MiMeDB: Showing metabocard for Iduronic acid (MMDBc0000218)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:40:10 UTC

Update Date

2024-04-30 19:31:32 UTC

Metabolite ID

MMDBc0000218

Metabolite Identification

Common Name

Iduronic acid

Description

Iduronic acid is a constituent of glycosaminoglycans heparin and heparan sulfate in varying proportions providing considerable diversity in sequence and biological function. The glycosaminoglycans (GAGs) are linear polysaccharides with alternating uronic acids (Iduronic acid and Glucuronic acid) and hexosamine residues, in which a limited set of monosaccharide units gives rise to a number of complex sequences by variable substitution with O-sulfate, N-sulfate, and N-acetyl groups. GAGs usually exist as the O-linked side-chains of proteoglycans, displaying a set of physiological functions which is remarkably wide and as yet incompletely explored. They may act as structural components of connective tissue and the extracellular matrix, or as specific ligands in the relationship between the cell surface and its surroundings. Heparan sulfate exists on the surface of most or all mammalian cells and can display a remarkable range of different sequence motifs; its range of interactions and possible functions reflect its structural complexity. The main repeat unit of heparin structurally resembles the protein binding sequences in heparan sulfate, but contains a higher percentage of sulfated residues. Utilized therapeutically as an anticoagulant and readily available in good quantities heparin serves as a useful model for heparan sulfate. Theoretical and experimental studies indicate that L-Iduronic acid residues of glycosaminoglycans are in equilibrium of different conformations, the relative proportion of conformers being a function of sulfation pattern and sequence. This unique conformational flexibility may provide an explanation for the stronger binding and associated higher biological activities of Iduronic acid-containing glycosaminoglycans (such as heparin, heparan sulfate and dermatan sulfate) as compared with other GAGs having similar charge density but with the more rigid glucuronic acid as the major uronic acid residue. Dermatan sulfates and heparins, which contain L-Iduronic acid in their backbone, show higher low-density lipoprotein (LDL)-affinity than chondroitin sulfates, which contain only D-glucuronic acid. Though confirming a non-specific, predominantly electrostatic interaction between GAGs and LDL, these results indicate modulation of LDL affinity by the polysaccharide backbone. Naturally oversulfated dermatan sulfate (SO3H/COOH ca. 1.2), mainly oversulfated at C-2 of Iduronic acid residues, show comparatively higher anticoagulant activity. (PMID: 3076283 , 8466951 , 8542607 , 11087707 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      34.538 -22.171   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      35.871 -18.320   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      33.204 -18.320   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      37.205 -22.171   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      30.536 -19.860   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      31.870 -22.171   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      38.539 -18.320   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      34.538 -20.631   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      35.871 -19.860   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      33.204 -19.860   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      37.205 -20.631   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      31.870 -20.631   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      38.539 -19.860   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   11                                                            
CONECT    5   12                                                            
CONECT    6   12                                                            
CONECT    7   13                                                            
CONECT    8    1    9   10                                                  
CONECT    9    2    8   11                                                  
CONECT   10    3    8   12                                                  
CONECT   11    4    9   13                                                  
CONECT   12    5    6   10                                                  
CONECT   13    7   11                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
Iduronate	Generator
L-Iduronate	HMDB
L-Iduronic acid	HMDB
Acid, iduronic	HMDB
(2S,3R,4R,5S)-2,3,4,5-Tetrahydroxy-6-oxohexanoate	HMDB
Iduronic acid	MeSH

Molecular Formula

C₆H₁₀O₇

Average Mass

194.1394

Monoisotopic Mass

194.042652674

IUPAC Name

(2S,3R,4R,5S)-2,3,4,5-tetrahydroxy-6-oxohexanoic acid

Traditional Name

iduronic acid

CAS Registry Number

3402-98-0

SMILES

O[C@H](C=O)[C@H](O)[C@@H](O)[C@H](O)C(O)=O

InChI Identifier

InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h1-5,8-11H,(H,12,13)/t2-,3+,4-,5+/m1/s1

InChI Key

IAJILQKETJEXLJ-LECHCGJUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glucuronic acid derivatives. Glucuronic acid derivatives are compounds containing a glucuronic acid moiety (or a derivative), which consists of a glucose moiety with the C6 carbon oxidized to a carboxylic acid.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glucuronic acid derivatives

Alternative Parents

Substituents

Glucuronic acid or derivatives
Hexose monosaccharide
Medium-chain hydroxy acid
Medium-chain fatty acid
Beta-hydroxy acid
Hydroxy fatty acid
Monosaccharide
Fatty acyl
Hydroxy acid
Fatty acid
Alpha-hydroxy acid
Beta-hydroxy aldehyde
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Aldehyde
Carbonyl group
Alcohol
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	100 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-3.2	ChemAxon
logS	-0.29	ALOGPS
pKa (Strongest Acidic)	3.24	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	135.29 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	37.21 m³·mol⁻¹	ChemAxon
Polarizability	16.1 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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 (Non-derivatized) - 70eV, Positive	splash10-000i-9700000000-cdaf9f94e02e4e7ba7d2	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positive	splash10-009i-4212940000-02a8091c226f3a41d70e	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-056s-2900000000-86606b8382ffe403bc8e	2016-08-02	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-9500000000-af67bc97552641417bee	2016-08-02	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9100000000-205a7cff1e298283a080	2016-08-02	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-05p9-9700000000-ee070fab487c9f3e49b7	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4r-9400000000-284825e422ba9585f17b	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9100000000-64d4f9d758e2a4eeba68	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00fr-9300000000-77aa1619935fe785e397	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a6r-9000000000-da4be7e32a829503c021	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a6r-9000000000-c1c9308cd925f43d015f	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01y5-7900000000-df218a4e340a0ff668c1	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03kl-9100000000-d22d4d2644d77203331d	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08fu-9000000000-93301767b758d212114f	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Lysosome

Biospecimen Locations

Blood
Feces
Fibroblasts
Urine

Tissue Locations

Fibroblasts

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192008	Heparan sulfate glucosamine 3-O-sulfotransferase 3B1	Enzyme	Q9Y662	Homo sapiens
MMDBp0192009	Heparan sulfate glucosamine 3-O-sulfotransferase 3A1	Enzyme	Q9Y663	Homo sapiens
MMDBp0192017	Heparan sulfate glucosamine 3-O-sulfotransferase 4	Enzyme	Q9Y661	Homo sapiens
MMDBp0192020	Heparan sulfate glucosamine 3-O-sulfotransferase 2	Enzyme	Q9Y278	Homo sapiens
MMDBp0192118	UDP-glucuronosyltransferase 2B4	Enzyme	P06133	Homo sapiens
MMDBp0192135	UDP-glucuronosyltransferase 1-4	Enzyme	P22310	Homo sapiens
MMDBp0192137	UDP-glucuronosyltransferase 2B7	Enzyme	P16662	Homo sapiens
MMDBp0192140	UDP-glucuronosyltransferase 1-1	Enzyme	P22309	Homo sapiens
MMDBp0192141	UDP-glucuronosyltransferase 1-9	Enzyme	O60656	Homo sapiens
MMDBp0192146	UDP-glucuronosyltransferase 1-6	Enzyme	P19224	Homo sapiens
MMDBp0193146	Alpha-L-iduronidase	Enzyme	P35475	Homo sapiens
MMDBp0193585	Carbohydrate sulfotransferase 14	Enzyme	Q8NCH0	Homo sapiens
MMDBp0195882	Dermatan-sulfate epimerase	Enzyme	Q9UL01	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0001500	Hydrogen Ion	Hydrogen Ion	Solute carrier family 17 (acidic sugar transporter), member 5	Transport of Iduronate, Lysososmal	VMH	10581036 2768261 9852127
MMDBr0005560	Iduronic acid	Iduronic acid	Not Available	Transport of L-Iduronate	VMH	30371894

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	Bacteroidetes	6	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	1	Human feces	Metabolic reconstruction
Bacteria	Proteobacteria	1	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified							HMDB
Human Urine	Detected and Quantified	0.017	0.15	umol/mmol creatinine	Adult (>18 years old)	Not Specified	Normal	HMDB	T. TOIDA, G. QIU, T. MATSUNAGA, Y. SAGEHASHI and T. IMANARI. Gas Chromatography-Mass Spectrometric Determinations of Iduronic and Glucuronic Acids in Glycosaminoglycans after Reduction of Carboxylic Group Using Sodium Borodeuteride, Analytical Sciences, 1992, 8(6), 799.
Human Fibroblasts	Detected but not Quantified				Not Specified	Not Specified	Normal	HMDB	34986597
Human Blood	Detected but not Quantified							HMDB

External Links

HMDB ID

HMDB0002704

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023047

KNApSAcK ID

Not Available

Chemspider ID

17794

KEGG Compound ID

C06472

BioCyc ID

Not Available

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

24769

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Ginsberg LC, Di Ferrante DT, Di Ferrante N: A substrate for direct measurement of L-iduronic acid 2-sulfate sulfatase. Carbohydr Res. 1978 Jul;64:225-35. doi: 10.1016/s0008-6215(00)83703-9. [PubMed:98232 ]
Casu B, Petitou M, Provasoli M, Sinay P: Conformational flexibility: a new concept for explaining binding and biological properties of iduronic acid-containing glycosaminoglycans. Trends Biochem Sci. 1988 Jun;13(6):221-5. doi: 10.1016/0968-0004(88)90088-6. [PubMed:3076283 ]
Inoue H, Otsu K, Suzuki S, Nakanishi Y: Difference between N-acetylgalactosamine 4-sulfate 6-O-sulfotransferases from human serum and squid cartilage in specificity toward the terminal and interior portion of chondroitin sulfate. J Biol Chem. 1986 Apr 5;261(10):4470-5. [PubMed:3082866 ]
Gigli M, Ghiselli G, Torri G, Naggi A, Rizzo V: A comparative study of low-density lipoprotein interaction with glycosaminoglycans. Biochim Biophys Acta. 1993 Apr 7;1167(2):211-7. doi: 10.1016/0005-2760(93)90164-5. [PubMed:8466951 ]
Bartolucci C, Cellai L, Iannelli MA, Lamba D, Liverani L, Mascellani G, Perola E: Inhibition of human leukocyte elastase by chemically and naturally oversulfated galactosaminoglycans. Carbohydr Res. 1995 Oct 23;276(2):401-8. doi: 10.1016/0008-6215(95)00179-w. [PubMed:8542607 ]
Mulloy B, Forster MJ: Conformation and dynamics of heparin and heparan sulfate. Glycobiology. 2000 Nov;10(11):1147-56. doi: 10.1093/glycob/10.11.1147. [PubMed:11087707 ]
Cheng F, Petersson P, Arroyo-Yanguas Y, Westergren-Thorsson G: Differences in the uptake and nuclear localization of anti-proliferative heparan sulfate between human lung fibroblasts and human lung carcinoma cells. J Cell Biochem. 2001;83(4):597-606. doi: 10.1002/jcb.1254. [PubMed:11746503 ]
Fuller M, Meikle PJ, Hopwood JJ: Glycosaminoglycan degradation fragments in mucopolysaccharidosis I. Glycobiology. 2004 May;14(5):443-50. doi: 10.1093/glycob/cwh049. Epub 2004 Jan 12. [PubMed:14718373 ]

Showing metabocard for Iduronic acid (MMDBc0000218)

MOL for #<Metabolite:0x00007fa4b5697ad8>

3D MOL for #<Metabolite:0x00007fa4b5697ad8>

3D SDF for #<Metabolite:0x00007fa4b5697ad8>

3D-SDF for #<Metabolite:0x00007fa4b5697ad8>

PDB for #<Metabolite:0x00007fa4b5697ad8>

3D PDB for #<Metabolite:0x00007fa4b5697ad8>

SMILES for #<Metabolite:0x00007fa4b5697ad8>

INCHI for #<Metabolite:0x00007fa4b5697ad8>

Structure for #<Metabolite:0x00007fa4b5697ad8>

3D Structure for #<Metabolite:0x00007fa4b5697ad8>