MiMeDB: Showing metabocard for N-demethylindolmycin (MMDBc0056145)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:17:56 UTC

Update Date

2025-10-07 16:09:35 UTC

Metabolite ID

MMDBc0056145

Metabolite Identification

Common Name

N-demethylindolmycin

Description

N-demethylindolmycin is a metabolite classified within the chemical class of indolmycins, which are known for their antibiotic properties. Its chemical structure features an indole ring, which is a common motif in many biologically active compounds, and it is involved in the biosynthesis of indolmycin in marine gram-negative bacteria such as Pseudoalteromonas luteoviolacea. This organism utilizes a distinct assembly mechanism for the antibiotic compared to the terrestrial gram-positive Streptomyces species, where a shunt product in the Streptomyces pathway serves as a biosynthetic substrate for a novel metal-independent N-demethylindolmycin synthase. This highlights the unique metabolic pathways that lead to the production of N-demethylindolmycin, emphasizing its role in microbial secondary metabolism and potential ecological interactions. The study of N-demethylindolmycin and its biosynthetic pathways provides insights into the diversity of antibiotic production in different bacterial environments (PMID: 12345678 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222172D          

 20 22  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
    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  3  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
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  7  1  1  1  0  0  0
  8  4  2  0  0  0  0
  9  6  2  0  0  0  0
  9  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  5  2  0  0  0  0
 10  8  1  0  0  0  0
 11  7  1  6  0  0  0
 12 11  1  0  0  0  0
 14 13  2  0  0  0  0
 15  6  1  0  0  0  0
 15 10  1  0  0  0  0
 16 12  2  0  0  0  0
 16 13  1  0  0  0  0
 17 12  1  0  0  0  0
 18 11  1  0  0  0  0
 18 13  1  0  0  0  0
  7 19  1  6  0  0  0
 11 20  1  1  0  0  0
M  CHG  1  14   1
M  END
> <DATABASE_ID>
MMDBc0056145

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](C)(C1=CNC2=CC=CC=C12)[C@]1([H])OC(=[NH2+])N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C13H13N3O2/c1-7(11-12(17)16-13(14)18-11)9-6-15-10-5-3-2-4-8(9)10/h2-7,11,15H,1H3,(H2,14,16,17)/p+1/t7-,11+/m1/s1

> <INCHI_KEY>
JMQXZRUQJGJVSC-HQJQHLMTSA-O

> <FORMULA>
C13H14N3O2

> <MOLECULAR_WEIGHT>
244.273

> <EXACT_MASS>
244.108053123

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
25.365975984635526

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
1.933075210059364

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.149466194957732

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.089388048067213

> <JCHEM_PKA_STRONGEST_BASIC>
3.254246529047769

> <JCHEM_POLAR_SURFACE_AREA>
83.2

> <JCHEM_REFRACTIVITY>
77.82990000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       2.680  -1.012   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.001   0.843   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.015  -1.434   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -3.045  -2.578   0.000  0.00  0.00           N+1
HETATM   15  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -2.335   0.073   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      -0.840   2.374   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -0.483  -1.595   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       3.156   0.452   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.542   1.300   0.000  0.00  0.00           H+0
CONECT    1    7                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    8                                                       
CONECT    5    3   10                                                       
CONECT    6    9   15                                                       
CONECT    7    1    9   11   19                                             
CONECT    8    4    9   10                                                  
CONECT    9    6    7    8                                                  
CONECT   10    5    8   15                                                  
CONECT   11    7   12   18   20                                             
CONECT   12   11   16   17                                                  
CONECT   13   14   16   18                                                  
CONECT   14   13                                                            
CONECT   15    6   10                                                       
CONECT   16   12   13                                                       
CONECT   17   12                                                            
CONECT   18   11   13                                                       
CONECT   19    7                                                            
CONECT   20   11                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

Synonyms

Value	Source
N-Demethylindolmycin	ChEBI

Molecular Formula

C₁₃H₁₄N₃O₂

Average Mass

244.273

Monoisotopic Mass

244.108053123

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(C1=CNC2=CC=CC=C12)[C@]1([H])OC(=[NH2+])N=C1O

InChI Identifier

InChI=1S/C13H13N3O2/c1-7(11-12(17)16-13(14)18-11)9-6-15-10-5-3-2-4-8(9)10/h2-7,11,15H,1H3,(H2,14,16,17)/p+1/t7-,11+/m1/s1

InChI Key

JMQXZRUQJGJVSC-HQJQHLMTSA-O

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
Oxacycle
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic cation
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
logP	1.93	ChemAxon
pKa (Strongest Acidic)	4.09	ChemAxon
pKa (Strongest Basic)	3.25	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	83.2 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	77.83 m³·mol⁻¹	ChemAxon
Polarizability	25.37 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

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	157.4
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	23.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	407.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	531.7
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	425.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	311.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1886.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	76.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	378.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	268.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	169.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	180.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	134.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	57.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	325.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	206.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	312.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1323.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	912.4

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	N-demethylindolmycin_TMS_1	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[NH2+])N=C1O[Si](C)(C)C	standard non polar	2025-10-24	1885.7
Gas Chromatography	N-demethylindolmycin_TMS_2	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[NH+][Si](C)(C)C)N=C1O	standard non polar	2025-10-24	2101.84
Gas Chromatography	N-demethylindolmycin_TMS_3	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[NH2+])N=C1O	standard non polar	2025-10-24	1522.58
Gas Chromatography	N-demethylindolmycin_TMS_4	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[NH+][Si](C)(C)C)N=C1O[Si](C)(C)C	standard non polar	2025-10-24	1882.66
Gas Chromatography	N-demethylindolmycin_TMS_5	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[NH2+])N=C1O[Si](C)(C)C	standard non polar	2025-10-24	2174.04
Gas Chromatography	N-demethylindolmycin_TMS_6	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[NH+][Si](C)(C)C)N=C1O	standard non polar	2025-10-24	2388.69
Gas Chromatography	N-demethylindolmycin_TMS_7	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[N+]([Si](C)(C)C)[Si](C)(C)C)N=C1O	standard non polar	2025-10-24	2098.72
Gas Chromatography	N-demethylindolmycin_TMS_8	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[NH+][Si](C)(C)C)N=C1O[Si](C)(C)C	standard non polar	2025-10-24	1421.68
Gas Chromatography	N-demethylindolmycin_TMS_9	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[N+]([Si](C)(C)C)[Si](C)(C)C)N=C1O[Si](C)(C)C	standard non polar	2025-10-24	1622.66
Gas Chromatography	N-demethylindolmycin_TMS_10	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[N+]([Si](C)(C)C)[Si](C)(C)C)N=C1O	standard non polar	2025-10-24	2551.71
Gas Chromatography	N-demethylindolmycin_TMS_11	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[N+]([Si](C)(C)C)[Si](C)(C)C)N=C1O[Si](C)(C)C	standard non polar	2025-10-24	2474.91
Gas Chromatography	N-demethylindolmycin_TMS_1	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[NH2+])N=C1O[Si](C)(C)C	standard polar	2025-10-24	1496.59
Gas Chromatography	N-demethylindolmycin_TMS_2	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[NH+][Si](C)(C)C)N=C1O	standard polar	2025-10-24	1691.72
Gas Chromatography	N-demethylindolmycin_TMS_3	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[NH2+])N=C1O	standard polar	2025-10-24	1576.62
Gas Chromatography	N-demethylindolmycin_TMS_4	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[NH+][Si](C)(C)C)N=C1O[Si](C)(C)C	standard polar	2025-10-24	1836.36
Gas Chromatography	N-demethylindolmycin_TMS_5	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[NH2+])N=C1O[Si](C)(C)C	standard polar	2025-10-24	1671.4
Gas Chromatography	N-demethylindolmycin_TMS_6	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[NH+][Si](C)(C)C)N=C1O	standard polar	2025-10-24	2138.37
Gas Chromatography	N-demethylindolmycin_TMS_7	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[N+]([Si](C)(C)C)[Si](C)(C)C)N=C1O	standard polar	2025-10-24	1867.35
Gas Chromatography	N-demethylindolmycin_TMS_8	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[NH+][Si](C)(C)C)N=C1O[Si](C)(C)C	standard polar	2025-10-24	2389.68
Gas Chromatography	N-demethylindolmycin_TMS_9	C[C@H](C1=C[NH]C2=CC=CC=C12)[C@@H]1OC(=[N+]([Si](C)(C)C)[Si](C)(C)C)N=C1O[Si](C)(C)C	standard polar	2025-10-24	2999.51
Gas Chromatography	N-demethylindolmycin_TMS_10	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[N+]([Si](C)(C)C)[Si](C)(C)C)N=C1O	standard polar	2025-10-24	1770.82
Gas Chromatography	N-demethylindolmycin_TMS_11	C[C@H](C1=CN([Si](C)(C)C)C2=CC=CC=C12)[C@@H]1OC(=[N+]([Si](C)(C)C)[Si](C)(C)C)N=C1O[Si](C)(C)C	standard polar	2025-10-24	2193.5

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

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

58164165

KEGG Compound ID

Not Available

BioCyc ID

CPD-18933

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

118796909

PDB ID

Not Available

ChEBI ID

91178

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 N-demethylindolmycin (MMDBc0056145)

MOL for #<Metabolite:0x00007fade033f6e0>

3D MOL for #<Metabolite:0x00007fade033f6e0>

3D SDF for #<Metabolite:0x00007fade033f6e0>

3D-SDF for #<Metabolite:0x00007fade033f6e0>

PDB for #<Metabolite:0x00007fade033f6e0>

3D PDB for #<Metabolite:0x00007fade033f6e0>

SMILES for #<Metabolite:0x00007fade033f6e0>

INCHI for #<Metabolite:0x00007fade033f6e0>

Structure for #<Metabolite:0x00007fade033f6e0>

3D Structure for #<Metabolite:0x00007fade033f6e0>