NP-MRD: Showing NP-Card for Heparan sulfate (NP0001418)

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Record Information

Version

1.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2020-11-24 22:23:18 UTC

NP-MRD ID

NP0001418

Secondary Accession Numbers

None

Natural Product 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

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


  Mrv1652305271900142D          

 39 40  0  0  1  0            999 V2000
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.2704   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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 36 39  2  0  0  0  0
M  END

HMDB0000693
     RDKit          3D
Heparan sulfate
 64 65  0  0  0  0  0  0  0  0999 V2000
   -5.5153    1.4647   -1.0106 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.2400    1.5693    0.0907 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6108    2.0259    1.4798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4421    1.9010    2.2473 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6397    2.3593    3.8289 S   0  0  0  0  0  6  0  0  0  0  0  0
   -0.4694    1.1532    4.7089 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1403    3.0356    4.0385 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6635    0.1463    0.1551 C   0  0  2  0  0  0  0  0  0  0  0  0
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    2.2977    0.9703    1.1179 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5863    1.0849    0.7865 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8510    2.5295    0.5020 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0
  2  3  1  0
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  8  9  2  0
  8 10  2  0
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M  END


  Mrv1652305271900142D          

 39 40  0  0  1  0            999 V2000
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 36 39  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0001418

> <DATABASE_NAME>
NP-MRD

> <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

> <FORMULA>
C14H25NO21S3

> <MOLECULAR_WEIGHT>
639.52

> <EXACT_MASS>
639.008120351

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
52.50687075361865

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(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

> <ALOGPS_LOGP>
-2.18

> <JCHEM_LOGP>
-8.12290777905686

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
-2.3327485898693743

> <JCHEM_PKA_STRONGEST_ACIDIC>
-3.270986019053157

> <JCHEM_PKA_STRONGEST_BASIC>
1.9907100004031326

> <JCHEM_POLAR_SURFACE_AREA>
326.73999999999995

> <JCHEM_REFRACTIVITY>
121.59679999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.95e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000693
     RDKit          3D
Heparan sulfate
 64 65  0  0  0  0  0  0  0  0999 V2000
   -5.5153    1.4647   -1.0106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3155    0.8739   -1.4168 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3822    0.8512   -0.3675 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3378    1.6536   -0.7507 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400    1.5693    0.0907 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6108    2.0259    1.4798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4421    1.9010    2.2473 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6397    2.3593    3.8289 S   0  0  0  0  0  6  0  0  0  0  0  0
   -0.4694    1.1532    4.7089 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4350    3.3754    4.1391 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1403    3.0356    4.0385 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6635    0.1463    0.1551 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6612    0.2151   -0.1785 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5572   -0.1182    0.8188 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2977    0.9703    1.1179 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5863    1.0849    0.7865 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8510    2.5295    0.5020 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9869    2.9680    0.1704 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8507    3.4948    0.5854 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1295    0.2652   -0.3165 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5318    1.0245   -1.4094 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8607    0.7825   -1.7618 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1689   -0.7833   -0.8393 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7991   -1.8431   -1.4561 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3952   -1.2835    0.3945 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7230   -2.3998   -0.0057 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2122   -3.8051    0.7448 S   0  0  0  0  0  6  0  0  0  0  0  0
    3.5732   -4.1608    0.2104 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2842   -4.9209    0.3673 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3551   -3.6188    2.4046 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5460   -0.7123   -0.6753 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2560   -2.0513   -0.6879 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9563   -0.5789   -0.0649 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8751   -1.4777   -0.7027 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8381   -1.2579   -2.0323 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5328   -2.6027   -2.8051 S   0  0  0  0  0  6  0  0  0  0  0  0
   -5.6913   -3.0414   -1.9352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5040   -3.7054   -2.9173 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0287   -2.2213   -4.3548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2088    1.4561   -1.8695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9276    0.9049   -0.1696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3464    2.5158   -0.6378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8692    1.3169    0.5054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4604    2.2769   -0.2677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9413    3.0801    1.4142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3955    1.3845    1.9099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1825    3.8640    3.4877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7258   -0.1933    1.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0243   -0.4147    1.7557 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2029    0.8678    1.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0348    4.4570    0.8187 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0237   -0.3287   -0.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9923   -0.2958   -2.0368 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1153    1.4595   -2.5970 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5278    0.9960   -0.9055 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4384   -0.2848   -1.5076 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9941   -1.5970   -2.4035 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1845   -1.4779    1.1555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9711   -4.2716    2.8025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6913   -0.2990   -1.7181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6755   -2.5498    0.0572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9025   -0.7811    1.0222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6609   -2.4680   -0.5388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7957   -2.7793   -4.6220 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  2  0
  8 11  1  0
  5 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
 16 20  1  0
 20 21  1  0
 21 22  1  0
 20 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  2  0
 27 29  2  0
 27 30  1  0
 12 31  1  0
 31 32  1  0
 31 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  2  0
 36 38  2  0
 36 39  1  0
 33  3  1  0
 25 14  1  0
  1 40  1  0
  1 41  1  0
  1 42  1  0
  3 43  1  1
  5 44  1  6
  6 45  1  0
  6 46  1  0
 11 47  1  0
 12 48  1  1
 14 49  1  1
 16 50  1  1
 19 51  1  0
 20 52  1  1
 22 53  1  0
 22 54  1  0
 22 55  1  0
 23 56  1  6
 24 57  1  0
 25 58  1  1
 30 59  1  0
 31 60  1  6
 32 61  1  0
 33 62  1  1
 34 63  1  0
 39 64  1  0
M  END

