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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2022-09-09 20:28:48 UTC

Update Date

2022-09-22 18:34:48 UTC

HMDB ID

HMDB0341333

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Indolmycin

Description

Structure

MOL SDF PDB SMILES InChI

  Mrv0541 05301214532D          

 21 23  0  0  0  0            999 V2000
    1.4358   -0.5422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3763   -2.1658    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
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  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
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5363    0.4514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0792   -0.7681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6313   -1.3812    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2508    0.0389    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4500    1.2719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2587   -0.8543    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6908    0.2424    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2903    0.6962    0.0000 H   0  0  0  0  0  0  0  0  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
  8  1  1  1  0  0  0
  9  5  2  0  0  0  0
 10  7  2  0  0  0  0
 10  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11  6  2  0  0  0  0
 11  9  1  0  0  0  0
 12  8  1  6  0  0  0
 13 12  1  0  0  0  0
 15  2  1  4  0  0  0
 15 14  2  0  0  0  0
 16  7  1  0  0  0  0
 16 11  1  0  0  0  0
 17 13  2  0  0  0  0
 17 14  1  0  0  0  0
 18 13  1  0  0  0  0
 19 12  1  0  0  0  0
 19 14  1  0  0  0  0
  8 20  1  6  0  0  0
 12 21  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0341333

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](C)(C1=CNC2=CC=CC=C12)[C@]1([H])OC(=NC)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H15N3O2/c1-8(12-13(18)17-14(15-2)19-12)10-7-16-11-6-4-3-5-9(10)11/h3-8,12,16H,1-2H3,(H,15,17,18)/t8-,12+/m1/s1

> <INCHI_KEY>
GNTVWGDQPXCYBV-PELKAZGASA-N

> <FORMULA>
C14H15N3O2

> <MOLECULAR_WEIGHT>
257.2878

> <EXACT_MASS>
257.116426739

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
27.18234599107551

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylimino)-2,5-dihydro-1,3-oxazol-4-ol

> <ALOGPS_LOGP>
2.18

> <JCHEM_LOGP>
2.6048372823333334

> <ALOGPS_LOGS>
-3.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.238545763439017

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.636447678394688

> <JCHEM_PKA_STRONGEST_BASIC>
2.0396374817712806

> <JCHEM_POLAR_SURFACE_AREA>
69.97

> <JCHEM_REFRACTIVITY>
71.5117

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.77e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylimino)-5H-1,3-oxazol-4-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-MAY-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-MAY-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    8                                                            
CONECT    2   15                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    3    9                                                       
CONECT    6    4   11                                                       
CONECT    7   10   16                                                       
CONECT    8    1   10   12   20                                             
CONECT    9    5   10   11                                                  
CONECT   10    7    8    9                                                  
CONECT   11    6    9   16                                                  
CONECT   12    8   13   19   21                                             
CONECT   13   12   17   18                                                  
CONECT   14   15   17   19                                                  
CONECT   15    2   14                                                       
CONECT   16    7   11                                                       
CONECT   17   13   14                                                       
CONECT   18   13                                                            
CONECT   19   12   14                                                       
CONECT   20    8                                                            
CONECT   21   12                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(-)-Indolmycin	ChEBI
(1R,5S)-(-)-5-(1-indol-3-Ylethyl)-2-(methylamino)-2-oxazolin-4-one	ChEBI
(5S,6R)-(-)-Indolmycin	ChEBI
Indolemycin	ChEBI
PA 155 a	ChEBI
PA-155-a	ChEBI
Indolmycin, (S-(r,s))-isomer	MeSH
Indolmycin, (r,s)-(+-)-isomer	MeSH
Indolmycin, (R-(r,s))-isomer	MeSH

Chemical Formula

C₁₄H₁₅N₃O₂

Average Molecular Weight

257.2878

Monoisotopic Molecular Weight

257.116426739

IUPAC Name

(5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylimino)-2,5-dihydro-1,3-oxazol-4-ol

Traditional Name

(5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylimino)-5H-1,3-oxazol-4-ol

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(C1=CNC2=CC=CC=C12)[C@]1([H])OC(=NC)N=C1O

InChI Identifier

InChI=1S/C14H15N3O2/c1-8(12-13(18)17-14(15-2)19-12)10-7-16-11-6-4-3-5-9(10)11/h3-8,12,16H,1-2H3,(H,15,17,18)/t8-,12+/m1/s1

InChI Key

GNTVWGDQPXCYBV-PELKAZGASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

3-alkylindoles

Alternative Parents

Substituents

3-alkylindole
Substituted pyrrole
Benzenoid
Oxazoline
Pyrrole
Heteroaromatic compound
Isourea
N-acylimine
Carboxylic acid derivative
Carboximidamide
Oxacycle
Azacycle
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

1,3-oxazoles (CHEBI:79394 )
indoles (CHEBI:79394 )
secondary amino compound (CHEBI:79394 )

Ontology

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	2.18	ALOGPS
logP	2.6	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	5.64	ChemAxon
pKa (Strongest Basic)	2.04	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	69.97 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	71.51 m³·mol⁻¹	ChemAxon
Polarizability	27.18 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 Kovats Retention Indices

Not Available

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indolmycin 10V, Positive-QTOF	splash10-0a4i-0190000000-ec694aceccccd2027108	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indolmycin 20V, Positive-QTOF	splash10-0540-3940000000-1d47a35dfb38971346a2	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indolmycin 40V, Positive-QTOF	splash10-052f-3900000000-0d07ae3c667e5be94812	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indolmycin 10V, Negative-QTOF	splash10-0a4i-4090000000-a9fa4313d02fe42fb0b9	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indolmycin 20V, Negative-QTOF	splash10-056r-2290000000-5e5a4242f6351db0c5ec	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Indolmycin 40V, Negative-QTOF	splash10-0006-9200000000-f7342c4048fc7dbebc97	2019-02-23	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

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

C00026624

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

CPD0-920

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

210263

PDB ID

Not Available

ChEBI ID

79394

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

Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920 ]

Showing metabocard for Indolmycin (HMDB0341333)

MOL for HMDB0341333 (Indolmycin)

3D MOL for HMDB0341333 (Indolmycin)

3D SDF for HMDB0341333 (Indolmycin)

3D-SDF for HMDB0341333 (Indolmycin)

PDB for HMDB0341333 (Indolmycin)

3D PDB for HMDB0341333 (Indolmycin)

SMILES for HMDB0341333 (Indolmycin)

INCHI for HMDB0341333 (Indolmycin)

Structure for HMDB0341333 (Indolmycin)

3D Structure for HMDB0341333 (Indolmycin)

Predicted Kovats Retention Indices

MS/MS Spectra