDALLTN
MarkerDB IDMDB00000166
Good Scents IDrw1068121
References
Synthesis ReferenceDu, Niansheng; Yang, Jianhua; Rena, Kasimu. Method for isolation of allantoin from Cistanche deserticola. Faming Zhuanli Shenqing Gongkai Shuomingshu (2006), 5pp.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Putative 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase
General function:
Not Available
Specific function:
Catalyzes the stereoselective decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) to (S)-allantoin (Potential).
Gene Name:
PRHOXNB
Uniprot ID:
A6NGE7
Molecular weight:
19129.52
Reactions
2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline → Allantoin + CO(2)details