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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2)transporters (1) Show 3 proteins XML

enzymes (2)transporters (1) Show 3 proteins

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 09:13:06 UTC

Update Date

2021-10-01 21:23:36 UTC

HMDB ID

HMDB0251697

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Edaravone

Description

Edaravone, also known as radicut or c.i. developer 1, belongs to the class of organic compounds known as pyrazolones. Pyrazolones are compounds containing a pyrazole ring which bears a ketone. Based on a literature review a significant number of articles have been published on Edaravone. This compound has been identified in human blood as reported by (PMID: 31557052 ). Edaravone is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Edaravone 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                                 23-FEB-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 4021                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-15         0                                  
HETATM    1  O   UNK     0       8.503   0.912   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0       5.792   0.483   0.000  0.00  0.00           N+0
HETATM    3  N   UNK     0       4.546   1.388   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       6.562   2.852   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.022   2.852   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.038   1.388   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.792  -1.057   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.117   4.098   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.458  -1.827   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.126  -1.827   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.458  -3.367   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.126  -3.367   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.792  -4.137   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    3    6    7                                                  
CONECT    3    2    5                                                       
CONECT    4    5    6                                                       
CONECT    5    3    4    8                                                  
CONECT    6    1    2    4                                                  
CONECT    7    2    9   10                                                  
CONECT    8    5                                                            
CONECT    9    7   11                                                       
CONECT   10    7   12                                                       
CONECT   11    9   13                                                       
CONECT   12   10   13                                                       
CONECT   13   11   12                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1-Phenyl-3-methyl-5-oxo-2-pyrazoline	ChEBI
2,4-Dihydro-5-methyl-2-phenyl-3H-pyrazol-3-one	ChEBI
3-Methyl-1-phenyl-2-pyrazolin-5-one	ChEBI
3-Methyl-1-phenyl-5-pyrazolone	ChEBI
3-Methyl-1-phenylpyrazol-5-one	ChEBI
C.I. developer 1	ChEBI
Developer Z	ChEBI
Methylphenylpyrazolone	ChEBI
Norphenazone	ChEBI
Phenyl methyl pyrazolone	ChEBI
Phenylmethylpyrazolone	ChEBI
Radicut	ChEBI
Radicava	Kegg
1-Phenyl-3-methyl-5-pyrazolone	MeSH
MCI 186	MeSH
MCI-186	MeSH
Edarabone	MeSH
Norantipyrine	MeSH
1 Phenyl 3 methyl 5 pyrazolone	MeSH
3 Methyl 1 phenyl 2 pyrazolin 5 one	MeSH

Chemical Formula

C₁₀H₁₀N₂O

Average Molecular Weight

174.203

Monoisotopic Molecular Weight

174.07931295

IUPAC Name

3-methyl-1-phenyl-4,5-dihydro-1H-pyrazol-5-one

Traditional Name

edaravone

CAS Registry Number

Not Available

SMILES

CC1=NN(C(=O)C1)C1=CC=CC=C1

InChI Identifier

InChI=1S/C10H10N2O/c1-8-7-10(13)12(11-8)9-5-3-2-4-6-9/h2-6H,7H2,1H3

InChI Key

QELUYTUMUWHWMC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrazolones. Pyrazolones are compounds containing a pyrazole ring which bears a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azolines

Sub Class

Pyrazolines

Direct Parent

Pyrazolones

Alternative Parents

Substituents

Benzenoid
Pyrazolinone
Monocyclic benzene moiety
Azacycle
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

ring assembly (CHEBI:31530 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0251697)

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	0.53	ALOGPS
logP	1.53	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	13.45	ChemAxon
pKa (Strongest Basic)	-1.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	32.67 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	49.49 m³·mol⁻¹	ChemAxon
Polarizability	18.61 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	136.172	30932474
DeepCCS	[M-H]-	133.776	30932474
DeepCCS	[M-2H]-	168.611	30932474
DeepCCS	[M+Na]+	143.07	30932474
AllCCS	[M+H]+	138.2	32859911
AllCCS	[M+H-H2O]+	133.8	32859911
AllCCS	[M+NH4]+	142.3	32859911
AllCCS	[M+Na]+	143.5	32859911
AllCCS	[M-H]-	139.2	32859911
AllCCS	[M+Na-2H]-	139.7	32859911
AllCCS	[M+HCOO]-	140.4	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	13.6631 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.25 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2127.9 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	443.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	153.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	261.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	131.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	487.9 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	551.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	100.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1126.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	419.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1352.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	323.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	357.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	432.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	289.5 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	59.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Edaravone	CC1=NN(C(=O)C1)C1=CC=CC=C1	2395.3	Standard polar	33892256
Edaravone	CC1=NN(C(=O)C1)C1=CC=CC=C1	1747.2	Standard non polar	33892256
Edaravone	CC1=NN(C(=O)C1)C1=CC=CC=C1	1648.4	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 - Edaravone GC-MS (Non-derivatized) - 70eV, Positive	splash10-000x-7900000000-1b63674e9e61b0415592	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Edaravone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Edaravone LC-ESI-qTof , Positive-QTOF	splash10-004i-1900000000-9c17dd936441a10926dc	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Edaravone , positive-QTOF	splash10-004i-1900000000-9c17dd936441a10926dc	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 10V, Positive-QTOF	splash10-004i-0900000000-e9a7118da8dd61cf703d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 20V, Positive-QTOF	splash10-004i-1900000000-96343e3befaa9cf0a207	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 40V, Positive-QTOF	splash10-0006-9100000000-aeca339c7e738592814a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 10V, Negative-QTOF	splash10-00di-0900000000-f624c623e550dc22aaa3	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 20V, Negative-QTOF	splash10-00di-1900000000-2012f697925d920763a6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 40V, Negative-QTOF	splash10-0006-9100000000-d2d3b4076db8592d0461	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 10V, Positive-QTOF	splash10-004i-0900000000-99e013a33d61f5b2babb	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 20V, Positive-QTOF	splash10-004i-0900000000-f092173f0b19729a2e6d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 40V, Positive-QTOF	splash10-004i-9200000000-344f8ae11a95707342e4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 10V, Negative-QTOF	splash10-00di-0900000000-eb2d5882d0b284199cab	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 20V, Negative-QTOF	splash10-00di-0900000000-4d7edbfa19219b7402ad	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Edaravone 40V, Negative-QTOF	splash10-0axu-9700000000-576a3531c2b1f5164af3	2021-10-12	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

DB12243

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

3881

KEGG Compound ID

C13008

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Edaravone

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

31530

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1191581

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 ]

Enzymes

Enzyme Details

1. Solute carrier family 22 member 6

General function:: Not Available
Specific function:: Involved in the renal elimination of endogenous and exogenous organic anions. Functions as organic anion exchanger when the uptake of one molecule of organic anion is coupled with an efflux of one molecule of endogenous dicarboxylic acid (glutarate, ketoglutarate, etc). Mediates the sodium-independent uptake of cidofovir, adefovir, 9-(2-phosphonylmethoxyethyl) guanine (PMEG), 9-(2-phosphonylmethoxyethyl) diaminopurine (PMEDAP), ochratoxin (OTA), acyclovir (ACV), 3'-azido-3-'deoxythymidine (AZT), cimetidine (CMD), 2,4-dichloro-phenoxyacetate (2,4-D), hippurate (HA), indoleacetate (IA), indoxyl sulfate (IS), 3-carboxy-4-methyl-5-propyl-2-furanpropionate (CMPF) and edaravone sulfate (By similarity). Mediates the sodium-independent uptake of p-aminohippurate (PAH) and 2,3-dimercapto-1-propanesulfonic acid (DMPS). PAH uptake is inhibited by p-chloromercuribenzenesulphonate (PCMBS), diethyl pyrocarbonate (DEPC), indomethacin, sulindac, diclofenac, carprofen, okadaic acid, furosemide, steviol, phorbol 12-myristate 13-acetate (PMA), calcium ionophore A23187, benzylpenicillin, bumetamide, losartan, probenecid, phenol red and glutarate (By similarity). PAH uptake is inhibited by benzothiazolylcysteine (BTC), S-chlorotrifluoroethylcysteine (CTFC), cysteine S-conjugates S-dichlorovinylcysteine (DCVC), urate, alpha-ketoglutarate and probenecid.
Gene Name:: SLC22A6
Uniprot ID:: Q9TSY7
Molecular weight:: 60588.3

Enzyme Details

2. Solute carrier family 22 member 6

General function:: Not Available
Specific function:: Involved in the renal elimination of endogenous and exogenous organic anions. Functions as organic anion exchanger when the uptake of one molecule of organic anion is coupled with an efflux of one molecule of endogenous dicarboxylic acid (glutarate, ketoglutarate, etc). Mediates the sodium-independent uptake of 2,3-dimercapto-1-propanesulfonic acid (DMPS), 9-(2-phosphonylmethoxyethyl) guanine (PMEG), 9-(2-phosphonylmethoxyethyl) diaminopurine (PMEDAP), ochratoxin (OTA), acyclovir (ACV), 3'-azido-3-'deoxythymidine (AZT), cimetidine (CMD) and edaravone sulfate. Mediates the sodium-independent uptake of p-aminohippurate (PAH), cidofovir, adefovir, 2,4-dichloro-phenoxyacetate (2,4-D), hippurate (HA), indoleacetate (IA), indoxyl sulfate (IS) and 3-carboxy-4-methyl-5-propyl-2-furanpropionate (CMPF). PAH uptake is inhibited by p-chloromercuribenzenesulphonate (PCMBS), diethyl pyrocarbonate (DEPC), indomethacin, sulindac, diclofenac, carprofen, okadaic acid, benzothiazolylcysteine (BTC), S-chlorotrifluoroethylcysteine (CTFC), cysteine S-conjugates S-dichlorovinylcysteine (DCVC), furosemide, steviol, phorbol 12-myristate 13-acetate (PMA), calcium ionophore A23187, benzylpenicillin, bumetamide, losartan, phenol red, urate and alpha-ketoglutarate (By similarity). PAH uptake is inhibited by glutarate and probenecid.
Gene Name:: SLC22A6
Uniprot ID:: O35956
Molecular weight:: 60765.66

Transporters

Enzyme Details

1. Solute carrier family 22 member 6

General function:: Involved in ion transmembrane transporter activity
Specific function:: Involved in the renal elimination of endogenous and exogenous organic anions. Functions as organic anion exchanger when the uptake of one molecule of organic anion is coupled with an efflux of one molecule of endogenous dicarboxylic acid (glutarate, ketoglutarate, etc). Mediates the sodium-independent uptake of 2,3-dimercapto-1-propanesulfonic acid (DMPS). Mediates the sodium-independent uptake of p- aminohippurate (PAH), ochratoxin (OTA), acyclovir (ACV), 3'-azido- 3-'deoxythymidine (AZT), cimetidine (CMD), 2,4-dichloro- phenoxyacetate (2,4-D), hippurate (HA), indoleacetate (IA), indoxyl sulfate (IS) and 3-carboxy-4-methyl-5-propyl-2- furanpropionate (CMPF), cidofovir, adefovir, 9-(2- phosphonylmethoxyethyl) guanine (PMEG), 9-(2- phosphonylmethoxyethyl) diaminopurine (PMEDAP) and edaravone sulfate. PAH uptake is inhibited by p- chloromercuribenzenesulphonate (PCMBS), diethyl pyrocarbonate (DEPC), sulindac, diclofenac, carprofen, glutarate and okadaic acid. PAH uptake is inhibited by benzothiazolylcysteine (BTC), S-chlorotrifluoroethylcysteine (CTFC), cysteine S-conjugates S-dichlorovinylcysteine (DCVC), furosemide, steviol, phorbol 12-myristate 13-acetate (PMA), calcium ionophore A23187, benzylpenicillin, furosemide, indomethacin, bumetamide, losartan, probenecid, phenol red, urate, and alpha-ketoglutarate
Gene Name:: SLC22A6
Uniprot ID:: Q4U2R8
Molecular weight:: 61815.8

Showing metabocard for Edaravone (HMDB0251697)

MOL for HMDB0251697 (Edaravone)

3D MOL for HMDB0251697 (Edaravone)

3D SDF for HMDB0251697 (Edaravone)

3D-SDF for HMDB0251697 (Edaravone)

PDB for HMDB0251697 (Edaravone)

3D PDB for HMDB0251697 (Edaravone)

SMILES for HMDB0251697 (Edaravone)

INCHI for HMDB0251697 (Edaravone)

Structure for HMDB0251697 (Edaravone)

3D Structure for HMDB0251697 (Edaravone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

Transporters