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    8  S   UNK     0       2.667  -3.080   0.000  0.00  0.00           S+0
HETATM    9  O   UNK     0       4.207  -3.080   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.127  -3.080   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       2.667  -1.540   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   24  S   UNK     0      -2.667  -9.240   0.000  0.00  0.00           S+0
HETATM   25  O   UNK     0      -1.897  -7.906   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -3.437 -10.574   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -4.001  -8.470   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      -4.001  -2.310   0.000  0.00  0.00           N+0
HETATM   35  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   36  S   UNK     0      -5.335   0.000   0.000  0.00  0.00           S+0
HETATM   37  O   UNK     0      -6.668   0.770   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -4.565   1.334   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -6.105  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   33                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12    5   13   31                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   28                                                  
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   14   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26   27                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   24                                                            
CONECT   28   16   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   12   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31    3   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   38   39                                             
CONECT   37   36                                                            
CONECT   38   36                                                            
CONECT   39   36                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   80    0
END

COMPND    HMDB0000693
HETATM    1  C1  UNL     1      -5.515   1.465  -1.011  1.00  0.00           C  
HETATM    2  O1  UNL     1      -4.315   0.874  -1.417  1.00  0.00           O  
HETATM    3  C2  UNL     1      -3.382   0.851  -0.368  1.00  0.00           C  
HETATM    4  O2  UNL     1      -2.338   1.654  -0.751  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.240   1.569   0.091  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.611   2.026   1.480  1.00  0.00           C  
HETATM    7  O3  UNL     1      -0.442   1.901   2.247  1.00  0.00           O  
HETATM    8  S1  UNL     1      -0.640   2.359   3.829  1.00  0.00           S  
HETATM    9  O4  UNL     1      -0.469   1.153   4.709  1.00  0.00           O  
HETATM   10  O5  UNL     1       0.435   3.375   4.139  1.00  0.00           O  
HETATM   11  O6  UNL     1      -2.140   3.036   4.039  1.00  0.00           O  
HETATM   12  C5  UNL     1      -0.663   0.146   0.155  1.00  0.00           C  
HETATM   13  O7  UNL     1       0.661   0.215  -0.179  1.00  0.00           O  
HETATM   14  C6  UNL     1       1.557  -0.118   0.819  1.00  0.00           C  
HETATM   15  O8  UNL     1       2.298   0.970   1.118  1.00  0.00           O  
HETATM   16  C7  UNL     1       3.586   1.085   0.787  1.00  0.00           C  
HETATM   17  C8  UNL     1       3.851   2.529   0.502  1.00  0.00           C  
HETATM   18  O9  UNL     1       4.987   2.968   0.170  1.00  0.00           O  
HETATM   19  O10 UNL     1       2.851   3.495   0.585  1.00  0.00           O  
HETATM   20  C9  UNL     1       4.129   0.265  -0.316  1.00  0.00           C  
HETATM   21  O11 UNL     1       4.532   1.024  -1.409  1.00  0.00           O  
HETATM   22  C10 UNL     1       5.861   0.783  -1.762  1.00  0.00           C  
HETATM   23  C11 UNL     1       3.169  -0.783  -0.839  1.00  0.00           C  
HETATM   24  O12 UNL     1       3.799  -1.843  -1.456  1.00  0.00           O  
HETATM   25  C12 UNL     1       2.395  -1.283   0.395  1.00  0.00           C  
HETATM   26  O13 UNL     1       1.723  -2.400  -0.006  1.00  0.00           O  
HETATM   27  S2  UNL     1       2.212  -3.805   0.745  1.00  0.00           S  
HETATM   28  O14 UNL     1       3.573  -4.161   0.210  1.00  0.00           O  
HETATM   29  O15 UNL     1       1.284  -4.921   0.367  1.00  0.00           O  
HETATM   30  O16 UNL     1       2.355  -3.619   2.405  1.00  0.00           O  
HETATM   31  C13 UNL     1      -1.546  -0.712  -0.675  1.00  0.00           C  
HETATM   32  O17 UNL     1      -1.256  -2.051  -0.688  1.00  0.00           O  
HETATM   33  C14 UNL     1      -2.956  -0.579  -0.065  1.00  0.00           C  
HETATM   34  N1  UNL     1      -3.875  -1.478  -0.703  1.00  0.00           N  
HETATM   35  O18 UNL     1      -3.838  -1.258  -2.032  1.00  0.00           O  
HETATM   36  S3  UNL     1      -4.533  -2.603  -2.805  1.00  0.00           S  
HETATM   37  O19 UNL     1      -5.691  -3.041  -1.935  1.00  0.00           O  
HETATM   38  O20 UNL     1      -3.504  -3.705  -2.917  1.00  0.00           O  
HETATM   39  O21 UNL     1      -5.029  -2.221  -4.355  1.00  0.00           O  
HETATM   40  H1  UNL     1      -6.209   1.456  -1.869  1.00  0.00           H  
HETATM   41  H2  UNL     1      -5.928   0.905  -0.170  1.00  0.00           H  
HETATM   42  H3  UNL     1      -5.346   2.516  -0.638  1.00  0.00           H  
HETATM   43  H4  UNL     1      -3.869   1.317   0.505  1.00  0.00           H  
HETATM   44  H5  UNL     1      -0.460   2.277  -0.268  1.00  0.00           H  
HETATM   45  H6  UNL     1      -1.941   3.080   1.414  1.00  0.00           H  
HETATM   46  H7  UNL     1      -2.395   1.385   1.910  1.00  0.00           H  
HETATM   47  H8  UNL     1      -2.182   3.864   3.488  1.00  0.00           H  
HETATM   48  H9  UNL     1      -0.726  -0.193   1.211  1.00  0.00           H  
HETATM   49  H10 UNL     1       1.024  -0.415   1.756  1.00  0.00           H  
HETATM   50  H11 UNL     1       4.203   0.868   1.713  1.00  0.00           H  
HETATM   51  H12 UNL     1       3.035   4.457   0.819  1.00  0.00           H  
HETATM   52  H13 UNL     1       5.024  -0.329  -0.002  1.00  0.00           H  
HETATM   53  H14 UNL     1       5.992  -0.296  -2.037  1.00  0.00           H  
HETATM   54  H15 UNL     1       6.115   1.459  -2.597  1.00  0.00           H  
HETATM   55  H16 UNL     1       6.528   0.996  -0.906  1.00  0.00           H  
HETATM   56  H17 UNL     1       2.438  -0.285  -1.508  1.00  0.00           H  
HETATM   57  H18 UNL     1       3.994  -1.597  -2.404  1.00  0.00           H  
HETATM   58  H19 UNL     1       3.184  -1.478   1.155  1.00  0.00           H  
HETATM   59  H20 UNL     1       2.971  -4.272   2.802  1.00  0.00           H  
HETATM   60  H21 UNL     1      -1.691  -0.299  -1.718  1.00  0.00           H  
HETATM   61  H22 UNL     1      -1.675  -2.550   0.057  1.00  0.00           H  
HETATM   62  H23 UNL     1      -2.902  -0.781   1.022  1.00  0.00           H  
HETATM   63  H24 UNL     1      -3.661  -2.468  -0.539  1.00  0.00           H  
HETATM   64  H25 UNL     1      -5.796  -2.779  -4.622  1.00  0.00           H  
CONECT    1    2   40   41   42
CONECT    2    3
CONECT    3    4   33   43
CONECT    4    5
CONECT    5    6   12   44
CONECT    6    7   45   46
CONECT    7    8
CONECT    8    9    9   10   10
CONECT    8   11
CONECT   11   47
CONECT   12   13   31   48
CONECT   13   14
CONECT   14   15   25   49
CONECT   15   16
CONECT   16   17   20   50
CONECT   17   18   18   19
CONECT   19   51
CONECT   20   21   23   52
CONECT   21   22
CONECT   22   53   54   55
CONECT   23   24   25   56
CONECT   24   57
CONECT   25   26   58
CONECT   26   27
CONECT   27   28   28   29   29
CONECT   27   30
CONECT   30   59
CONECT   31   32   33   60
CONECT   32   61
CONECT   33   34   62
CONECT   34   35   63
CONECT   35   36
CONECT   36   37   37   38   38
CONECT   36   39
CONECT   39   64
END

HMDB0000693
     RDKit          3D
Heparan sulfate
 64 65  0  0  0  0  0  0  0  0999 V2000
   -5.5153    1.4647   -1.0106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3155    0.8739   -1.4168 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3822    0.8512   -0.3675 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3378    1.6536   -0.7507 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400    1.5693    0.0907 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6108    2.0259    1.4798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4421    1.9010    2.2473 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6397    2.3593    3.8289 S   0  0  0  0  0  6  0  0  0  0  0  0
   -0.4694    1.1532    4.7089 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4350    3.3754    4.1391 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1403    3.0356    4.0385 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6635    0.1463    0.1551 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6612    0.2151   -0.1785 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5572   -0.1182    0.8188 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2977    0.9703    1.1179 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5863    1.0849    0.7865 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8510    2.5295    0.5020 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9869    2.9680    0.1704 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8507    3.4948    0.5854 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1295    0.2652   -0.3165 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5318    1.0245   -1.4094 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8607    0.7825   -1.7618 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1689   -0.7833   -0.8393 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7991   -1.8431   -1.4561 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3952   -1.2835    0.3945 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7230   -2.3998   -0.0057 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2122   -3.8051    0.7448 S   0  0  0  0  0  6  0  0  0  0  0  0
    3.5732   -4.1608    0.2104 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2842   -4.9209    0.3673 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3551   -3.6188    2.4046 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5460   -0.7123   -0.6753 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2560   -2.0513   -0.6879 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9563   -0.5789   -0.0649 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8751   -1.4777   -0.7027 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8381   -1.2579   -2.0323 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5328   -2.6027   -2.8051 S   0  0  0  0  0  6  0  0  0  0  0  0
   -5.6913   -3.0414   -1.9352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5040   -3.7054   -2.9173 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0287   -2.2213   -4.3548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2088    1.4561   -1.8695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9276    0.9049   -0.1696 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3464    2.5158   -0.6378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8692    1.3169    0.5054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4604    2.2769   -0.2677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9413    3.0801    1.4142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3955    1.3845    1.9099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1825    3.8640    3.4877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7258   -0.1933    1.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0243   -0.4147    1.7557 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2029    0.8678    1.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0348    4.4570    0.8187 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0237   -0.3287   -0.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9923   -0.2958   -2.0368 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1153    1.4595   -2.5970 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5278    0.9960   -0.9055 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4384   -0.2848   -1.5076 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9941   -1.5970   -2.4035 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1845   -1.4779    1.1555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9711   -4.2716    2.8025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6913   -0.2990   -1.7181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6755   -2.5498    0.0572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9025   -0.7811    1.0222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6609   -2.4680   -0.5388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7957   -2.7793   -4.6220 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  2  0
  8 11  1  0
  5 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
 16 20  1  0
 20 21  1  0
 21 22  1  0
 20 23  1  0
 23 24  1  0
 23 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  2  0
 27 29  2  0
 27 30  1  0
 12 31  1  0
 31 32  1  0
 31 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  2  0
 36 38  2  0
 36 39  1  0
 33  3  1  0
 25 14  1  0
  1 40  1  0
  1 41  1  0
  1 42  1  0
  3 43  1  1
  5 44  1  6
  6 45  1  0
  6 46  1  0
 11 47  1  0
 12 48  1  1
 14 49  1  1
 16 50  1  1
 19 51  1  0
 20 52  1  1
 22 53  1  0
 22 54  1  0
 22 55  1  0
 23 56  1  6
 24 57  1  0
 25 58  1  1
 30 59  1  0
 31 60  1  6
 32 61  1  0
 33 62  1  1
 34 63  1  0
 39 64  1  0
M  END

View in JSmol

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 Mass

639.5200 Da

Monoisotopic Mass

639.00812 Da

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

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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

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	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0000693

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

General References

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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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Showing NP-Card for Heparan sulfate (NP0001418)

MOL for NP0001418 (Heparan sulfate)

3D MOL for NP0001418 (Heparan sulfate)

3D SDF for NP0001418 (Heparan sulfate)

3D-SDF for NP0001418 (Heparan sulfate)

PDB for NP0001418 (Heparan sulfate)

3D PDB for NP0001418 (Heparan sulfate)

SMILES for NP0001418 (Heparan sulfate)

INCHI for NP0001418 (Heparan sulfate)

Structure for NP0001418 (Heparan sulfate)

3D Structure for NP0001418 (Heparan sulfate)