Human Metabolome Database Version 3.5

Showing metabocard for Heparan sulfate (HMDB00693)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-01-28 19:27:25 -0700
Secondary Accession Numbers None
Metabolite Identification
Common Name Heparan sulfate
Description Heparan sulfate is a heteropolysaccharide that is similar in structure to heparin. It accumulates in individuals with mucopolysaccharidosis. Heparan sulfate (HS) is a linear polysaccharide found in all animal tissues. It occurs as a proteoglycan (PG) in which two or three HS chains are attached in close proximity to cell suface or extracellular matrix proteins.[1][2] It is in this form that HS binds to a variety of protein ligands and regulates a wide variety of biological activities, including developmental processes, angiogenesis, blood coagulation and tumour metastasis. (Wikipedia).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
  1. alpha-Idosane
  2. Heparan N-sulfate
  3. Heparan N-sulphate
  4. Heparan sulfate
  5. Heparan sulphate
  6. Heparatan sulfate
  7. Heparatan sulphate
  8. Heparitin
  9. Heparitin monosulfate
  10. Heparitin monosulphate
  11. Heparitin sulfate
  12. Heparitin sulphate
  13. HHS 5
  14. N-Acetylheparan sulfate
  15. N-Acetylheparan sulphate
  16. Suleparoid
  17. Tavidan
Chemical Formula C14H23NO21S3
Average Molecular Weight 637.522
Monoisotopic Molecular Weight 636.992468873
IUPAC Name (2S,3R,4R,5S,6R)-4-hydroxy-3-methoxy-6-{[(2S,3R,4S,5S,6R)-6-methoxy-4-oxido-5-[(sulfooxy)amino]-2-[(sulfooxy)methyl]oxan-3-yl]oxy}-5-(sulfooxy)oxane-2-carboxylate
Traditional IUPAC Name (2S,3R,4R,5S,6R)-4-hydroxy-3-methoxy-6-{[(2S,3R,4S,5S,6R)-6-methoxy-4-oxido-5-[(sulfooxy)amino]-2-[(sulfooxy)methyl]oxan-3-yl]oxy}-5-(sulfooxy)oxane-2-carboxylate
CAS Registry Number 9050-30-0
SMILES Not Available
InChI Identifier InChI=1S/C14H24NO21S3/c1-29-9-7(17)10(35-38(23,24)25)14(34-11(9)12(18)19)33-8-4(3-31-37(20,21)22)32-13(30-2)5(6(8)16)15-36-39(26,27)28/h4-11,13-15,17H,3H2,1-2H3,(H,18,19)(H,20,21,22)(H,23,24,25)(H,26,27,28)/q-1/p-1/t4-,5-,6-,7+,8-,9+,10-,11-,13+,14+/m0/s1
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Carbohydrates and Carbohydrate Conjugates
Class Disaccharides
Sub Class Dihexoses
Other Descriptors
  • Aliphatic Heteropolycyclic Compounds
  • Acetal
  • Carboxylic Acid Salt
  • Dialkyl Ether
  • Glucosamine
  • Glucuronic Acid Or Derivative
  • Glucuronide
  • Glycosyl Compound
  • Mannosamine
  • O Glycosyl Compound
  • Organic Hydroxylamine
  • Organic Hyponitrite
  • Organic Sulfuric Acid
  • Organic Sulfuric Acid Monoester
  • Oxane
  • Secondary Alcohol
  • Sugar Acid
  • Sulfate Ester
Direct Parent Dihexoses
Status Detected and Quantified
  • Endogenous
Biofunction Not Available
Application Not Available
Cellular locations Not Available
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
LogP -8.1 ChemAxon
Hydrogen Acceptor Count 19 ChemAxon
Hydrogen Donor Count 5 ChemAxon
Polar Surface Area 332.4 A2 ChemAxon
Rotatable Bond Count 13 ChemAxon
Refractivity 142.98 ChemAxon
Polarizability 52.51 ChemAxon
Formal Charge -2 ChemAxon
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations Not Available
Biofluid Locations
  • Blood
Tissue Location
  • Muscle
  • Skeletal Muscle
  • Fibroblasts
  • Intestine
  • Neuron
  • Pancreas
  • Placenta
  • Testes
  • Kidney
  • Liver
  • Epidermis
  • Nerve Cells
  • Platelet
  • Spleen
  • Uterus
Pathways Not Available
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
0.5 (0.0-1.0) uM Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 2.6 (1.4-6.1) uM Adult (>18 years old) Both Liver disease with gastrointestinal bleeding
Associated Disorders and Diseases
Disease References
Liver disease
  • McKee RF, Hodson S, Dawes J, Garden OJ, Carter DC: Plasma concentrations of endogenous heparinoids in portal hypertension. Gut. 1992 Nov;33(11):1549-52. Pubmed: 1452082 Link_out
      Associated OMIM IDs None
      DrugBank ID Not Available
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB022184
