MiMeDB: Showing metabocard for Fe(III)dicitrate (MMDBc0031611)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:41:21 UTC

Update Date

2022-08-31 18:22:29 UTC

Metabolite ID

MMDBc0031611

Metabolite Identification

Common Name

Fe(III)dicitrate

Description

Fe(iii)dicitrate is the complex formed between iron(III) and citrate. It is a substrate for the E. coli transport protein known as FecA. FecA is the outer membrane receptor protein in the Fe3+ dicitrate transport system.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 07301213352D          

 27 24  0  0  0  0            999 V2000
    0.3654    0.3235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0635   -0.8034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3654    1.1485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8885   -0.8034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0635   -0.5015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3490   -0.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3490    1.5610    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0799    1.5610    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3010   -0.0890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3010   -1.5179    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0635   -1.3265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7780   -0.0890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7615    0.6255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5658    0.3235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2638   -0.8034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5658    1.1485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0888   -0.8034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1369   -0.5015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8513   -0.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8513    1.5610    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2803    1.5610    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5013   -0.0890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5013   -1.5179    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1369   -1.3265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4224   -0.0890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4388    0.6255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.1679    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  1  1  0  0  0  0
  6  2  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  5  1  0  0  0  0
 13  6  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 19 14  1  0  0  0  0
 19 15  1  0  0  0  0
 19 18  1  0  0  0  0
 20 16  1  0  0  0  0
 21 16  1  0  0  0  0
 22 17  1  0  0  0  0
 23 17  1  0  0  0  0
 24 18  1  0  0  0  0
 25 18  1  0  0  0  0
 26 19  1  0  0  0  0
M  END


  Mrv0541 07301213352D          

 27 24  0  0  0  0            999 V2000
    0.3654    0.3235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0635   -0.8034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3654    1.1485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8885   -0.8034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0635   -0.5015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3490   -0.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3490    1.5610    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0799    1.5610    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3010   -0.0890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3010   -1.5179    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0635   -1.3265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7780   -0.0890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7615    0.6255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5658    0.3235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2638   -0.8034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5658    1.1485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0888   -0.8034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1369   -0.5015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8513   -0.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8513    1.5610    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2803    1.5610    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5013   -0.0890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5013   -1.5179    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1369   -1.3265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4224   -0.0890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4388    0.6255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.1679    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  1  1  0  0  0  0
  6  2  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  5  1  0  0  0  0
 13  6  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 19 14  1  0  0  0  0
 19 15  1  0  0  0  0
 19 18  1  0  0  0  0
 20 16  1  0  0  0  0
 21 16  1  0  0  0  0
 22 17  1  0  0  0  0
 23 17  1  0  0  0  0
 24 18  1  0  0  0  0
 25 18  1  0  0  0  0
 26 19  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031611

> <DATABASE_NAME>
MIME

> <SMILES>
[Fe].OC(O)CC(O)(CC(O)O)C(O)O.OC(O)CC(O)(CC(O)O)C(O)O

> <INCHI_IDENTIFIER>
InChI=1S/2C6H14O7.Fe/c2*7-3(8)1-6(13,5(11)12)2-4(9)10;/h2*3-5,7-13H,1-2H2;

> <INCHI_KEY>
BWHIDISYXGEZJU-UHFFFAOYSA-N

> <FORMULA>
C12H28FeO14

> <MOLECULAR_WEIGHT>
452.187

> <EXACT_MASS>
452.082847737

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.47273018862575

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
bis(3-(dihydroxymethyl)pentane-1,1,3,5,5-pentol) iron

> <JCHEM_LOGP>
-3.157412904

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.142894692965799

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.130197835632575

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7782423417763242

> <JCHEM_POLAR_SURFACE_AREA>
141.61

> <JCHEM_REFRACTIVITY>
38.69129999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
bis(3-(dihydroxymethyl)pentane-1,1,3,5,5-pentol) iron

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-JUL-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27 Fe   UNK     0       0.000   0.000   0.000  0.00  0.00          Fe+0
CONECT    1    3    6                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7    8                                                  
CONECT    4    2    9   10                                                  
CONECT    5    6   11   12                                                  
CONECT    6    1    2    5   13                                             
CONECT    7    3                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    5                                                            
CONECT   13    6                                                            
CONECT   14   16   19                                                       
CONECT   15   17   19                                                       
CONECT   16   14   20   21                                                  
CONECT   17   15   22   23                                                  
CONECT   18   19   24   25                                                  
CONECT   19   14   15   18   26                                             
CONECT   20   16                                                            
CONECT   21   16                                                            
CONECT   22   17                                                            
CONECT   23   17                                                            
CONECT   24   18                                                            
CONECT   25   18                                                            
CONECT   26   19                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   48    0
END

Synonyms

Value	Source
Fe(III)dicitric acid	Generator

Molecular Formula

C₁₂H₂₈FeO₁₄

Average Mass

452.187

Monoisotopic Mass

452.082847737

IUPAC Name

bis(3-(dihydroxymethyl)pentane-1,1,3,5,5-pentol) iron

Traditional Name

bis(3-(dihydroxymethyl)pentane-1,1,3,5,5-pentol) iron

CAS Registry Number

Not Available

SMILES

[Fe].OC(O)CC(O)(CC(O)O)C(O)O.OC(O)CC(O)(CC(O)O)C(O)O

InChI Identifier

InChI=1S/2C6H14O7.Fe/c2*7-3(8)1-6(13,5(11)12)2-4(9)10;/h2*3-5,7-13H,1-2H2;

InChI Key

BWHIDISYXGEZJU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar alcohols

Alternative Parents

Substituents

Sugar alcohol
Tertiary alcohol
Organic transition metal salt
1,1-diol
Polyol
Carbonyl hydrate
Hydrocarbon derivative
Organic salt
Alcohol
Aliphatic acyclic compound

Molecular Framework

Not Available

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.2	ChemAxon
pKa (Strongest Acidic)	11.13	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	141.61 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	38.69 m³·mol⁻¹	ChemAxon
Polarizability	17.47 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_6_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0000900000-2520f3b30a5864d90710	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0000900000-2520f3b30a5864d90710	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0000900000-2520f3b30a5864d90710	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0000900000-acb20658066243e1a640	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-0000900000-acb20658066243e1a640	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0udi-0000900000-acb20658066243e1a640	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

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

Metabolic Reactions

Not Available

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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	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

440954

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS: ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. [PubMed:26481353 ]

Showing metabocard for Fe(III)dicitrate (MMDBc0031611)

MOL for #<Metabolite:0x00007fecec366c18>

3D MOL for #<Metabolite:0x00007fecec366c18>

3D SDF for #<Metabolite:0x00007fecec366c18>

3D-SDF for #<Metabolite:0x00007fecec366c18>

PDB for #<Metabolite:0x00007fecec366c18>

3D PDB for #<Metabolite:0x00007fecec366c18>

SMILES for #<Metabolite:0x00007fecec366c18>

INCHI for #<Metabolite:0x00007fecec366c18>

Structure for #<Metabolite:0x00007fecec366c18>

3D Structure for #<Metabolite:0x00007fecec366c18>