MiMeDB: Showing metabocard for Indolmycin (MMDBc0015608)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:23:49 UTC

Update Date

2025-10-07 16:04:15 UTC

Metabolite ID

MMDBc0015608

Metabolite Identification

Common Name

Indolmycin

Description

Indolmycin is a microbial natural product belonging to the class of indole alkaloids. Its chemical structure features a bicyclic indole ring system that is crucial for its biological activity. Indolmycin functions primarily as an inhibitor of bacterial tryptophanyl-tRNA synthetase (TrpRS), a key enzyme involved in protein synthesis. The binding affinity of indolmycin for EcTrpRS has been reported with a Kd of 0.71 ± 0.1 μM (PMID:40945024 ). It selectively targets TrpRS, which catalyzes the formation of tryptophanyl-AMP and the transfer of tryptophan to tRNATrp, thereby playing a significant role in the synthesis of proteins in bacteria (PMID:38457660 ). Variations in the TrpRS structure, such as substitutions in the cytosolic form, can limit indolmycin binding (PMID:40023769 ). Research has also focused on the design and synthesis of indolmycin derivatives to enhance antibacterial activity against resistant strains like methicillin-resistant Staphylococcus aureus (PMID:35963132 ). Additionally, genome analysis has identified RIPP-like peptides that may influence the algicidal effects of indolmycin, highlighting its potential in various biological pathways (PMID:35610407 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152108232D          

 21 23  0  0  1  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  1  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  2  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  6  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  1  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  1  0  0  0
 12 21  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0015608

> <DATABASE_NAME>
MIME

> <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+/m0/s1

> <INCHI_KEY>
GNTVWGDQPXCYBV-QPUJVOFHSA-N

> <FORMULA>
C14H15N3O2

> <MOLECULAR_WEIGHT>
257.293

> <EXACT_MASS>
257.116426735

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
27.402695749601726

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.18

> <JCHEM_LOGP>
2.5147734385828318

> <ALOGPS_LOGS>
-3.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.238544909082739

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.98953427482532

> <JCHEM_PKA_STRONGEST_BASIC>
2.0325517899465324

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0       2.680  -1.012   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.569  -4.043   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.001   0.843   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.015  -1.434   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -3.045  -2.578   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      -2.335   0.073   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0      -0.840   2.374   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -0.483  -1.595   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0       3.156   0.452   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.542   1.300   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

Synonyms

Not Available

Molecular Formula

C₁₄H₁₅N₃O₂

Average Mass

257.293

Monoisotopic Mass

257.116426735

IUPAC Name

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

Traditional Name

(5R)-5-[(1S)-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+/m0/s1

InChI Key

GNTVWGDQPXCYBV-QPUJVOFHSA-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
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Oxacycle
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Imine
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.078 g/L	ALOGPS
logP	2.18	ALOGPS
logP	2.51	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	3.99	ChemAxon
pKa (Strongest Basic)	2.03	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	27.4 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

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Actinobacteria	1		Metabolic reconstruction
Bacteria	Actinobacteria	1		Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78443582

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

12310808

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Indolmycin (MMDBc0015608)

MOL for #<Metabolite:0x00007f8de40423c8>

3D MOL for #<Metabolite:0x00007f8de40423c8>

3D SDF for #<Metabolite:0x00007f8de40423c8>

3D-SDF for #<Metabolite:0x00007f8de40423c8>

PDB for #<Metabolite:0x00007f8de40423c8>

3D PDB for #<Metabolite:0x00007f8de40423c8>

SMILES for #<Metabolite:0x00007f8de40423c8>

INCHI for #<Metabolite:0x00007f8de40423c8>

Structure for #<Metabolite:0x00007f8de40423c8>

3D Structure for #<Metabolite:0x00007f8de40423c8>