MiMeDB: Showing metabocard for Vibrioferrin (MMDBc0024570)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 14:22:07 UTC

Update Date

2025-10-07 16:07:28 UTC

Metabolite ID

MMDBc0024570

Metabolite Identification

Common Name

Vibrioferrin

Description

Vibrioferrin is a carboxylate class siderophore produced by certain bacteria, notably Vibrio parahaemolyticus and Photobacterium damselae subsp. It plays a crucial role in iron acquisition, which is essential for bacterial growth and metabolism, particularly in iron-limited environments. The chemical structure of vibrioferrin consists of a complex arrangement of carboxylate groups that facilitate the chelation of iron ions, enabling the bacteria to effectively capture and transport iron. In Vibrio parahaemolyticus, the expression of genes involved in vibrioferrin utilization is regulated by the iron-responsive repressor Fur and the small RNA RyhB, highlighting its importance in iron homeostasis (PMID:40024720 ). Additionally, metagenomic analyses have shown that genes involved in the biosynthesis of vibrioferrin are more abundant in certain environmental conditions, such as the presence of glacial colloids (PMID:40980733 ). The synthesis of vibrioferrin is encoded by a novel genomic island, which allows marine pathogens to thrive in low-iron environments (PMID:39662786 ). Overall, vibrioferrin is integral to the survival and competitive advantage of bacteria in various ecological niches.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152116222D          

 31 31  0  0  1  0            999 V2000
   -1.0558    1.6913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8951    0.0352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6797    0.2901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2202    0.4805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6905   -0.5590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7723    1.0936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0775   -0.0070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7301   -1.0887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4752   -0.3041    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2820    0.5872    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5173    1.8783    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5792    0.9221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2490    0.8000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3259   -0.4747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1781   -1.7018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5371   -1.2602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8649    2.5120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9268    1.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2598   -0.0491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0157    1.7274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2928   -0.2619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6689    1.1392    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  5  4  1  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 15  6  1  1  0  0  0
 15  7  1  0  0  0  0
 15 13  1  0  0  0  0
 16  3  1  0  0  0  0
 16 14  1  0  0  0  0
 17  4  1  4  0  0  0
 17 12  2  0  0  0  0
 18  8  1  0  0  0  0
 18  9  1  0  0  0  0
 18 16  1  0  0  0  0
 19  9  2  0  0  0  0
 20 10  2  0  0  0  0
 21 10  1  0  0  0  0
 22 11  2  0  0  0  0
 23 12  1  0  0  0  0
 24 13  2  0  0  0  0
 25 13  1  0  0  0  0
 26 14  2  0  0  0  0
 27 14  1  0  0  0  0
 15 28  1  6  0  0  0
 29 16  1  0  0  0  0
 30  5  1  0  0  0  0
 30 11  1  0  0  0  0
  8 31  1  1  0  0  0
M  END


  Mrv1652305152116222D          

 31 31  0  0  1  0            999 V2000
   -1.0558    1.6913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8951    0.0352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6797    0.2901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2202    0.4805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6905   -0.5590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7723    1.0936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0775   -0.0070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7301   -1.0887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4752   -0.3041    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2820    0.5872    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5173    1.8783    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5792    0.9221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2490    0.8000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3259   -0.4747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1781   -1.7018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5371   -1.2602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8649    2.5120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9268    1.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2598   -0.0491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0157    1.7274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2928   -0.2619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6689    1.1392    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  5  4  1  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 15  6  1  1  0  0  0
 15  7  1  0  0  0  0
 15 13  1  0  0  0  0
 16  3  1  0  0  0  0
 16 14  1  0  0  0  0
 17  4  1  4  0  0  0
 17 12  2  0  0  0  0
 18  8  1  0  0  0  0
 18  9  1  0  0  0  0
 18 16  1  0  0  0  0
 19  9  2  0  0  0  0
 20 10  2  0  0  0  0
 21 10  1  0  0  0  0
 22 11  2  0  0  0  0
 23 12  1  0  0  0  0
 24 13  2  0  0  0  0
 25 13  1  0  0  0  0
 26 14  2  0  0  0  0
 27 14  1  0  0  0  0
 15 28  1  6  0  0  0
 29 16  1  0  0  0  0
 30  5  1  0  0  0  0
 30 11  1  0  0  0  0
  8 31  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0024570

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](C)(N1C(=O)CCC1(O)C(O)=O)C(O)=NCCOC(=O)C[C@](O)(CC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H22N2O12/c1-8(18-9(19)2-3-16(18,29)14(26)27)12(23)17-4-5-30-11(22)7-15(28,13(24)25)6-10(20)21/h8,28-29H,2-7H2,1H3,(H,17,23)(H,20,21)(H,24,25)(H,26,27)/t8-,15+,16?/m0/s1

> <INCHI_KEY>
IGQXNKDXMPSELX-BIAKFKOBSA-N

> <FORMULA>
C16H22N2O12

> <MOLECULAR_WEIGHT>
434.354

> <EXACT_MASS>
434.117274156

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
39.1286047215366

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-[2-(2-{[(2S)-2-(2-carboxy-2-hydroxy-5-oxopyrrolidin-1-yl)-1-hydroxypropylidene]amino}ethoxy)-2-oxoethyl]-2-hydroxybutanedioic acid

> <ALOGPS_LOGP>
-1.60

> <JCHEM_LOGP>
-3.0195062109521773

> <ALOGPS_LOGS>
-2.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.463746778242973

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.966974910735377

> <JCHEM_PKA_STRONGEST_BASIC>
2.339554356971613

> <JCHEM_POLAR_SURFACE_AREA>
231.55999999999995

> <JCHEM_REFRACTIVITY>
90.88039999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.20e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-[2-(2-{[(2S)-2-(2-carboxy-2-hydroxy-5-oxopyrrolidin-1-yl)-1-hydroxypropylidene]amino}ethoxy)-2-oxoethyl]-2-hydroxybutanedioic 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      -1.971   3.157   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.404   0.066   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.869   0.542   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -11.611   0.897   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -10.622  -1.043   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -12.642   2.041   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -9.478  -0.013   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.795   0.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -12.563  -2.032   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.090   3.224   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -12.087  -0.568   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -4.260   1.096   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0     -12.166   3.506   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0     -14.148   1.721   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -9.798   1.493   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -2.475  -0.886   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0     -11.532  -3.177   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0     -14.069  -2.352   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       1.614   4.689   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       3.597   2.904   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0     -13.552  -0.092   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.029   3.224   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -8.013  -0.489   0.000  0.00  0.00           O+0
HETATM   31  H   UNK     0      -3.115   2.127   0.000  0.00  0.00           H+0
CONECT    1    8                                                            
CONECT    2    3    9                                                       
CONECT    3    2   16                                                       
CONECT    4    5   17                                                       
CONECT    5    4   30                                                       
CONECT    6   10   15                                                       
CONECT    7   11   15                                                       
CONECT    8    1   12   18   31                                             
CONECT    9    2   18   19                                                  
CONECT   10    6   20   21                                                  
CONECT   11    7   22   30                                                  
CONECT   12    8   17   23                                                  
CONECT   13   15   24   25                                                  
CONECT   14   16   26   27                                                  
CONECT   15    6    7   13   28                                             
CONECT   16    3   14   18   29                                             
CONECT   17    4   12                                                       
CONECT   18    8    9   16                                                  
CONECT   19    9                                                            
CONECT   20   10                                                            
CONECT   21   10                                                            
CONECT   22   11                                                            
CONECT   23   12                                                            
CONECT   24   13                                                            
CONECT   25   13                                                            
CONECT   26   14                                                            
CONECT   27   14                                                            
CONECT   28   15                                                            
CONECT   29   16                                                            
CONECT   30    5   11                                                       
CONECT   31    8                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   62    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₂₂N₂O₁₂

Average Mass

434.354

Monoisotopic Mass

434.117274156

IUPAC Name

(2R)-2-[2-(2-{[(2S)-2-(2-carboxy-2-hydroxy-5-oxopyrrolidin-1-yl)-1-hydroxypropylidene]amino}ethoxy)-2-oxoethyl]-2-hydroxybutanedioic acid

Traditional Name

(2R)-2-[2-(2-{[(2S)-2-(2-carboxy-2-hydroxy-5-oxopyrrolidin-1-yl)-1-hydroxypropylidene]amino}ethoxy)-2-oxoethyl]-2-hydroxybutanedioic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(N1C(=O)CCC1(O)C(O)=O)C(O)=NCCOC(=O)C[C@](O)(CC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C16H22N2O12/c1-8(18-9(19)2-3-16(18,29)14(26)27)12(23)17-4-5-30-11(22)7-15(28,13(24)25)6-10(20)21/h8,28-29H,2-7H2,1H3,(H,17,23)(H,20,21)(H,24,25)(H,26,27)/t8-,15+,16?/m0/s1

InChI Key

IGQXNKDXMPSELX-BIAKFKOBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetracarboxylic acids and derivatives. These are carboxylic acids containing exactly four carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tetracarboxylic acids and derivatives

Direct Parent

Tetracarboxylic acids and derivatives

Alternative Parents

Substituents

Tetracarboxylic acid or derivatives
Alanine or derivatives
Alpha-amino acid or derivatives
Oxoproline
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Fatty acid ester
Alpha-hydroxy acid
Pyrrolidone
2-pyrrolidone
Hydroxy acid
N-alkylpyrrolidine
Fatty acyl
Tertiary alcohol
Tertiary carboxylic acid amide
Pyrrolidine
Secondary carboxylic acid amide
Carboxamide group
Lactam
Carboxylic acid ester
Alkanolamine
Carboxylic acid
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Alcohol
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

tertiary alcohol (CHEBI:84585 )
carboxylic ester (CHEBI:84585 )
tricarboxylic acid (CHEBI:84585 )
pyrrolidin-2-ones (CHEBI:84585 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.2 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-3	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	2.97	ChemAxon
pKa (Strongest Basic)	2.34	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	231.56 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	90.88 m³·mol⁻¹	ChemAxon
Polarizability	39.13 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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	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

C00029220

Chemspider ID

9277261

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11102119

PDB ID

Not Available

ChEBI ID

84585

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 Vibrioferrin (MMDBc0024570)

MOL for #<Metabolite:0x00007f8dc8012f68>

3D MOL for #<Metabolite:0x00007f8dc8012f68>

3D SDF for #<Metabolite:0x00007f8dc8012f68>

3D-SDF for #<Metabolite:0x00007f8dc8012f68>

PDB for #<Metabolite:0x00007f8dc8012f68>

3D PDB for #<Metabolite:0x00007f8dc8012f68>

SMILES for #<Metabolite:0x00007f8dc8012f68>

INCHI for #<Metabolite:0x00007f8dc8012f68>

Structure for #<Metabolite:0x00007f8dc8012f68>

3D Structure for #<Metabolite:0x00007f8dc8012f68>