Bovine Metabolome Database: Showing metabocard for Heparan sulfate (BMDB0000693)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (10) Show 10 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:35:00 UTC

Update Date

2020-05-11 20:55:08 UTC

BMDB ID

BMDB0000693

Secondary Accession Numbers

BMDB00693

Metabolite Identification

Common Name

Heparan sulfate

Description

Heparan sulfate, also known as heparitin or alpha-idosane, belongs to the class of organic compounds known as disaccharide sulfates. These are disaccharides carrying one or more sulfate group on a sugar unit. Based on a literature review a significant number of articles have been published on Heparan sulfate.

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
Heparan sulfuric acid	Generator
Heparan sulphate	Generator
Heparan sulphuric acid	Generator
alpha-Idosane	HMDB
Heparan N-sulfate	HMDB
Heparan N-sulphate	HMDB
Heparatan sulfate	HMDB
Heparatan sulphate	HMDB
Heparitin	HMDB
Heparitin monosulfate	HMDB
Heparitin monosulphate	HMDB
Heparitin sulfate	HMDB
Heparitin sulphate	HMDB
HHS 5	HMDB
N-Acetylheparan sulfate	HMDB
N-Acetylheparan sulphate	HMDB
Suleparoid	HMDB
Tavidan	HMDB
(2S,3R,4R,5S,6R)-4-Hydroxy-6-{[(2S,3R,4S,5S,6R)-4-hydroxy-6-methoxy-5-[(sulfooxy)amino]-2-[(sulfooxy)methyl]oxan-3-yl]oxy}-3-methoxy-5-(sulfooxy)oxane-2-carboxylate	HMDB
(2S,3R,4R,5S,6R)-4-Hydroxy-6-{[(2S,3R,4S,5S,6R)-4-hydroxy-6-methoxy-5-[(sulphooxy)amino]-2-[(sulphooxy)methyl]oxan-3-yl]oxy}-3-methoxy-5-(sulphooxy)oxane-2-carboxylate	HMDB
(2S,3R,4R,5S,6R)-4-Hydroxy-6-{[(2S,3R,4S,5S,6R)-4-hydroxy-6-methoxy-5-[(sulphooxy)amino]-2-[(sulphooxy)methyl]oxan-3-yl]oxy}-3-methoxy-5-(sulphooxy)oxane-2-carboxylic acid	HMDB

Chemical Formula

C₁₄H₂₅NO₂₁S₃

Average Molecular Weight

639.52

Monoisotopic Molecular Weight

639.008120351

IUPAC Name

(2S,3R,4R,5S,6R)-4-hydroxy-6-{[(2S,3R,4S,5S,6R)-4-hydroxy-6-methoxy-5-[(sulfooxy)amino]-2-[(sulfooxy)methyl]oxan-3-yl]oxy}-3-methoxy-5-(sulfooxy)oxane-2-carboxylic acid

Traditional Name

(2S,3R,4R,5S,6R)-4-hydroxy-6-{[(2S,3R,4S,5S,6R)-4-hydroxy-6-methoxy-5-[(sulfooxy)amino]-2-[(sulfooxy)methyl]oxan-3-yl]oxy}-3-methoxy-5-(sulfooxy)oxane-2-carboxylic acid

CAS Registry Number

9050-30-0

SMILES

CO[C@@H]1O[C@@H](COS(O)(=O)=O)[C@H](O[C@@H]2O[C@@H]([C@H](OC)[C@@H](O)[C@@H]2OS(O)(=O)=O)C(O)=O)[C@@H](O)[C@@H]1NOS(O)(=O)=O

InChI Identifier

InChI=1S/C14H25NO21S3/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/h4-11,13-17H,3H2,1-2H3,(H,18,19)(H,20,21,22)(H,23,24,25)(H,26,27,28)/t4-,5-,6-,7+,8-,9+,10-,11-,13+,14+/m0/s1

InChI Key

AUQASCCBXZRMEG-RHKLHVFKSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as disaccharide sulfates. These are disaccharides carrying one or more sulfate group on a sugar unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Disaccharide sulfates

Alternative Parents

Substituents

Disaccharide sulfate
1-o-glucuronide
O-glucuronide
Glucuronic acid or derivatives
Glycosyl compound
O-glycosyl compound
Sulfuric acid ester
Alkyl sulfate
Sulfate-ester
Sulfuric acid monoester
Pyran
Oxane
Organic sulfuric acid or derivatives
Secondary alcohol
Acetal
Carboxylic acid derivative
Carboxylic acid
Dialkyl ether
Ether
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Alcohol
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Status

Expected but not Quantified

Origin

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	-2.2	ALOGPS
logP	-8.1	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	-3.3	ChemAxon
pKa (Strongest Basic)	1.99	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	326.74 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	121.6 m³·mol⁻¹	ChemAxon
Polarizability	52.51 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_16) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_17) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_18) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0kai-9400000000-404fa85a4342eafffaec	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-001i-9400000000-eec3b32ccab8e708c47b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-001i-9400000000-ad221bda41e892ec4944	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00dl-0029057000-552f350b2eda79515ae3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0fk9-1079141000-0b28aff1bbd9804b9bea	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-05fr-1394000000-5fa03687957fac5d0d21	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00kr-2923734000-0b76c8fcf07de6f623f2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-4903331000-2468d6710f7d484c4bc2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00xr-7901000000-aa930e030c48c4c24016	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0000019000-61194d75acd7b76eeb63	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000b-9380064000-507abf4005bb44c55d09	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0002-9232401000-8b2d59e928ea5f7d2bf8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-0000009000-37a3f7caf057b5f5103f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0006-3061394000-8c7732b97f391e56ce66	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0pb9-3291100000-baca1b5774273b60adc0	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Epidermis
Fibroblasts
Intestine
Kidney
Liver
Neuron
Pancreas
Placenta
Platelet
Skeletal Muscle
Spleen
Testis

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Pancreas	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Platelet	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Skeletal Muscle	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Testis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000693

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022184

KNApSAcK ID

Not Available

Chemspider ID

74854259

KEGG Compound ID

C00925

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Heparan sulfate

METLIN ID

Not Available

PubChem Compound

53477715

PDB ID

Not Available

ChEBI ID

Not Available

References

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)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. N-acetylglucosamine-6-sulfatase

General function:: Inorganic ion transport and metabolism
Specific function:: Not Available
Gene Name:: GNS
Uniprot ID:: Q1LZH9
Molecular weight:: 62776.0

Enzyme Details

2. Cartilage oligomeric matrix protein

General function:: Involved in calcium ion binding
Specific function:: May play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as the collagens and fibronectin. Can mediate the interaction of chondrocytes with the cartilage extracellular matrix through interaction with cell surface integrin receptors. Could play a role in the pathogenesis of osteoarthritis. Potent suppressor of apoptosis in both primary chondrocytes and transformed cells. Suppresses apoptosis by blocking the activation of caspase-3 and by inducing the IAP family of survival proteins (BIRC3, BIRC2, BIRC5 and XIAP). Essential for maintaining a vascular smooth muscle cells (VSMCs) contractile/differentiated phenotype under physiological and pathological stimuli. Maintains this phenotype of VSMCs by interacting with ITGA7 (By similarity).
Gene Name:: COMP
Uniprot ID:: P35445
Molecular weight:: 82362.0

Enzyme Details

3. Vascular endothelial growth factor A

General function:: Involved in cytokine activity
Specific function:: Growth factor active in angiogenesis, vasculogenesis and endothelial cell growth. Induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis and induces permeabilization of blood vessels. Binds to the FLT1/VEGFR1 and KDR/VEGFR2 receptors, heparan sulfate and heparin (By similarity). Binding to NRP1 receptor initiates a signaling pathway needed for motor neuron axon guidance and cell body migration, including for the caudal migration of facial motor neurons from rhombomere 4 to rhombomere 6 during embryonic development (By similarity).
Gene Name:: VEGFA
Uniprot ID:: P15691
Molecular weight:: 22310.0

Enzyme Details

4. Prolargin

General function:: Cell wall/membrane/envelope biogenesis
Specific function:: May anchor basement membranes to the underlying connective tissue.
Gene Name:: PRELP
Uniprot ID:: Q9GKN8
Molecular weight:: 43683.0

Enzyme Details

5. Glypican 6

General function:: Involved in heparan sulfate proteoglycan binding
Specific function:: Cell surface proteoglycan that bears heparan sulfate.
Gene Name:: GPC6
Uniprot ID:: A1L539
Molecular weight:: 17550.0

Enzyme Details

6. GPC5 protein

General function:: Involved in heparan sulfate proteoglycan binding
Specific function:: Cell surface proteoglycan that bears heparan sulfate.
Gene Name:: GPC5
Uniprot ID:: A7MB84
Molecular weight:: 66355.0

Enzyme Details

7. Syndecan-2

General function:: Involved in cytoskeletal protein binding
Specific function:: Cell surface proteoglycan that bears heparan sulfate. Regulates dendritic arbor morphogenesis (By similarity).
Gene Name:: SDC2
Uniprot ID:: Q58DD4
Molecular weight:: 22399.0

Enzyme Details

8. Syndecan-1

General function:: Involved in cytoskeletal protein binding
Specific function:: Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP.
Gene Name:: SDC1
Uniprot ID:: Q08DZ5
Molecular weight:: 32316.0

Enzyme Details

9. Glypican 3

General function:: Involved in heparan sulfate proteoglycan binding
Specific function:: Cell surface proteoglycan that bears heparan sulfate.
Gene Name:: GPC3
Uniprot ID:: Q3ZBZ6
Molecular weight:: 65458.0

Enzyme Details

10. Glypican-1

General function:: Not Available
Specific function:: Cell surface proteoglycan that bears heparan sulfate. Binds, via the heparan sulfate side chains, alpha-4 (V) collagen and participates in Schwann cell myelination (By similarity). May act as a catalyst in increasing the rate of conversion of prion protein PRPN (C) to PRNP (Sc) via associating (via the heparan sulfate side chains) with both forms of PRPN, targeting them to lipid rafts and facilitating their interaction. Required for proper skeletal muscle differentiation by sequestering FGF2 in lipid rafts preventing its binding to receptors (FGFRs) and inhibiting the FGF-mediated signaling (By similarity).
Gene Name:: GPC1
Uniprot ID:: G3X745
Molecular weight:: 61007.0

Showing metabocard for Heparan sulfate (BMDB0000693)

Structure for BMDB0000693 (Heparan sulfate)

Enzymes