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Showing metabocard for Pentosan Polysulfate (HMDB0014824)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:50 UTC
Update Date2022-03-07 02:51:45 UTC
HMDB IDHMDB0014824
Secondary Accession Numbers
  • HMDB14824
Metabolite Identification
Common NamePentosan Polysulfate
DescriptionPentosan Polysulfate, also known as SP 54, tavan or hoe bay 946, belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Pentosan Polysulfate is a drug which is used for the relief of bladder pain or discomfort associated with interstitial cystitis. Pentosan Polysulfate is an extremely weak basic (essentially neutral) compound (based on its pKa). Pentosan Polysulfate is a low molecular weight heparin-like compound. Outside of the human body, Pentosan Polysulfate is found, on average, in the highest concentration within tamarinds and figs. Pentosan Polysulfate has also been detected, but not quantified in, garden onions. This could make pentosan polysulfate a potential biomarker for the consumption of these foods. It inhibits the growth of SW13 adrenocortical cells transfected with FGF-4 and tumorigenicity of MCF-7 breast carcinoma cells transfected with FGF-1 or FGF-4. It is a sulfated pentosyl polysaccharide with heparin-like properties. It has been shown to interact also with the heparin-binding site of FGFR-1. It has anticoagulant and fibrinolytic effects. Pentosan Polysulfate is only found in individuals that have used or taken this drug.
Structure
Data?1582753224
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0014824 (Pentosan Polysulfate)

686
  Mrv0541 02231214552D          

 35 36  0  0  1  0            999 V2000
    4.2365    1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.5234    1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    9.9524   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.3799    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0944   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8089    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2379    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2379   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2379    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6668   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8240    0.5231    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6490    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9359    0.5231    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1109    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.3649    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.5398   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3950    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2200   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6655   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9509    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.8089    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0944   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.5234   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2365   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.5234   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6655   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.8089   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  1 14  1  0  0  0  0
  1 18  2  0  0  0  0
  1 19  2  0  0  0  0
  2  9  1  0  0  0  0
  2 15  1  0  0  0  0
  2 20  2  0  0  0  0
  2 21  2  0  0  0  0
  3 10  1  0  0  0  0
  3 16  1  0  0  0  0
  3 22  2  0  0  0  0
  3 23  2  0  0  0  0
  4 11  1  0  0  0  0
  4 17  1  0  0  0  0
  4 24  2  0  0  0  0
  4 25  2  0  0  0  0
 26  5  1  6  0  0  0
 29  5  1  1  0  0  0
  6 29  1  0  0  0  0
  6 35  1  0  0  0  0
  7 33  1  0  0  0  0
  7 34  1  0  0  0  0
 27  8  1  1  0  0  0
 28  9  1  6  0  0  0
 30 10  1  1  0  0  0
 31 11  1  6  0  0  0
 32 12  1  6  0  0  0
 34 13  1  1  0  0  0
 26 27  1  0  0  0  0
 26 33  1  0  0  0  0
 27 31  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 32  1  0  0  0  0
 31 34  1  0  0  0  0
 32 35  1  0  0  0  0
M  END
Download

3D MOL for HMDB0014824 (Pentosan Polysulfate)

HMDB0014824
     RDKit          3D
Pentosan Polysulfate
 53 54  0  0  0  0  0  0  0  0999 V2000
   -3.4362   -0.3147   -4.1378 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6785    0.2878   -2.7838 S   0  0  0  0  0  6  0  0  0  0  0  0
   -4.9915   -0.2494   -2.2863 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7319    1.9554   -2.9738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4103   -0.1890   -1.7931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8529   -1.0088   -0.7539 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1169   -2.3228   -0.8348 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0364   -3.2767   -1.3139 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6454   -2.8067    0.5052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8815   -1.9031    1.1983 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0339   -0.5914    0.7991 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2568   -0.4069   -0.3425 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6612    0.6006   -0.0541 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5337    1.6660   -1.1010 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3987    1.3421   -2.1457 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6569    1.8702   -1.7743 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4708    3.2617   -1.6990 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9695    1.2967   -0.4086 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3139    0.9609   -0.3921 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0886    1.7756    0.8256 S   0  0  0  0  0  6  0  0  0  0  0  0
    4.3250    1.6795    2.1355 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3083    3.2237    0.4555 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6175    1.1200    1.1224 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0967    0.0667   -0.1277 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5106   -0.4393    1.0886 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0780   -2.0117    0.9778 S   0  0  0  0  0  6  0  0  0  0  0  0
    2.2205   -2.8631    0.0906 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0238   -2.6076    2.3572 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6744   -2.0753    0.4671 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5026   -0.3529    0.5425 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2044   -0.9777    1.5734 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1386    0.0923    2.4416 S   0  0  0  0  0  6  0  0  0  0  0  0
   -5.5900   -0.1032    2.1890 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8653   -0.1765    3.9140 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6657    1.6947    2.1779 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3799    2.3651   -2.3257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9569   -1.1496   -0.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2957   -2.3023   -1.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4522   -2.9734   -2.1592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5072   -3.1613    1.1155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0214   -3.7137    0.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7389    0.0856    1.6238 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5486    0.9917    0.9775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4813    1.7533   -1.5322 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7610    2.6881   -0.6825 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4113    1.5786   -2.5049 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4981    3.6235   -2.6244 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7809    2.0224    0.4024 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8822    0.5346    0.3491 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2086   -0.6445   -0.9616 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7578   -2.6838   -0.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7691    0.7210    0.5861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1553    2.0478    1.4129 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  2  0
 20 23  1  0
 18 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  2  0
 26 29  1  0
 11 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  2  0
 32 34  2  0
 32 35  1  0
 30  6  1  0
 24 13  1  0
  4 36  1  0
  6 37  1  6
  7 38  1  6
  8 39  1  0
  9 40  1  0
  9 41  1  0
 11 42  1  1
 13 43  1  1
 14 44  1  0
 14 45  1  0
 16 46  1  6
 17 47  1  0
 18 48  1  1
 23 49  1  0
 24 50  1  6
 29 51  1  0
 30 52  1  6
 35 53  1  0
M  END
Download

3D SDF for HMDB0014824 (Pentosan Polysulfate)

686
  Mrv0541 02231214552D          

 35 36  0  0  1  0            999 V2000
    4.2365    1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.5234    1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    9.9524   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.3799    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0944   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8089    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2379    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2379   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2379    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6668   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8240    0.5231    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6490    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9359    0.5231    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1109    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.3649    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.5398   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3950    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2200   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6655   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9509    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.8089    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.0944   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.5234   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2365   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.5234   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6655   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.8089   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  1 14  1  0  0  0  0
  1 18  2  0  0  0  0
  1 19  2  0  0  0  0
  2  9  1  0  0  0  0
  2 15  1  0  0  0  0
  2 20  2  0  0  0  0
  2 21  2  0  0  0  0
  3 10  1  0  0  0  0
  3 16  1  0  0  0  0
  3 22  2  0  0  0  0
  3 23  2  0  0  0  0
  4 11  1  0  0  0  0
  4 17  1  0  0  0  0
  4 24  2  0  0  0  0
  4 25  2  0  0  0  0
 26  5  1  6  0  0  0
 29  5  1  1  0  0  0
  6 29  1  0  0  0  0
  6 35  1  0  0  0  0
  7 33  1  0  0  0  0
  7 34  1  0  0  0  0
 27  8  1  1  0  0  0
 28  9  1  6  0  0  0
 30 10  1  1  0  0  0
 31 11  1  6  0  0  0
 32 12  1  6  0  0  0
 34 13  1  1  0  0  0
 26 27  1  0  0  0  0
 26 33  1  0  0  0  0
 27 31  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 32  1  0  0  0  0
 31 34  1  0  0  0  0
 32 35  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014824

> <DATABASE_NAME>
hmdb

> <SMILES>
O[C@@H]1CO[C@@H](O[C@@H]2CO[C@@H](O)[C@H](OS(O)(=O)=O)[C@H]2OS(O)(=O)=O)[C@H](OS(O)(=O)=O)[C@H]1OS(O)(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O21S4/c11-3-1-26-10(8(31-35(22,23)24)5(3)28-32(13,14)15)27-4-2-25-9(12)7(30-34(19,20)21)6(4)29-33(16,17)18/h3-12H,1-2H2,(H,13,14,15)(H,16,17,18)(H,19,20,21)(H,22,23,24)/t3-,4-,5+,6+,7-,8-,9-,10+/m1/s1

> <INCHI_KEY>
FCCNSUIJIOOXEZ-SJYYZXOBSA-N

> <FORMULA>
C10H18O21S4

> <MOLECULAR_WEIGHT>
602.497

> <EXACT_MASS>
601.922340398

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
46.16655886325522

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S,3R,4S,5R)-5-hydroxy-2-{[(3R,4S,5R,6R)-6-hydroxy-4,5-bis(sulfooxy)oxan-3-yl]oxy}-4-(sulfooxy)oxan-3-yl]oxidanesulfonic acid

> <ALOGPS_LOGP>
-2.49

> <JCHEM_LOGP>
-11.39932632632439

> <ALOGPS_LOGS>
-2.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
-2.5074635017282665

> <JCHEM_PKA_STRONGEST_ACIDIC>
-2.9445776264001253

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5627096412501187

> <JCHEM_POLAR_SURFACE_AREA>
322.54999999999995

> <JCHEM_REFRACTIVITY>
96.37889999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.49e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentosan polysulfate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0014824 (Pentosan Polysulfate)

HMDB0014824
     RDKit          3D
Pentosan Polysulfate
 53 54  0  0  0  0  0  0  0  0999 V2000
   -3.4362   -0.3147   -4.1378 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6785    0.2878   -2.7838 S   0  0  0  0  0  6  0  0  0  0  0  0
   -4.9915   -0.2494   -2.2863 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7319    1.9554   -2.9738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4103   -0.1890   -1.7931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8529   -1.0088   -0.7539 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1169   -2.3228   -0.8348 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0364   -3.2767   -1.3139 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6454   -2.8067    0.5052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8815   -1.9031    1.1983 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0339   -0.5914    0.7991 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2568   -0.4069   -0.3425 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6612    0.6006   -0.0541 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5337    1.6660   -1.1010 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3987    1.3421   -2.1457 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6569    1.8702   -1.7743 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4708    3.2617   -1.6990 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9695    1.2967   -0.4086 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3139    0.9609   -0.3921 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0886    1.7756    0.8256 S   0  0  0  0  0  6  0  0  0  0  0  0
    4.3250    1.6795    2.1355 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3083    3.2237    0.4555 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6175    1.1200    1.1224 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0967    0.0667   -0.1277 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5106   -0.4393    1.0886 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0780   -2.0117    0.9778 S   0  0  0  0  0  6  0  0  0  0  0  0
    2.2205   -2.8631    0.0906 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0238   -2.6076    2.3572 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6744   -2.0753    0.4671 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5026   -0.3529    0.5425 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2044   -0.9777    1.5734 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1386    0.0923    2.4416 S   0  0  0  0  0  6  0  0  0  0  0  0
   -5.5900   -0.1032    2.1890 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8653   -0.1765    3.9140 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6657    1.6947    2.1779 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3799    2.3651   -2.3257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9569   -1.1496   -0.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2957   -2.3023   -1.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4522   -2.9734   -2.1592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5072   -3.1613    1.1155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0214   -3.7137    0.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7389    0.0856    1.6238 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5486    0.9917    0.9775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4813    1.7533   -1.5322 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7610    2.6881   -0.6825 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4113    1.5786   -2.5049 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4981    3.6235   -2.6244 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7809    2.0224    0.4024 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8822    0.5346    0.3491 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2086   -0.6445   -0.9616 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7578   -2.6838   -0.3045 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7691    0.7210    0.5861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1553    2.0478    1.4129 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  2  0
 20 23  1  0
 18 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  2  0
 26 29  1  0
 11 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  2  0
 32 34  2  0
 32 35  1  0
 30  6  1  0
 24 13  1  0
  4 36  1  0
  6 37  1  6
  7 38  1  6
  8 39  1  0
  9 40  1  0
  9 41  1  0
 11 42  1  1
 13 43  1  1
 14 44  1  0
 14 45  1  0
 16 46  1  6
 17 47  1  0
 18 48  1  1
 23 49  1  0
 24 50  1  6
 29 51  1  0
 30 52  1  6
 35 53  1  0
M  END
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PDB for HMDB0014824 (Pentosan Polysulfate)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 686                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  S   UNK     0       7.908   2.310   0.000  0.00  0.00           S+0
HETATM    2  S   UNK     0      15.910   2.310   0.000  0.00  0.00           S+0
HETATM    3  S   UNK     0      18.578  -0.770   0.000  0.00  0.00           S+0
HETATM    4  S   UNK     0       5.241  -0.770   0.000  0.00  0.00           S+0
HETATM    5  O   UNK     0      11.909   0.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      13.243  -2.310   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       9.242  -3.080   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       9.242   1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      14.577   1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      17.244   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.574   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      17.244  -3.080   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       6.574  -3.080   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       6.574   3.080   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      17.244   3.080   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      19.911  -1.540   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.907  -1.540   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       7.138   0.976   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       8.678   3.644   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      16.680   0.976   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      15.140   3.644   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      19.348   0.564   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      17.808  -2.104   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       4.471   0.564   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       6.011  -2.104   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      10.576  -0.770   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.242   0.000   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      14.577   0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      13.243  -0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      15.910  -0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.908  -0.770   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      15.910  -2.310   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      10.576  -2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       7.908  -2.310   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      14.577  -3.080   0.000  0.00  0.00           C+0
CONECT    1    8   14   18   19                                             
CONECT    2    9   15   20   21                                             
CONECT    3   10   16   22   23                                             
CONECT    4   11   17   24   25                                             
CONECT    5   26   29                                                       
CONECT    6   29   35                                                       
CONECT    7   33   34                                                       
CONECT    8    1   27                                                       
CONECT    9    2   28                                                       
CONECT   10    3   30                                                       
CONECT   11    4   31                                                       
CONECT   12   32                                                            
CONECT   13   34                                                            
CONECT   14    1                                                            
CONECT   15    2                                                            
CONECT   16    3                                                            
CONECT   17    4                                                            
CONECT   18    1                                                            
CONECT   19    1                                                            
CONECT   20    2                                                            
CONECT   21    2                                                            
CONECT   22    3                                                            
CONECT   23    3                                                            
CONECT   24    4                                                            
CONECT   25    4                                                            
CONECT   26    5   27   33                                                  
CONECT   27    8   26   31                                                  
CONECT   28    9   29   30                                                  
CONECT   29    5    6   28                                                  
CONECT   30   10   28   32                                                  
CONECT   31   11   27   34                                                  
CONECT   32   12   30   35                                                  
CONECT   33    7   26                                                       
CONECT   34    7   13   31                                                  
CONECT   35    6   32                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   72    0
END
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3D PDB for HMDB0014824 (Pentosan Polysulfate)

COMPND    HMDB0014824
HETATM    1  O1  UNL     1      -3.436  -0.315  -4.138  1.00  0.00           O  
HETATM    2  S1  UNL     1      -3.679   0.288  -2.784  1.00  0.00           S  
HETATM    3  O2  UNL     1      -4.991  -0.249  -2.286  1.00  0.00           O  
HETATM    4  O3  UNL     1      -3.732   1.955  -2.974  1.00  0.00           O  
HETATM    5  O4  UNL     1      -2.410  -0.189  -1.793  1.00  0.00           O  
HETATM    6  C1  UNL     1      -2.853  -1.009  -0.754  1.00  0.00           C  
HETATM    7  C2  UNL     1      -2.117  -2.323  -0.835  1.00  0.00           C  
HETATM    8  O5  UNL     1      -3.036  -3.277  -1.314  1.00  0.00           O  
HETATM    9  C3  UNL     1      -1.645  -2.807   0.505  1.00  0.00           C  
HETATM   10  O6  UNL     1      -0.881  -1.903   1.198  1.00  0.00           O  
HETATM   11  C4  UNL     1      -1.034  -0.591   0.799  1.00  0.00           C  
HETATM   12  O7  UNL     1      -0.257  -0.407  -0.343  1.00  0.00           O  
HETATM   13  C5  UNL     1       0.661   0.601  -0.054  1.00  0.00           C  
HETATM   14  C6  UNL     1       0.534   1.666  -1.101  1.00  0.00           C  
HETATM   15  O8  UNL     1       1.399   1.342  -2.146  1.00  0.00           O  
HETATM   16  C7  UNL     1       2.657   1.870  -1.774  1.00  0.00           C  
HETATM   17  O9  UNL     1       2.471   3.262  -1.699  1.00  0.00           O  
HETATM   18  C8  UNL     1       2.969   1.297  -0.409  1.00  0.00           C  
HETATM   19  O10 UNL     1       4.314   0.961  -0.392  1.00  0.00           O  
HETATM   20  S2  UNL     1       5.089   1.776   0.826  1.00  0.00           S  
HETATM   21  O11 UNL     1       4.325   1.680   2.135  1.00  0.00           O  
HETATM   22  O12 UNL     1       5.308   3.224   0.456  1.00  0.00           O  
HETATM   23  O13 UNL     1       6.618   1.120   1.122  1.00  0.00           O  
HETATM   24  C9  UNL     1       2.097   0.067  -0.128  1.00  0.00           C  
HETATM   25  O14 UNL     1       2.511  -0.439   1.089  1.00  0.00           O  
HETATM   26  S3  UNL     1       3.078  -2.012   0.978  1.00  0.00           S  
HETATM   27  O15 UNL     1       2.220  -2.863   0.091  1.00  0.00           O  
HETATM   28  O16 UNL     1       3.024  -2.608   2.357  1.00  0.00           O  
HETATM   29  O17 UNL     1       4.674  -2.075   0.467  1.00  0.00           O  
HETATM   30  C10 UNL     1      -2.503  -0.353   0.542  1.00  0.00           C  
HETATM   31  O18 UNL     1      -3.204  -0.978   1.573  1.00  0.00           O  
HETATM   32  S4  UNL     1      -4.139   0.092   2.442  1.00  0.00           S  
HETATM   33  O19 UNL     1      -5.590  -0.103   2.189  1.00  0.00           O  
HETATM   34  O20 UNL     1      -3.865  -0.176   3.914  1.00  0.00           O  
HETATM   35  O21 UNL     1      -3.666   1.695   2.178  1.00  0.00           O  
HETATM   36  H1  UNL     1      -4.380   2.365  -2.326  1.00  0.00           H  
HETATM   37  H2  UNL     1      -3.957  -1.150  -0.835  1.00  0.00           H  
HETATM   38  H3  UNL     1      -1.296  -2.302  -1.577  1.00  0.00           H  
HETATM   39  H4  UNL     1      -3.452  -2.973  -2.159  1.00  0.00           H  
HETATM   40  H5  UNL     1      -2.507  -3.161   1.115  1.00  0.00           H  
HETATM   41  H6  UNL     1      -1.021  -3.714   0.322  1.00  0.00           H  
HETATM   42  H7  UNL     1      -0.739   0.086   1.624  1.00  0.00           H  
HETATM   43  H8  UNL     1       0.549   0.992   0.977  1.00  0.00           H  
HETATM   44  H9  UNL     1      -0.481   1.753  -1.532  1.00  0.00           H  
HETATM   45  H10 UNL     1       0.761   2.688  -0.682  1.00  0.00           H  
HETATM   46  H11 UNL     1       3.411   1.579  -2.505  1.00  0.00           H  
HETATM   47  H12 UNL     1       2.498   3.623  -2.624  1.00  0.00           H  
HETATM   48  H13 UNL     1       2.781   2.022   0.402  1.00  0.00           H  
HETATM   49  H14 UNL     1       6.882   0.535   0.349  1.00  0.00           H  
HETATM   50  H15 UNL     1       2.209  -0.645  -0.962  1.00  0.00           H  
HETATM   51  H16 UNL     1       4.758  -2.684  -0.305  1.00  0.00           H  
HETATM   52  H17 UNL     1      -2.769   0.721   0.586  1.00  0.00           H  
HETATM   53  H18 UNL     1      -4.155   2.048   1.413  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    3    4    5
CONECT    4   36
CONECT    5    6
CONECT    6    7   30   37
CONECT    7    8    9   38
CONECT    8   39
CONECT    9   10   40   41
CONECT   10   11
CONECT   11   12   30   42
CONECT   12   13
CONECT   13   14   24   43
CONECT   14   15   44   45
CONECT   15   16
CONECT   16   17   18   46
CONECT   17   47
CONECT   18   19   24   48
CONECT   19   20
CONECT   20   21   21   22   22
CONECT   20   23
CONECT   23   49
CONECT   24   25   50
CONECT   25   26
CONECT   26   27   27   28   28
CONECT   26   29
CONECT   29   51
CONECT   30   31   52
CONECT   31   32
CONECT   32   33   33   34   34
CONECT   32   35
CONECT   35   53
END
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SMILES for HMDB0014824 (Pentosan Polysulfate)

O[C@@H]1CO[C@@H](O[C@@H]2CO[C@@H](O)[C@H](OS(O)(=O)=O)[C@H]2OS(O)(=O)=O)[C@H](OS(O)(=O)=O)[C@H]1OS(O)(=O)=O
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INCHI for HMDB0014824 (Pentosan Polysulfate)

InChI=1S/C10H18O21S4/c11-3-1-26-10(8(31-35(22,23)24)5(3)28-32(13,14)15)27-4-2-25-9(12)7(30-34(19,20)21)6(4)29-33(16,17)18/h3-12H,1-2H2,(H,13,14,15)(H,16,17,18)(H,19,20,21)(H,22,23,24)/t3-,4-,5+,6+,7-,8-,9-,10+/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC10H18O21S4
Average Molecular Weight602.497
Monoisotopic Molecular Weight601.922340398
IUPAC Name[(2S,3R,4S,5R)-5-hydroxy-2-{[(3R,4S,5R,6R)-6-hydroxy-4,5-bis(sulfooxy)oxan-3-yl]oxy}-4-(sulfooxy)oxan-3-yl]oxidanesulfonic acid
Traditional Namepentosan polysulfate
CAS Registry Number37300-21-3
SMILES
O[C@@H]1CO[C@@H](O[C@@H]2CO[C@@H](O)[C@H](OS(O)(=O)=O)[C@H]2OS(O)(=O)=O)[C@H](OS(O)(=O)=O)[C@H]1OS(O)(=O)=O
InChI Identifier
InChI=1S/C10H18O21S4/c11-3-1-26-10(8(31-35(22,23)24)5(3)28-32(13,14)15)27-4-2-25-9(12)7(30-34(19,20)21)6(4)29-33(16,17)18/h3-12H,1-2H2,(H,13,14,15)(H,16,17,18)(H,19,20,21)(H,22,23,24)/t3-,4-,5+,6+,7-,8-,9-,10+/m1/s1
InChI KeyFCCNSUIJIOOXEZ-SJYYZXOBSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentO-glycosyl compounds
Alternative Parents
Substituents
  • Disaccharide
  • O-glycosyl compound
  • Oxane
  • Sulfuric acid ester
  • Alkyl sulfate
  • Sulfate-ester
  • Sulfuric acid monoester
  • Organic sulfuric acid or derivatives
  • Hemiacetal
  • Secondary alcohol
  • Oxacycle
  • Acetal
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility3.49 g/LNot Available
LogP-8Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00686 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00686 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00686
Phenol Explorer Compound IDNot Available
FooDB IDFDB019140
KNApSAcK IDNot Available
Chemspider ID34595
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPentosan polysulfate
METLIN IDNot Available
PubChem Compound37720
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Heparin-binding growth factor 2
General function:
Involved in growth factor activity
Specific function:
The heparin-binding growth factors are angiogenic agents in vivo and are potent mitogens for a variety of cell types in vitro. There are differences in the tissue distribution and concentration of these 2 growth factors
Gene Name:
FGF2
Uniprot ID:
P09038
Molecular weight:
30769.7
References
  1. Zugmaier G, Favoni R, Jaeger R, Rosen N, Knabbe C: Polysulfated heparinoids selectively inactivate heparin-binding angiogenesis factors. Ann N Y Acad Sci. 1999;886:243-8. [PubMed:10667230 ]
  2. Mucha S, Melen-Mucha G, Stepien T, Godlewski A, Stepien H: Effects of pentosan polysulfate sodium on the estrogen-induced pituitary prolactinoma in Fischer 344 rats. Oncol Rep. 2002 Nov-Dec;9(6):1385-9. [PubMed:12375053 ]
  3. Pluda JM, Shay LE, Foli A, Tannenbaum S, Cohen PJ, Goldspiel BR, Adamo D, Cooper MR, Broder S, Yarchoan R: Administration of pentosan polysulfate to patients with human immunodeficiency virus-associated Kaposi's sarcoma. J Natl Cancer Inst. 1993 Oct 6;85(19):1585-92. [PubMed:7692072 ]
  4. McLeskey SW, Zhang L, Kharbanda S, Kurebayashi J, Lippman ME, Dickson RB, Kern FG: Fibroblast growth factor overexpressing breast carcinoma cells as models of angiogenesis and metastasis. Breast Cancer Res Treat. 1996;39(1):103-17. [PubMed:8738610 ]
  5. Jerebtsova M, Wong E, Przygodzki R, Tang P, Ray PE: A novel role of fibroblast growth factor-2 and pentosan polysulfate in the pathogenesis of intestinal bleeding in mice. Am J Physiol Heart Circ Physiol. 2007 Feb;292(2):H743-50. Epub 2006 Oct 27. [PubMed:17071728 ]
Enzyme Details
2. Heparin-binding growth factor 1
General function:
Involved in fibroblast growth factor receptor binding
Specific function:
The heparin-binding growth factors are angiogenic agents in vivo and are potent mitogens for a variety of cell types in vitro. There are differences in the tissue distribution and concentration of these 2 growth factors
Gene Name:
FGF1
Uniprot ID:
P05230
Molecular weight:
17459.6
References
  1. Pascu C, Ljungh A, Wadstrom T: Staphylococci bind heparin-binding host growth factors. Curr Microbiol. 1996 Apr;32(4):201-7. [PubMed:8867461 ]
  2. Zenjari C, Boilly-Marer Y, Desbiens X, Oudghir M, Hondermarck H, Boilly B: Experimental evidence for FGF-1 control of blastema cell proliferation during limb regeneration of the amphibian Pleurodeles waltl. Int J Dev Biol. 1996 Oct;40(5):965-71. [PubMed:8946244 ]
  3. Jerebtsova M, Wong E, Przygodzki R, Tang P, Ray PE: A novel role of fibroblast growth factor-2 and pentosan polysulfate in the pathogenesis of intestinal bleeding in mice. Am J Physiol Heart Circ Physiol. 2007 Feb;292(2):H743-50. Epub 2006 Oct 27. [PubMed:17071728 ]
Enzyme Details
3. Fibroblast growth factor 4
General function:
Involved in growth factor activity
Specific function:
Can transform NIH 3T3 cells from a human stomach tumor (hst) and from karposi's sarcoma (KS3). It has a mitogenic activity
Gene Name:
FGF4
Uniprot ID:
P08620
Molecular weight:
22047.4
References
  1. Zugmaier G, Lippman ME, Wellstein A: Inhibition by pentosan polysulfate (PPS) of heparin-binding growth factors released from tumor cells and blockage by PPS of tumor growth in animals. J Natl Cancer Inst. 1992 Nov 18;84(22):1716-24. [PubMed:1279186 ]
  2. McLeskey SW, Zhang L, Kharbanda S, Kurebayashi J, Lippman ME, Dickson RB, Kern FG: Fibroblast growth factor overexpressing breast carcinoma cells as models of angiogenesis and metastasis. Breast Cancer Res Treat. 1996;39(1):103-17. [PubMed:8738610 ]
  3. Wellstein A, Zugmaier G, Califano JA 3rd, Kern F, Paik S, Lippman ME: Tumor growth dependent on Kaposi's sarcoma-derived fibroblast growth factor inhibited by pentosan polysulfate. J Natl Cancer Inst. 1991 May 15;83(10):716-20. [PubMed:1708834 ]