      KNApSAcK ID Not Available
      Chemspider ID Not Available
      KEGG Compound ID C00925 Link_out
      BioCyc ID CPD-7177 Link_out
      BiGG ID Not Available
      Wikipedia Link Heparan sulfate Link_out
      NuGOwiki Link HMDB00693 Link_out
      Metagene Link HMDB00693 Link_out
      METLIN ID Not Available
      PubChem Compound 53477714 Link_out
      PDB ID Not Available
      ChEBI ID Not Available
      Synthesis Reference Meier, Bernd Horst; Meier, Nele. Manufacture and use of modified adducts of polysaccharides and chitosan or chitin and a process to improve the preparation of polysaccharide-drug conjugates. PCT Int. Appl. (2007), 67pp. CODEN: PIXXD2 WO 2007122269 A1 20071101 CAN 147:487869 AN 2007:1237349
      Material Safety Data Sheet (MSDS) Download (PDF)
      General References
      1. Inoue H, Otsu K, Yoneda M, Kimata K, Suzuki S, Nakanishi Y: Glycosaminoglycan sulfotransferases in human and animal sera. J Biol Chem. 1986 Apr 5;261(10):4460-9. Pubmed: 3457007 Link_out
      2. Nader HB, Lopes CC, Rocha HA, Santos EA, Dietrich CP: Heparins and heparinoids: occurrence, structure and mechanism of antithrombotic and hemorrhagic activities. Curr Pharm Des. 2004;10(9):951-66. Pubmed: 15078126 Link_out
      3. Henriquez JP, Casar JC, Fuentealba L, Carey DJ, Brandan E: Extracellular matrix histone H1 binds to perlecan, is present in regenerating skeletal muscle and stimulates myoblast proliferation. J Cell Sci. 2002 May 15;115(Pt 10):2041-51. Pubmed: 11973346 Link_out
      4. Hjelm Cluff A, Malmstrom A, Tingaker B, David G, Ekman-Ordeberg G: Normal labor associated with changes in uterine heparan sulfate proteoglycan expression and localization. Acta Obstet Gynecol Scand. 2005 Mar;84(3):217-24. Pubmed: 15715528 Link_out
      5. Yu WH, Yu S, Meng Q, Brew K, Woessner JF Jr: TIMP-3 binds to sulfated glycosaminoglycans of the extracellular matrix. J Biol Chem. 2000 Oct 6;275(40):31226-32. Pubmed: 10900194 Link_out
      6. Subramanian G, LeBlanc RA, Wardley RC, Fuller AO: Defective entry of herpes simplex virus types 1 and 2 into porcine cells and lack of infection in infant pigs indicate species tropism. J Gen Virol. 1995 Sep;76 ( Pt 9):2375-9. Pubmed: 7561780 Link_out
      7. Jenniskens GJ, Veerkamp JH, van Kuppevelt TH: Heparan sulfates in skeletal muscle development and physiology. J Cell Physiol. 2006 Feb;206(2):283-94. Pubmed: 15991249 Link_out
      8. Maeda T, Alexander CM, Friedl A: Induction of syndecan-1 expression in stromal fibroblasts promotes proliferation of human breast cancer cells. Cancer Res. 2004 Jan 15;64(2):612-21. Pubmed: 14744776 Link_out
      9. Sher I, Zisman-Rozen S, Eliahu L, Whitelock JM, Maas-Szabowski N, Yamada Y, Breitkreutz D, Fusenig NE, Arikawa-Hirasawa E, Iozzo RV, Bergman R, Ron D: Targeting perlecan in human keratinocytes reveals novel roles for perlecan in epidermal formation. J Biol Chem. 2006 Feb 24;281(8):5178-87. Epub 2005 Nov 2. Pubmed: 16269412 Link_out
      10. Savas PS, Hemsley KM, Hopwood JJ: Intracerebral injection of sulfamidase delays neuropathology in murine MPS-IIIA. Mol Genet Metab. 2004 Aug;82(4):273-85. Pubmed: 15308125 Link_out
      11. Chernousov MA, Rothblum K, Tyler WA, Stahl RC, Carey DJ: Schwann cells synthesize type V collagen that contains a novel alpha 4 chain. Molecular cloning, biochemical characterization, and high affinity heparin binding of alpha 4(V) collagen. J Biol Chem. 2000 Sep 8;275(36):28208-15. Pubmed: 10852920 Link_out
      12. Chikama S, Iida S, Inoue M, Kawagoe N, Tomiyasu K, Matsuoka K, Noda S, Takazono I: Role of heparan sulfate proteoglycan (syndecan-1) on the renal epithelial cells during calcium oxalate monohydrate crystal attachment. Kurume Med J. 2002;49(4):201-10. Pubmed: 12652971 Link_out
      13. Kosir MA, Foley-Loudon PA, Finkenauer R, Tennenberg SD: Multiple heparanases are expressed in polymorphonuclear cells. J Surg Res. 2002 Mar;103(1):100-8. Pubmed: 11855924 Link_out
      14. Myette JR, Shriver Z, Liu J, Venkataraman G, Rosenberg R, Sasisekharan R: Expression in Escherichia coli, purification and kinetic characterization of human heparan sulfate 3-O-sulfotransferase-1. Biochem Biophys Res Commun. 2002 Feb 1;290(4):1206-13. Pubmed: 11811991 Link_out
      15. Barnett MW, Fisher CE, Perona-Wright G, Davies JA: Signalling by glial cell line-derived neurotrophic factor (GDNF) requires heparan sulphate glycosaminoglycan. J Cell Sci. 2002 Dec 1;115(Pt 23):4495-503. Pubmed: 12414995 Link_out
      16. Wasserman L, Abramovici A, Shlesinger H, Goldman JA, Allalouf D: Histochemical localization of acidic glycosaminoglycans in normal human placentae. Placenta. 1983 Jan-Apr;4(1):101-8. Pubmed: 6406996 Link_out
      17. Haimov-Kochman R, Friedmann Y, Prus D, Goldman-Wohl DS, Greenfield C, Anteby EY, Aviv A, Vlodavsky I, Yagel S: Localization of heparanase in normal and pathological human placenta. Mol Hum Reprod. 2002 Jun;8(6):566-73. Pubmed: 12029075 Link_out
      18. Dempsey LA, Plummer TB, Coombes SL, Platt JL: Heparanase expression in invasive trophoblasts and acute vascular damage. Glycobiology. 2000 May;10(5):467-75. Pubmed: 10764835 Link_out
      19. Leu SJ, Chen N, Chen CC, Todorovic V, Bai T, Juric V, Liu Y, Yan G, Lam SC, Lau LF: Targeted mutagenesis of the angiogenic protein CCN1 (CYR61). Selective inactivation of integrin alpha6beta1-heparan sulfate proteoglycan coreceptor-mediated cellular functions. J Biol Chem. 2004 Oct 15;279(42):44177-87. Epub 2004 Aug 17. Pubmed: 15322081 Link_out
      20. Lensen JF, Rops AL, Wijnhoven TJ, Hafmans T, Feitz WF, Oosterwijk E, Banas B, Bindels RJ, van den Heuvel LP, van der Vlag J, Berden JH, van Kuppevelt TH: Localization and functional characterization of glycosaminoglycan domains in the normal human kidney as revealed by phage display-derived single chain antibodies. J Am Soc Nephrol. 2005 May;16(5):1279-88. Epub 2005 Mar 23. Pubmed: 15788473 Link_out

      Name: UDP-glucuronosyltransferase 2B4
      Reactions: Not Available
      Gene Name: UGT2B4
      Uniprot ID: P06133 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: UDP-glucuronosyltransferase 1-4
      Reactions: Not Available
      Gene Name: UGT1A4
      Uniprot ID: P22310 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: UDP-glucuronosyltransferase 2B7
      Reactions: Not Available
      Gene Name: UGT2B7
      Uniprot ID: P16662 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: UDP-glucuronosyltransferase 1-1
      Reactions: Not Available
      Gene Name: UGT1A1
      Uniprot ID: P22309 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: UDP-glucuronosyltransferase 1-9
      Reactions: Not Available
      Gene Name: UGT1A9
      Uniprot ID: O60656 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: UDP-glucuronosyltransferase 1-6
      Reactions: Not Available
      Gene Name: UGT1A6
      Uniprot ID: P19224 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3
      Reactions: Not Available
      Gene Name: B3GAT3
      Uniprot ID: O94766 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Iduronate 2-sulfatase
      Reactions: Not Available
      Gene Name: IDS
      Uniprot ID: P22304 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Basement membrane-specific heparan sulfate proteoglycan core protein
      Reactions: Not Available
      Gene Name: HSPG2
      Uniprot ID: P98160 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Syndecan-1
      Reactions: Not Available
      Gene Name: SDC1
      Uniprot ID: P18827 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Syndecan-4
      Reactions: Not Available
      Gene Name: SDC4
      Uniprot ID: P31431 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Beta-1,3-galactosyltransferase 6
      Reactions: Not Available
      Gene Name: B3GALT6
      Uniprot ID: Q96L58 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Syndecan-2
      Reactions: Not Available
      Gene Name: SDC2
      Uniprot ID: P34741 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA