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Showing metabocard for 3-Methyloxindole (HMDB0304943)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-10-01 18:04:09 UTC
Update Date2022-09-22 18:35:14 UTC
HMDB IDHMDB0304943
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Methyloxindole
Description3-methyloxindole belongs to the class of organic compounds known as indolines. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene to form 2,3-dihydroindole. 3-methyloxindole is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304943 (3-Methyloxindole)


  Mrv1533004231517542D          

 11 12  0  0  0  0            999 V2000
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  2 11  1  0  0  0  0
  6 11  1  0  0  0  0
M  END
Download

3D MOL for HMDB0304943 (3-Methyloxindole)

HMDB0304943
     RDKit          3D

 20 21  0  0  0  0  0  0  0  0999 V2000
   -2.1610   -0.8415   -0.5414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4343   -0.0553    0.5329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6341    1.3879    0.3886 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7544    1.9587    0.5211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3874    1.9987    0.0853 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6131    0.9904    0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9821    1.0325   -0.2251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7059   -0.1418   -0.2098 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0766   -1.3544    0.0565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7269   -1.4107    0.3092 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0212   -0.2219    0.2888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1830   -0.4460   -0.7343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5463   -0.7901   -1.4818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1761   -1.9139   -0.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6655   -0.4363    1.5494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2617    3.0213   -0.0656 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4137    1.9989   -0.4246 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7716   -0.1254   -0.4058 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6368   -2.2926    0.0719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2555   -2.3588    0.5136 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11  2  1  0
 11  6  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  5 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
M  END
Download

3D SDF for HMDB0304943 (3-Methyloxindole)


  Mrv1533004231517542D          

 11 12  0  0  0  0            999 V2000
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  2 11  1  0  0  0  0
  6 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304943

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1C(=O)NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C9H9NO/c1-6-7-4-2-3-5-8(7)10-9(6)11/h2-6H,1H3,(H,10,11)

> <INCHI_KEY>
BBZCPUCZKLTAJQ-UHFFFAOYSA-N

> <FORMULA>
C9H9NO

> <MOLECULAR_WEIGHT>
147.177

> <EXACT_MASS>
147.068413914

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
15.608428466269345

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methyl-2,3-dihydro-1H-indol-2-one

> <ALOGPS_LOGP>
1.46

> <JCHEM_LOGP>
1.6150364653333331

> <ALOGPS_LOGS>
-1.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.262031675224211

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.306488389952733

> <JCHEM_PKA_STRONGEST_BASIC>
-5.118340195069035

> <JCHEM_POLAR_SURFACE_AREA>
29.1

> <JCHEM_REFRACTIVITY>
44.1594

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.68e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methyloxindole

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0304943 (3-Methyloxindole)

HMDB0304943
     RDKit          3D

 20 21  0  0  0  0  0  0  0  0999 V2000
   -2.1610   -0.8415   -0.5414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4343   -0.0553    0.5329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6341    1.3879    0.3886 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7544    1.9587    0.5211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3874    1.9987    0.0853 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6131    0.9904    0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9821    1.0325   -0.2251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7059   -0.1418   -0.2098 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0766   -1.3544    0.0565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7269   -1.4107    0.3092 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0212   -0.2219    0.2888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1830   -0.4460   -0.7343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5463   -0.7901   -1.4818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1761   -1.9139   -0.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6655   -0.4363    1.5494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2617    3.0213   -0.0656 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4137    1.9989   -0.4246 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7716   -0.1254   -0.4058 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6368   -2.2926    0.0719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2555   -2.3588    0.5136 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11  2  1  0
 11  6  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  5 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
M  END
Download

PDB for HMDB0304943 (3-Methyloxindole)

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.320  -1.303   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    2    6                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for HMDB0304943 (3-Methyloxindole)

COMPND    HMDB0304943
HETATM    1  C1  UNL     1      -2.161  -0.841  -0.541  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.434  -0.055   0.533  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.634   1.388   0.389  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.754   1.959   0.521  1.00  0.00           O  
HETATM    5  N1  UNL     1      -0.387   1.999   0.085  1.00  0.00           N  
HETATM    6  C4  UNL     1       0.613   0.990   0.029  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.982   1.032  -0.225  1.00  0.00           C  
HETATM    8  C6  UNL     1       2.706  -0.142  -0.210  1.00  0.00           C  
HETATM    9  C7  UNL     1       2.077  -1.354   0.056  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.727  -1.411   0.309  1.00  0.00           C  
HETATM   11  C9  UNL     1       0.021  -0.222   0.289  1.00  0.00           C  
HETATM   12  H1  UNL     1      -3.183  -0.446  -0.734  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.546  -0.790  -1.482  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.176  -1.914  -0.258  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.666  -0.436   1.549  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.262   3.021  -0.066  1.00  0.00           H  
HETATM   17  H6  UNL     1       2.414   1.999  -0.425  1.00  0.00           H  
HETATM   18  H7  UNL     1       3.772  -0.125  -0.406  1.00  0.00           H  
HETATM   19  H8  UNL     1       2.637  -2.293   0.072  1.00  0.00           H  
HETATM   20  H9  UNL     1       0.256  -2.359   0.514  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3   11   15
CONECT    3    4    4    5
CONECT    5    6   16
CONECT    6    7    7   11
CONECT    7    8   17
CONECT    8    9    9   18
CONECT    9   10   19
CONECT   10   11   11   20
END
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SMILES for HMDB0304943 (3-Methyloxindole)

