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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 02:01:54 UTC

Update Date

2021-09-26 22:58:58 UTC

HMDB ID

HMDB0248602

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Arkofix

Description

Arkofix, also known as DMDHEU, belongs to the class of organic compounds known as imidazolidinones. These are organic compounds containing an imidazolidinone moiety, which is an imidazolidine ring bearing a ketone. Based on a literature review very few articles have been published on Arkofix. This compound has been identified in human blood as reported by (PMID: 31557052 ). Arkofix is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Arkofix 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

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       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.060   2.080   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.290  -0.290   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.011  -2.943   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
CONECT    1    2   12                                                       
CONECT    2    1    3    6                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    2    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8                                                            
CONECT   10    4                                                            
CONECT   11    3                                                            
CONECT   12    1                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
DMDHEU	MeSH
Dimethylol dihydroxyethyleneurea	MeSH
Dimethyloldihydroxyethyleneurea	MeSH

Chemical Formula

C₅H₁₀N₂O₅

Average Molecular Weight

178.144

Monoisotopic Molecular Weight

178.05897143

IUPAC Name

4,5-dihydroxy-1,3-bis(hydroxymethyl)imidazolidin-2-one

Traditional Name

4,5-dihydroxy-1,3-bis(hydroxymethyl)imidazolidin-2-one

CAS Registry Number

Not Available

SMILES

OCN1C(O)C(O)N(CO)C1=O

InChI Identifier

InChI=1S/C5H10N2O5/c8-1-6-3(10)4(11)7(2-9)5(6)12/h3-4,8-11H,1-2H2

InChI Key

ZEYUSQVGRCPBPG-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as imidazolidinones. These are organic compounds containing an imidazolidinone moiety, which is an imidazolidine ring bearing a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azolidines

Sub Class

Imidazolidines

Direct Parent

Imidazolidinones

Alternative Parents

Substituents

Imidazolidinone
Urea
Carbonic acid derivative
Azacycle
Alkanolamine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.4	ALOGPS
logP	-2.5	ChemAxon
logS	0.45	ALOGPS
pKa (Strongest Acidic)	11.75	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	104.47 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	35.02 m³·mol⁻¹	ChemAxon
Polarizability	15.65 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	130.456	30932474
DeepCCS	[M-H]-	126.826	30932474
DeepCCS	[M-2H]-	164.149	30932474
DeepCCS	[M+Na]+	139.436	30932474
AllCCS	[M+H]+	138.4	32859911
AllCCS	[M+H-H2O]+	134.3	32859911
AllCCS	[M+NH4]+	142.2	32859911
AllCCS	[M+Na]+	143.3	32859911
AllCCS	[M-H]-	131.7	32859911
AllCCS	[M+Na-2H]-	132.9	32859911
AllCCS	[M+HCOO]-	134.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Arkofix	OCN1C(O)C(O)N(CO)C1=O	3191.8	Standard polar	33892256
Arkofix	OCN1C(O)C(O)N(CO)C1=O	2203.8	Standard non polar	33892256
Arkofix	OCN1C(O)C(O)N(CO)C1=O	1878.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (Non-derivatized) - 70eV, Positive	splash10-001j-9700000000-1f2ac529ac363b6efb4f	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TMS_4_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TBDMS_3_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Arkofix GC-MS (TBDMS_4_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arkofix 10V, Positive-QTOF	splash10-004i-0900000000-09a38c30254dc171f658	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arkofix 20V, Positive-QTOF	splash10-0002-2900000000-63ee4fd7b1d8e3fd3b51	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arkofix 40V, Positive-QTOF	splash10-0aba-9000000000-210852ea61cc966c8a76	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arkofix 10V, Negative-QTOF	splash10-004i-1900000000-6e419989f78f38db5533	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arkofix 20V, Negative-QTOF	splash10-0006-9400000000-ffe9123a7b61d87790db	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Arkofix 40V, Negative-QTOF	splash10-0006-9000000000-83e509a330d1cd3ae0cf	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

15045

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15824

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for Arkofix (HMDB0248602)

MOL for HMDB0248602 (Arkofix)

3D MOL for HMDB0248602 (Arkofix)

3D SDF for HMDB0248602 (Arkofix)

3D-SDF for HMDB0248602 (Arkofix)

PDB for HMDB0248602 (Arkofix)

3D PDB for HMDB0248602 (Arkofix)

SMILES for HMDB0248602 (Arkofix)

INCHI for HMDB0248602 (Arkofix)

Structure for HMDB0248602 (Arkofix)

3D Structure for HMDB0248602 (Arkofix)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra