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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 19:53:17 UTC

Update Date

2021-09-26 23:15:14 UTC

HMDB ID

HMDB0258388

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Sorbinil

Description

Sorbinil belongs to the class of organic compounds known as hydantoins. These are heterocyclic compounds containing an imidazolidine substituted by ketone group at positions 2 and 4. Based on a literature review a significant number of articles have been published on Sorbinil. This compound has been identified in human blood as reported by (PMID: 31557052 ). Sorbinil is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Sorbinil 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

  Mrv1652309112121532D          

 17 19  0  0  0  0            999 V2000
   -0.9969   -1.3447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3946   -1.9084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3948   -1.6686    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5819   -0.8651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0205   -0.3014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8099   -0.5412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6200   -0.6971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9700   -1.4442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0186    0.0252    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4549    0.6275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6108    1.4377    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7078    0.2775    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1666    0.5021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9560    0.7419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5583    0.1782    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3713   -0.6253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1430    1.5454    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  6 12  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
  4 16  1  0  0  0  0
 14 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0258388

> <DATABASE_NAME>
hmdb

> <SMILES>
FC1=CC2=C(OCCC22NC(=O)NC2=O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C11H9FN2O3/c12-6-1-2-8-7(5-6)11(3-4-17-8)9(15)13-10(16)14-11/h1-2,5H,3-4H2,(H2,13,14,15,16)

> <INCHI_KEY>
LXANPKRCLVQAOG-UHFFFAOYSA-N

> <FORMULA>
C11H9FN2O3

> <MOLECULAR_WEIGHT>
236.202

> <EXACT_MASS>
236.059720321

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
20.84544542218064

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-fluoro-2,3-dihydrospiro[1-benzopyran-4,4'-imidazolidine]-2',5'-dione

> <ALOGPS_LOGP>
0.59

> <JCHEM_LOGP>
0.43563233500000015

> <ALOGPS_LOGS>
-1.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.51679357073898

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.672495156369035

> <JCHEM_PKA_STRONGEST_BASIC>
-4.853497835597696

> <JCHEM_POLAR_SURFACE_AREA>
67.42999999999999

> <JCHEM_REFRACTIVITY>
54.94470000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.63e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
sorbinil

> <JCHEM_VEBER_RULE>
0

$$$$

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      -1.861  -2.510   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.736  -3.562   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.737  -3.115   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.086  -1.615   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.038  -0.563   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.512  -1.010   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.024  -1.301   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -3.677  -2.696   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      -3.768   0.047   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -2.716   1.171   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.007   2.684   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0      -1.321   0.518   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       0.311   0.937   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.784   1.385   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.909   0.333   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.560  -1.167   0.000  0.00  0.00           C+0
HETATM   17  F   UNK     0       2.134   2.885   0.000  0.00  0.00           F+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   16                                                  
CONECT    5    4    6   13                                                  
CONECT    6    5    1    7   12                                             
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    6                                                       
CONECT   13    5   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15    4                                                       
CONECT   17   14                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

COMPND    HMDB0258388
HETATM    1  O1  UNL     1       3.484  -2.305  -0.961  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.618  -1.559  -0.402  1.00  0.00           C  
HETATM    3  N1  UNL     1       2.897  -0.573   0.585  1.00  0.00           N  
HETATM    4  C2  UNL     1       1.645   0.007   0.919  1.00  0.00           C  
HETATM    5  O2  UNL     1       1.410   0.620   1.997  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.735  -0.258  -0.223  1.00  0.00           C  
HETATM    7  C4  UNL     1       0.978   0.811  -1.261  1.00  0.00           C  
HETATM    8  C5  UNL     1       0.663   2.158  -0.696  1.00  0.00           C  
HETATM    9  O3  UNL     1      -0.497   2.160   0.124  1.00  0.00           O  
HETATM   10  C6  UNL     1      -1.263   1.012   0.314  1.00  0.00           C  
HETATM   11  C7  UNL     1      -2.609   1.080   0.669  1.00  0.00           C  
HETATM   12  C8  UNL     1      -3.362  -0.063   0.856  1.00  0.00           C  
HETATM   13  C9  UNL     1      -2.773  -1.304   0.690  1.00  0.00           C  
HETATM   14  F1  UNL     1      -3.506  -2.443   0.872  1.00  0.00           F  
HETATM   15  C10 UNL     1      -1.439  -1.364   0.339  1.00  0.00           C  
HETATM   16  C11 UNL     1      -0.682  -0.227   0.150  1.00  0.00           C  
HETATM   17  N2  UNL     1       1.200  -1.555  -0.647  1.00  0.00           N  
HETATM   18  H1  UNL     1       3.851  -0.324   0.989  1.00  0.00           H  
HETATM   19  H2  UNL     1       0.392   0.553  -2.168  1.00  0.00           H  
HETATM   20  H3  UNL     1       2.061   0.787  -1.499  1.00  0.00           H  
HETATM   21  H4  UNL     1       1.542   2.587  -0.169  1.00  0.00           H  
HETATM   22  H5  UNL     1       0.403   2.826  -1.569  1.00  0.00           H  
HETATM   23  H6  UNL     1      -3.047   2.082   0.793  1.00  0.00           H  
HETATM   24  H7  UNL     1      -4.420   0.033   1.135  1.00  0.00           H  
HETATM   25  H8  UNL     1      -0.994  -2.366   0.212  1.00  0.00           H  
HETATM   26  H9  UNL     1       0.713  -2.374  -1.050  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   17
CONECT    3    4   18
CONECT    4    5    5    6
CONECT    6    7   16   17
CONECT    7    8   19   20
CONECT    8    9   21   22
CONECT    9   10
CONECT   10   11   11   16
CONECT   11   12   23
CONECT   12   13   13   24
CONECT   13   14   15
CONECT   15   16   16   25
CONECT   17   26
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₁H₉FN₂O₃

Average Molecular Weight

236.202

Monoisotopic Molecular Weight

236.059720321

IUPAC Name

6-fluoro-2,3-dihydrospiro[1-benzopyran-4,4'-imidazolidine]-2',5'-dione

Traditional Name

sorbinil

CAS Registry Number

Not Available

SMILES

FC1=CC2=C(OCCC22NC(=O)NC2=O)C=C1

InChI Identifier

InChI=1S/C11H9FN2O3/c12-6-1-2-8-7(5-6)11(3-4-17-8)9(15)13-10(16)14-11/h1-2,5H,3-4H2,(H2,13,14,15,16)

InChI Key

LXANPKRCLVQAOG-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydantoins. These are heterocyclic compounds containing an imidazolidine substituted by ketone group at positions 2 and 4.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azolidines

Sub Class

Imidazolidines

Direct Parent

Hydantoins

Alternative Parents

Substituents

Hydantoin
Alpha-amino acid or derivatives
Chromane
1-benzopyran
Benzopyran
5-monosubstituted hydantoin
Alkyl aryl ether
N-acyl urea
Ureide
Aryl fluoride
Aryl halide
Benzenoid
Dicarboximide
Carbonic acid derivative
Urea
Carboxylic acid derivative
Oxacycle
Ether
Azacycle
Organic nitrogen compound
Organohalogen compound
Organofluoride
Organonitrogen compound
Carbonyl group
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0258388)

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	0.59	ALOGPS
logP	0.44	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	8.67	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	67.43 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	54.94 m³·mol⁻¹	ChemAxon
Polarizability	20.85 Å³	ChemAxon
Number of Rings	3	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
DeepCCS	[M-2H]-	182.91	30932474
DeepCCS	[M+Na]+	158.066	30932474
AllCCS	[M+H]+	150.5	32859911
AllCCS	[M+H-H2O]+	146.4	32859911
AllCCS	[M+NH4]+	154.3	32859911
AllCCS	[M+Na]+	155.4	32859911
AllCCS	[M-H]-	150.8	32859911
AllCCS	[M+Na-2H]-	150.4	32859911
AllCCS	[M+HCOO]-	150.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Sorbinil	FC1=CC2=C(OCCC22NC(=O)NC2=O)C=C1	3818.7	Standard polar	33892256
Sorbinil	FC1=CC2=C(OCCC22NC(=O)NC2=O)C=C1	1956.5	Standard non polar	33892256
Sorbinil	FC1=CC2=C(OCCC22NC(=O)NC2=O)C=C1	2178.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Sorbinil,1TMS,isomer #1	C[Si](C)(C)N1C(=O)NC(=O)C12CCOC1=CC=C(F)C=C12	2189.6	Semi standard non polar	33892256
Sorbinil,1TMS,isomer #1	C[Si](C)(C)N1C(=O)NC(=O)C12CCOC1=CC=C(F)C=C12	2129.1	Standard non polar	33892256
Sorbinil,1TMS,isomer #1	C[Si](C)(C)N1C(=O)NC(=O)C12CCOC1=CC=C(F)C=C12	3149.1	Standard polar	33892256
Sorbinil,1TMS,isomer #2	C[Si](C)(C)N1C(=O)NC2(CCOC3=CC=C(F)C=C32)C1=O	2184.8	Semi standard non polar	33892256
Sorbinil,1TMS,isomer #2	C[Si](C)(C)N1C(=O)NC2(CCOC3=CC=C(F)C=C32)C1=O	2055.6	Standard non polar	33892256
Sorbinil,1TMS,isomer #2	C[Si](C)(C)N1C(=O)NC2(CCOC3=CC=C(F)C=C32)C1=O	3082.0	Standard polar	33892256
Sorbinil,2TMS,isomer #1	C[Si](C)(C)N1C(=O)N([Si](C)(C)C)C2(CCOC3=CC=C(F)C=C32)C1=O	2063.6	Semi standard non polar	33892256
Sorbinil,2TMS,isomer #1	C[Si](C)(C)N1C(=O)N([Si](C)(C)C)C2(CCOC3=CC=C(F)C=C32)C1=O	2157.0	Standard non polar	33892256
Sorbinil,2TMS,isomer #1	C[Si](C)(C)N1C(=O)N([Si](C)(C)C)C2(CCOC3=CC=C(F)C=C32)C1=O	2736.9	Standard polar	33892256
Sorbinil,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)NC(=O)C12CCOC1=CC=C(F)C=C12	2422.0	Semi standard non polar	33892256
Sorbinil,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)NC(=O)C12CCOC1=CC=C(F)C=C12	2360.1	Standard non polar	33892256
Sorbinil,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)NC(=O)C12CCOC1=CC=C(F)C=C12	3245.5	Standard polar	33892256
Sorbinil,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)NC2(CCOC3=CC=C(F)C=C32)C1=O	2438.2	Semi standard non polar	33892256
Sorbinil,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)NC2(CCOC3=CC=C(F)C=C32)C1=O	2288.4	Standard non polar	33892256
Sorbinil,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C(=O)NC2(CCOC3=CC=C(F)C=C32)C1=O	3181.5	Standard polar	33892256
Sorbinil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)N([Si](C)(C)C(C)(C)C)C2(CCOC3=CC=C(F)C=C32)C1=O	2485.8	Semi standard non polar	33892256
Sorbinil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)N([Si](C)(C)C(C)(C)C)C2(CCOC3=CC=C(F)C=C32)C1=O	2622.3	Standard non polar	33892256
Sorbinil,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)N([Si](C)(C)C(C)(C)C)C2(CCOC3=CC=C(F)C=C32)C1=O	2882.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Sorbinil GC-MS (Non-derivatized) - 70eV, Positive	splash10-014l-0910000000-d86641decb0ee92d374e	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Sorbinil GC-MS (Non-derivatized) - 70eV, Positive	Not Available	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

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

5062

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Sorbinil

METLIN ID

Not Available

PubChem Compound

5252

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 Sorbinil (HMDB0258388)

MOL for HMDB0258388 (Sorbinil)

3D MOL for HMDB0258388 (Sorbinil)

3D SDF for HMDB0258388 (Sorbinil)

3D-SDF for HMDB0258388 (Sorbinil)

PDB for HMDB0258388 (Sorbinil)

3D PDB for HMDB0258388 (Sorbinil)

SMILES for HMDB0258388 (Sorbinil)

INCHI for HMDB0258388 (Sorbinil)

Structure for HMDB0258388 (Sorbinil)

3D Structure for HMDB0258388 (Sorbinil)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra