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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-07-09 16:10:00 UTC

Update Date

2023-02-21 17:30:17 UTC

HMDB ID

HMDB0060967

Secondary Accession Numbers

HMDB60967

Metabolite Identification

Common Name

S-nirvanol

Description

S-nirvanol is a metabolite of mephenytoin. Mephenytoin (marketed as Mesantoin by Novartis) is a hydantoin, used as an anticonvulsant. It was introduced approximately 10 years after phenytoin, in the late 1940s. The significant metabolite of mephenytoin is nirvanol (5-ethyl-5-phenylhydantoin), which was the first hydantoin (briefly used as a hypnotic). However, nirvanol is quite toxic and mephenytoin was only considered after other less toxic anticonvulsants had failed. It can cause potentially fatal blood dyscrasia in 1% of patients. (Wikipedia )

Structure

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

  Mrv0541 07091309092D          

 15 16  0  0  0  0            999 V2000
    4.1889    2.2349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3819    2.4065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1738    3.6327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9188    2.8480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9807    3.8042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4709    2.2349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5328    3.1911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2778    2.4065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4973    1.3085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4174    0.5238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8299    1.7934    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2424    0.5238    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1624    1.3085    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2819    1.5634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9324   -0.1436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  6  2  0  0  0  0
  8  7  1  0  0  0  0
 11  2  1  6  0  0  0
 11  8  1  1  0  0  0
 11  9  1  0  0  0  0
 12  9  2  0  0  0  0
 12 10  1  0  0  0  0
 13 10  2  0  0  0  0
 13 11  1  0  0  0  0
 14  9  1  0  0  0  0
 15 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060967

> <DATABASE_NAME>
hmdb

> <SMILES>
CC[C@]1(N=C(O)N=C1O)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C11H12N2O2/c1-2-11(8-6-4-3-5-7-8)9(14)12-10(15)13-11/h3-7H,2H2,1H3,(H2,12,13,14,15)/t11-/m0/s1

> <INCHI_KEY>
UDTWZFJEMMUFLC-NSHDSACASA-N

> <FORMULA>
C11H12N2O2

> <MOLECULAR_WEIGHT>
204.2252

> <EXACT_MASS>
204.089877638

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
20.90467583575281

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4S)-4-ethyl-4-phenyl-4H-imidazole-2,5-diol

> <ALOGPS_LOGP>
1.30

> <JCHEM_LOGP>
2.6949021496666656

> <ALOGPS_LOGS>
-2.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.801612685169788

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.489484647743836

> <JCHEM_PKA_STRONGEST_BASIC>
-0.2241287430422253

> <JCHEM_POLAR_SURFACE_AREA>
65.18

> <JCHEM_REFRACTIVITY>
55.6847

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.71e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S)-5-ethyl-5-phenylimidazole-2,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-JUL-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JUL-13         0                                  
HETATM    1  C   UNK     0       7.819   4.172   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.313   4.492   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.191   6.781   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.715   5.316   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.697   7.101   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.746   4.172   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.728   5.957   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.252   4.492   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.528   2.443   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.512   0.978   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.282   3.348   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       6.052   0.978   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       4.036   2.443   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       7.993   2.918   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       3.607  -0.268   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1   11                                                       
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    8                                                       
CONECT    7    5    8                                                       
CONECT    8    6    7   11                                                  
CONECT    9   11   12   14                                                  
CONECT   10   12   13   15                                                  
CONECT   11    2    8    9   13                                             
CONECT   12    9   10                                                       
CONECT   13   10   11                                                       
CONECT   14    9                                                            
CONECT   15   10                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

COMPND    HMDB0060967
HETATM    1  C1  UNL     1      -0.294   1.560   1.874  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.878   1.620   0.478  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.839   0.228  -0.150  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.563  -0.216  -0.209  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.039  -1.087   0.739  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.350  -1.540   0.734  1.00  0.00           C  
HETATM    7  C7  UNL     1       3.215  -1.118  -0.239  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.752  -0.246  -1.195  1.00  0.00           C  
HETATM    9  C9  UNL     1       1.426   0.207  -1.184  1.00  0.00           C  
HETATM   10  N1  UNL     1      -1.653  -0.601   0.690  1.00  0.00           N  
HETATM   11  C10 UNL     1      -2.639  -1.042   0.010  1.00  0.00           C  
HETATM   12  O1  UNL     1      -3.678  -1.896   0.465  1.00  0.00           O  
HETATM   13  N2  UNL     1      -2.552  -0.543  -1.317  1.00  0.00           N  
HETATM   14  C11 UNL     1      -1.516   0.201  -1.447  1.00  0.00           C  
HETATM   15  O2  UNL     1      -1.173   0.832  -2.649  1.00  0.00           O  
HETATM   16  H1  UNL     1      -0.755   2.372   2.499  1.00  0.00           H  
HETATM   17  H2  UNL     1       0.815   1.667   1.875  1.00  0.00           H  
HETATM   18  H3  UNL     1      -0.523   0.601   2.381  1.00  0.00           H  
HETATM   19  H4  UNL     1      -0.265   2.270  -0.161  1.00  0.00           H  
HETATM   20  H5  UNL     1      -1.907   2.022   0.514  1.00  0.00           H  
HETATM   21  H6  UNL     1       0.396  -1.441   1.519  1.00  0.00           H  
HETATM   22  H7  UNL     1       2.726  -2.226   1.481  1.00  0.00           H  
HETATM   23  H8  UNL     1       4.254  -1.481  -0.238  1.00  0.00           H  
HETATM   24  H9  UNL     1       3.437   0.084  -1.961  1.00  0.00           H  
HETATM   25  H10 UNL     1       1.111   0.893  -1.959  1.00  0.00           H  
HETATM   26  H11 UNL     1      -4.443  -1.401   0.939  1.00  0.00           H  
HETATM   27  H12 UNL     1      -0.971   0.279  -3.489  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3   19   20
CONECT    3    4   10   14
CONECT    4    5    5    9
CONECT    5    6   21
CONECT    6    7    7   22
CONECT    7    8   23
CONECT    8    9    9   24
CONECT    9   25
CONECT   10   11   11
CONECT   11   12   13
CONECT   12   26
CONECT   13   14   14
CONECT   14   15
CONECT   15   27
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₁H₁₂N₂O₂

Average Molecular Weight

204.2252

Monoisotopic Molecular Weight

204.089877638

IUPAC Name

(4S)-4-ethyl-4-phenyl-4H-imidazole-2,5-diol

Traditional Name

(5S)-5-ethyl-5-phenylimidazole-2,4-diol

CAS Registry Number

Not Available

SMILES

CC[C@]1(N=C(O)N=C1O)C1=CC=CC=C1

InChI Identifier

InChI=1S/C11H12N2O2/c1-2-11(8-6-4-3-5-7-8)9(14)12-10(15)13-11/h3-7H,2H2,1H3,(H2,12,13,14,15)/t11-/m0/s1

InChI Key

UDTWZFJEMMUFLC-NSHDSACASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylhydantoins. These are heterocyclic aromatic compounds containing an imiazolidinedione moiety substituted by a phenyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azolidines

Sub Class

Imidazolidines

Direct Parent

Phenylhydantoins

Alternative Parents

Substituents

5-phenylhydantoin
Phenylimidazolidine
Alpha-amino acid or derivatives
5-monosubstituted hydantoin
N-acyl urea
Ureide
Monocyclic benzene moiety
Benzenoid
Dicarboximide
Urea
Carbonic acid derivative
Carboxylic acid derivative
Azacycle
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060967)

Organ

Kidney (HMDB: HMDB0060967)
Liver (HMDB: HMDB0060967)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060967)

Cellular substructure

Cytoplasm (HMDB: HMDB0060967)
Membrane (HMDB: HMDB0060967)

Source

Endogenous

Endogenous (HMDB: HMDB0060967)

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
Water Solubility	0.27 g/L	ALOGPS
logP	1.3	ALOGPS
logP	2.69	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	4.49	ChemAxon
pKa (Strongest Basic)	-0.22	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	65.18 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.68 m³·mol⁻¹	ChemAxon
Polarizability	20.9 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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
DarkChem	[M+H]+	147.599	31661259
DarkChem	[M-H]-	144.855	31661259
DeepCCS	[M+H]+	145.576	30932474
DeepCCS	[M-H]-	143.181	30932474
DeepCCS	[M-2H]-	176.371	30932474
DeepCCS	[M+Na]+	151.489	30932474
AllCCS	[M+H]+	144.9	32859911
AllCCS	[M+H-H2O]+	140.6	32859911
AllCCS	[M+NH4]+	148.9	32859911
AllCCS	[M+Na]+	150.1	32859911
AllCCS	[M-H]-	146.6	32859911
AllCCS	[M+Na-2H]-	146.8	32859911
AllCCS	[M+HCOO]-	147.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
S-nirvanol	CC[C@]1(N=C(O)N=C1O)C1=CC=CC=C1	2892.7	Standard polar	33892256
S-nirvanol	CC[C@]1(N=C(O)N=C1O)C1=CC=CC=C1	1706.6	Standard non polar	33892256
S-nirvanol	CC[C@]1(N=C(O)N=C1O)C1=CC=CC=C1	1784.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
S-nirvanol,1TMS,isomer #1	CC[C@@]1(C2=CC=CC=C2)N=C(O[Si](C)(C)C)N=C1O	1838.0	Semi standard non polar	33892256
S-nirvanol,1TMS,isomer #2	CC[C@@]1(C2=CC=CC=C2)N=C(O)N=C1O[Si](C)(C)C	1844.8	Semi standard non polar	33892256
S-nirvanol,2TMS,isomer #1	CC[C@@]1(C2=CC=CC=C2)N=C(O[Si](C)(C)C)N=C1O[Si](C)(C)C	1868.0	Semi standard non polar	33892256
S-nirvanol,1TBDMS,isomer #1	CC[C@@]1(C2=CC=CC=C2)N=C(O[Si](C)(C)C(C)(C)C)N=C1O	2052.9	Semi standard non polar	33892256
S-nirvanol,1TBDMS,isomer #2	CC[C@@]1(C2=CC=CC=C2)N=C(O)N=C1O[Si](C)(C)C(C)(C)C	2046.4	Semi standard non polar	33892256
S-nirvanol,2TBDMS,isomer #1	CC[C@@]1(C2=CC=CC=C2)N=C(O[Si](C)(C)C(C)(C)C)N=C1O[Si](C)(C)C(C)(C)C	2221.9	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 - S-nirvanol GC-MS (Non-derivatized) - 70eV, Positive	splash10-003r-1900000000-73f9322c3f866afbddf2	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - S-nirvanol GC-MS (2 TMS) - 70eV, Positive	splash10-00si-7359000000-6dc0fe36504bf8bbaf39	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - S-nirvanol 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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 10V, Positive-QTOF	splash10-0a59-0790000000-a2a6ae44e2dbe82664af	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 20V, Positive-QTOF	splash10-001i-0900000000-815bac46b1859ce007ac	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 40V, Positive-QTOF	splash10-0uyi-6900000000-aa312761b55adcbd9c37	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 10V, Negative-QTOF	splash10-0udi-1390000000-8e73560b69c65c506d00	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 20V, Negative-QTOF	splash10-0w2c-6970000000-bcc16e733ca436e0fb0c	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 40V, Negative-QTOF	splash10-0f7o-9700000000-1961c2b34749594805c3	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 10V, Positive-QTOF	splash10-0a4i-0290000000-06f54373db5814a8969e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 20V, Positive-QTOF	splash10-067i-1920000000-71f36919fd604632c51e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 40V, Positive-QTOF	splash10-016r-7900000000-69e57df52ad7452f485c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 10V, Negative-QTOF	splash10-0udi-3190000000-26350db44a1504e6421e	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 20V, Negative-QTOF	splash10-0006-9300000000-3bd0854e0e599136828b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-nirvanol 40V, Negative-QTOF	splash10-0006-9100000000-93968538a87d194aec33	2021-09-23	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Nirvanol

METLIN ID

Not Available

PubChem Compound

6540813

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

Not Available

Showing metabocard for S-nirvanol (HMDB0060967)

MOL for HMDB0060967 (S-nirvanol)

3D MOL for HMDB0060967 (S-nirvanol)

3D SDF for HMDB0060967 (S-nirvanol)

3D-SDF for HMDB0060967 (S-nirvanol)

PDB for HMDB0060967 (S-nirvanol)

3D PDB for HMDB0060967 (S-nirvanol)

SMILES for HMDB0060967 (S-nirvanol)

INCHI for HMDB0060967 (S-nirvanol)

Structure for HMDB0060967 (S-nirvanol)

3D Structure for HMDB0060967 (S-nirvanol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra