MiMeDB: Showing metabocard for Kleboxymycin (MMDBc0028213)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 17:50:53 UTC

Update Date

2025-10-07 16:07:49 UTC

Metabolite ID

MMDBc0028213

Metabolite Identification

Common Name

Kleboxymycin

Description

Kleboxymycin is a tricyclic polyketide antibiotic belonging to the chemical class of polyketides. Its chemical structure features a complex arrangement that contributes to its potent cytotoxic properties, as evidenced by its higher cytotoxicity compared to tilivalline in TC50 cell culture assays (PMID:28972161 ). Kleboxymycin is synthesized via a biosynthetic gene cluster (BGC) that is prevalent among various strains of the Klebsiella oxytoca complex, with genomic analyses revealing that 34.7% of isolates carry kleboxymycin gene clusters (KGC) (PMID:40246208 ). The detection of the kleboxymycin BGC across multiple Klebsiella genome sequences indicates its widespread occurrence, with 88 out of 7170 genomes encoding this cluster (PMID:34142942 ). Moreover, whole-genome sequencing has shown that strains containing the kleboxymycin BGC possess additional virulence factors, suggesting their potential as human pathogens (PMID:32126585 ). The biosynthetic pathways for kleboxymycin and tilivalline appear to overlap, indicating a relationship between these compounds (PMID:28972161 ). Overall, kleboxymycin's intricate chemical structure and its involvement in antimicrobial resistance highlight its significance in clinical microbiology (PMID:40804599 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152119502D          

 19 21  0  0  1  0            999 V2000
    4.7050    1.2468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4911    1.6373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9194    0.9948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8068    2.3995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8795    2.0531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1184    1.1015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3084    1.5491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6293    2.3347    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2685    2.6074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4829    2.3555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1364    2.9855    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5691    1.1829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9614    2.9947    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8219    1.5325    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4431    3.4137    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7702    3.7247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5783    0.3580    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2966    3.0897    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5675    3.6889    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  7  2  0  0  0  0
 10  9  1  0  0  0  0
 11  8  1  0  0  0  0
 12  7  1  0  0  0  0
 13 10  1  0  0  0  0
 13 11  1  0  0  0  0
 14  6  1  0  0  0  0
 14  8  1  0  0  0  0
 14 12  1  0  0  0  0
 15  9  1  0  0  0  0
 11 16  1  6  0  0  0
 17 12  2  0  0  0  0
  8 18  1  6  0  0  0
 11 19  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0028213

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CCCN1C(=O)C1=C(N[C@@]2([H])O)C(O)=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C12H14N2O3/c15-9-5-1-3-7-10(9)13-11(16)8-4-2-6-14(8)12(7)17/h1,3,5,8,11,13,15-16H,2,4,6H2/t8-,11-/m0/s1

> <INCHI_KEY>
QEILHZZUMSPTRX-KWQFWETISA-N

> <FORMULA>
C12H14N2O3

> <MOLECULAR_WEIGHT>
234.255

> <EXACT_MASS>
234.100442319

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
23.921901449390234

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(7S,8S)-8,11-dihydroxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(10),11,13-trien-2-one

> <ALOGPS_LOGP>
0.42

> <JCHEM_LOGP>
1.020266699

> <ALOGPS_LOGS>
-0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.266675949934642

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.443615461724965

> <JCHEM_PKA_STRONGEST_BASIC>
-0.20051593908196264

> <JCHEM_POLAR_SURFACE_AREA>
72.8

> <JCHEM_REFRACTIVITY>
63.37660000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.30e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(7S,8S)-8,11-dihydroxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(10),11,13-trien-2-one

> <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       8.783   2.327   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.917   3.056   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.316   1.857   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.506   4.479   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.108   3.832   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.088   2.056   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.176   2.892   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.041   4.358   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.968   4.867   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.501   4.397   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.988   5.573   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.796   2.208   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       5.528   5.590   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       3.401   2.861   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       8.294   6.372   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.304   6.953   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.813   0.668   0.000  0.00  0.00           O+0
HETATM   18  H   UNK     0       2.420   5.767   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       4.793   6.886   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    1    9                                                       
CONECT    6    2   14                                                       
CONECT    7    3   10   12                                                  
CONECT    8    4   11   14   18                                             
CONECT    9    5   10   15                                                  
CONECT   10    7    9   13                                                  
CONECT   11    8   13   16   19                                             
CONECT   12    7   14   17                                                  
CONECT   13   10   11                                                       
CONECT   14    6    8   12                                                  
CONECT   15    9                                                            
CONECT   16   11                                                            
CONECT   17   12                                                            
CONECT   18    8                                                            
CONECT   19   11                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

Synonyms

Not Available

Molecular Formula

C₁₂H₁₄N₂O₃

Average Mass

234.255

Monoisotopic Mass

234.100442319

IUPAC Name

(7S,8S)-8,11-dihydroxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(10),11,13-trien-2-one

Traditional Name

(7S,8S)-8,11-dihydroxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(10),11,13-trien-2-one

CAS Registry Number

Not Available

SMILES

[H][C@@]12CCCN1C(=O)C1=C(N[C@@]2([H])O)C(O)=CC=C1

InChI Identifier

InChI=1S/C12H14N2O3/c15-9-5-1-3-7-10(9)13-11(16)8-4-2-6-14(8)12(7)17/h1,3,5,8,11,13,15-16H,2,4,6H2/t8-,11-/m0/s1

InChI Key

QEILHZZUMSPTRX-KWQFWETISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzodiazepines

Sub Class

1,4-benzodiazepines

Direct Parent

1,4-benzodiazepines

Alternative Parents

Substituents

1,4-benzodiazepine
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Secondary aliphatic/aromatic amine
Benzenoid
Vinylogous amide
Tertiary carboxylic acid amide
Pyrrolidine
Lactam
Carboxamide group
Amino acid or derivatives
Azacycle
Secondary amine
Carboxylic acid derivative
Alkanolamine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Amine
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	33 g/L	ALOGPS
logP	0.42	ALOGPS
logP	1.02	ChemAxon
logS	-0.85	ALOGPS
pKa (Strongest Acidic)	9.44	ChemAxon
pKa (Strongest Basic)	-0.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	72.8 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	63.38 m³·mol⁻¹	ChemAxon
Polarizability	23.92 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	Proteobacteria	1	Human ; Human feces; Human subgingival plaque	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

146684602

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Kleboxymycin (MMDBc0028213)

MOL for #<Metabolite:0x00007f8de9a12c90>

3D MOL for #<Metabolite:0x00007f8de9a12c90>

3D SDF for #<Metabolite:0x00007f8de9a12c90>

3D-SDF for #<Metabolite:0x00007f8de9a12c90>

PDB for #<Metabolite:0x00007f8de9a12c90>

3D PDB for #<Metabolite:0x00007f8de9a12c90>

SMILES for #<Metabolite:0x00007f8de9a12c90>

INCHI for #<Metabolite:0x00007f8de9a12c90>

Structure for #<Metabolite:0x00007f8de9a12c90>

3D Structure for #<Metabolite:0x00007f8de9a12c90>