MiMeDB: Showing metabocard for Vulnibactin 2 (MMDBc0007118)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:24:59 UTC

Update Date

2025-10-07 16:05:17 UTC

Metabolite ID

MMDBc0007118

Metabolite Identification

Common Name

Vulnibactin 2

Description

Vulnibactin 2 is a siderophore, a type of small molecule that chelates iron and is produced by certain bacteria. There is limited literature available on this metabolite, indicating that further research is needed to fully understand its properties and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152102242D          

 16 17  0  0  0  0            999 V2000
    2.1665    3.2361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884    0.9479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528    0.1942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034    1.6153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323    0.1080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830    1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526    0.7754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.2911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9731    0.6892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.7036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.7036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    2.1965    0.0000 O   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
  6  1  1  0  0  0  0
  7  4  2  0  0  0  0
  8  5  2  0  0  0  0
  8  7  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  1  0  0  0  0
 11  9  1  0  0  0  0
 12  9  1  0  0  0  0
 12 10  2  0  0  0  0
 13  8  1  0  0  0  0
 14 11  2  0  0  0  0
 15 11  1  0  0  0  0
 16  6  1  0  0  0  0
 16 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0007118

> <DATABASE_NAME>
MIME

> <SMILES>
CC1OC(=NC1C(O)=O)C1=CC=CC=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C11H11NO4/c1-6-9(11(14)15)12-10(16-6)7-4-2-3-5-8(7)13/h2-6,9,13H,1H3,(H,14,15)

> <INCHI_KEY>
RLUVVLOFTLKEDG-UHFFFAOYSA-N

> <FORMULA>
C11H11NO4

> <MOLECULAR_WEIGHT>
221.212

> <EXACT_MASS>
221.068807838

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
21.83517165616414

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(2-hydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxylic acid

> <ALOGPS_LOGP>
1.67

> <JCHEM_LOGP>
2.261418048

> <ALOGPS_LOGS>
-2.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.375573801854268

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3683583258009073

> <JCHEM_PKA_STRONGEST_BASIC>
-0.3432075637223281

> <JCHEM_POLAR_SURFACE_AREA>
79.12

> <JCHEM_REFRACTIVITY>
55.566600000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.68e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(2-hydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxylic acid

> <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       4.044   6.041   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.778   1.769   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.152   0.363   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.873   3.015   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.620   0.202   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.580   5.565   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.342   2.854   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.285   1.447   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   6.470   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.564   4.100   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334   8.010   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       0.088   5.565   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       1.816   1.286   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   8.780   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.667   8.780   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.104   4.100   0.000  0.00  0.00           O+0
CONECT    1    6                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    7                                                       
CONECT    5    3    8                                                       
CONECT    6    1    9   16                                                  
CONECT    7    4    8   10                                                  
CONECT    8    5    7   13                                                  
CONECT    9    6   11   12                                                  
CONECT   10    7   12   16                                                  
CONECT   11    9   14   15                                                  
CONECT   12    9   10                                                       
CONECT   13    8                                                            
CONECT   14   11                                                            
CONECT   15   11                                                            
CONECT   16    6   10                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₁₁NO₄

Average Mass

221.212

Monoisotopic Mass

221.068807838

IUPAC Name

2-(2-hydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxylic acid

Traditional Name

2-(2-hydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC1OC(=NC1C(O)=O)C1=CC=CC=C1O

InChI Identifier

InChI=1S/C11H11NO4/c1-6-9(11(14)15)12-10(16-6)7-4-2-3-5-8(7)13/h2-6,9,13H,1H3,(H,14,15)

InChI Key

RLUVVLOFTLKEDG-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Oxazoline
Carboxylic acid
Monocarboxylic acid or derivatives
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Azacycle
Oxacycle
Organopnictogen compound
Organooxygen compound
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.97 g/L	ALOGPS
logP	1.67	ALOGPS
logP	2.26	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	3.37	ChemAxon
pKa (Strongest Basic)	-0.34	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	79.12 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.57 m³·mol⁻¹	ChemAxon
Polarizability	21.84 Å³	ChemAxon
Number of Rings	2	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)	2025-10-23	239.2
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	64.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	374.1
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	505.4
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	401.7
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	300.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	1570.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	81.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	544.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	224.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	172.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	183.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	106.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	140.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	483.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	97.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	302.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1121.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	817.1

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Vulnibactin 2_TMS_1	CC1OC(C2=CC=CC=C2O)=NC1C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1678.51
Gas Chromatography	Vulnibactin 2_TMS_2	CC1OC(C2=CC=CC=C2O[Si](C)(C)C)=NC1C(=O)O	standard non polar	2025-10-23	2031.79
Gas Chromatography	Vulnibactin 2_TMS_3	CC1OC(C2=CC=CC=C2O[Si](C)(C)C)=NC1C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1672.97
Gas Chromatography	Vulnibactin 2_TMS_1	CC1OC(C2=CC=CC=C2O)=NC1C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1648.52
Gas Chromatography	Vulnibactin 2_TMS_2	CC1OC(C2=CC=CC=C2O[Si](C)(C)C)=NC1C(=O)O	standard polar	2025-10-23	1945.48
Gas Chromatography	Vulnibactin 2_TMS_3	CC1OC(C2=CC=CC=C2O[Si](C)(C)C)=NC1C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1730.32

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	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

78434767

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

136444984

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 Vulnibactin 2 (MMDBc0007118)

MOL for #<Metabolite:0x00007f2e082fbad8>

3D MOL for #<Metabolite:0x00007f2e082fbad8>

3D SDF for #<Metabolite:0x00007f2e082fbad8>

3D-SDF for #<Metabolite:0x00007f2e082fbad8>

PDB for #<Metabolite:0x00007f2e082fbad8>

3D PDB for #<Metabolite:0x00007f2e082fbad8>

SMILES for #<Metabolite:0x00007f2e082fbad8>

INCHI for #<Metabolite:0x00007f2e082fbad8>

Structure for #<Metabolite:0x00007f2e082fbad8>

3D Structure for #<Metabolite:0x00007f2e082fbad8>