CC1C(=O)NC2=CC=CC=C12
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INCHI for HMDB0304943 (3-Methyloxindole)

InChI=1S/C9H9NO/c1-6-7-4-2-3-5-8(7)10-9(6)11/h2-6H,1H3,(H,10,11)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,3-Dihydro-3-methyl-2H-indol-2-oneChEBI
3-Methyl-1,3-dihydroindol-2-oneChEBI
3-Methyl-2-oxindoleMeSH
Chemical FormulaC9H9NO
Average Molecular Weight147.177
Monoisotopic Molecular Weight147.068413914
IUPAC Name3-methyl-2,3-dihydro-1H-indol-2-one
Traditional Name3-methyloxindole
CAS Registry NumberNot Available
SMILES
CC1C(=O)NC2=CC=CC=C12
InChI Identifier
InChI=1S/C9H9NO/c1-6-7-4-2-3-5-8(7)10-9(6)11/h2-6H,1H3,(H,10,11)
InChI KeyBBZCPUCZKLTAJQ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indolines. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene to form 2,3-dihydroindole.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassIndolines
Direct ParentIndolines
Alternative Parents
Substituents
  • Dihydroindole
  • Benzenoid
  • Carboxamide group
  • Lactam
  • Secondary carboxylic acid amide
  • Azacycle
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.46ALOGPS
logP1.62ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)12.31ChemAxon
pKa (Strongest Basic)-5.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area29.1 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity44.16 m³·mol⁻¹ChemAxon
Polarizability15.61 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+129.2332859911
AllCCS[M+H-H2O]+124.46532859911
AllCCS[M+Na]+134.96132859911
AllCCS[M+NH4]+133.67732859911
AllCCS[M-H]-129.93332859911
AllCCS[M+Na-2H]-130.83432859911
AllCCS[M+HCOO]-131.8932859911
DeepCCS[M-2H]-162.86930932474
DeepCCS[M+Na]+138.21230932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Methyloxindole,1TMS,isomer #1CC1C(=O)N([Si](C)(C)C)C2=CC=CC=C211498.9Semi standard non polar33892256
3-Methyloxindole,1TMS,isomer #1CC1C(=O)N([Si](C)(C)C)C2=CC=CC=C211552.9Standard non polar33892256
3-Methyloxindole,1TMS,isomer #1CC1C(=O)N([Si](C)(C)C)C2=CC=CC=C211838.1Standard polar33892256
3-Methyloxindole,1TBDMS,isomer #1CC1C(=O)N([Si](C)(C)C(C)(C)C)C2=CC=CC=C211740.0Semi standard non polar33892256
3-Methyloxindole,1TBDMS,isomer #1CC1C(=O)N([Si](C)(C)C(C)(C)C)C2=CC=CC=C211790.4Standard non polar33892256
3-Methyloxindole,1TBDMS,isomer #1CC1C(=O)N([Si](C)(C)C(C)(C)C)C2=CC=CC=C211979.6Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyloxindole 10V, Positive-QTOFsplash10-0002-0900000000-7b55d189e95922af9f372021-10-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyloxindole 20V, Positive-QTOFsplash10-0002-0900000000-cea9330d77eab03f33942021-10-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyloxindole 40V, Positive-QTOFsplash10-0ufr-9700000000-f73f909d72f005c95b1e2021-10-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyloxindole 10V, Negative-QTOFsplash10-0002-0900000000-46c7adeffe51c18a37d62021-10-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyloxindole 20V, Negative-QTOFsplash10-0002-3900000000-ca8edd5d21083ea3a52e2021-10-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyloxindole 40V, Negative-QTOFsplash10-0006-9000000000-f3f899006742cd993cf22021-10-22Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC02366
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound150923
PDB IDNot Available
ChEBI ID17397
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. National Institute of Environmental Health Science (NIEHS) [Link]