Hmdb loader

Showing metabocard for Icariside D1 (HMDB0303758)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 04:24:36 UTC
Update Date2021-09-24 04:24:37 UTC
HMDB IDHMDB0303758
Secondary Accession NumbersNone
Metabolite Identification
Common NameIcariside D1
DescriptionIcariside d1 is a member of the class of compounds known as O-glycosyl compounds. O-glycosyl compounds are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Icariside d1 is soluble (in water) and a very weakly acidic compound (based on its pKa). Icariside d1 can be found in anise and pomegranate, which makes icariside d1 a potential biomarker for the consumption of these food products.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303758 (Icariside D1)


  Mrv0541 02241209482D          

 29 31  0  0  0  0            999 V2000
   -1.2891   -3.8951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -4.3076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175   -3.8951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175   -3.0701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -2.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -3.0701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -2.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -1.8327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -1.4203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -0.5953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -0.1829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175   -0.5953    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -0.1829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754    0.6421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1395    1.0545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1395    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8751    2.2534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0030    3.0687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4199    3.6517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891    1.0545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039    0.6421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175    1.0545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6093    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1923    2.4624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8183    3.1980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5882    3.4936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7175    4.3076    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6051    3.9941    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 13  1  0  0  0  0
 11 12  1  0  0  0  0
 11 22  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 21  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 24  1  0  0  0  0
 18 19  1  0  0  0  0
 18 26  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 29  1  0  0  0  0
 27 28  1  0  0  0  0
M  END
Download

3D MOL for HMDB0303758 (Icariside D1)

HMDB0303758
     RDKit          3D
Icariside D1
 57 59  0  0  0  0  0  0  0  0999 V2000
    7.5455    0.4569   -1.6405 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5661    1.2490   -1.0460 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9260    0.4200    0.0502 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8304    0.0254    1.0069 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2850   -0.7782   -0.6155 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0657   -0.9227    0.0103 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5732    0.3621    0.2416 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6090    0.2572    1.2276 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3447    0.6588    0.8323 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7649   -0.1537   -0.3049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4900    0.3735   -0.5617 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4909   -0.0778    0.2582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6425    0.6640    0.0419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1295    1.2334    1.2257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3739    2.0130    0.8822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4137    1.1600    0.2967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3647    0.5192    1.0760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3481   -0.2838    0.5562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4040   -0.4700   -0.7993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4633    0.1606   -1.6008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4892    0.9588   -1.0602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7146   -1.5488   -0.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8308   -2.0588    0.5305 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4797   -2.2812    0.2637 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5347   -2.5320    1.6475 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7988   -1.6112   -0.0411 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3801   -2.2870   -1.1411 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7870    1.1374    0.7099 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7370    2.4584    0.3299 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1935   -0.4650   -1.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8166    1.4876   -1.8079 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0661    2.1208   -0.6105 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3430   -0.4538    1.7100 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8972   -1.6820   -0.3668 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1314   -0.6514   -1.6903 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1612    0.7671   -0.6948 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6474    0.7496    1.6825 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4870    1.7023    0.4177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3706    0.0629   -1.2076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1698   -0.0866    1.3054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3271    0.4787    1.9942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3458    1.9176    1.5882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0723    2.7642    0.0996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7522    2.5801    1.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3219    0.6651    2.1457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0766   -0.7721    1.1781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1714   -1.0978   -1.2155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5535   -0.0217   -2.6739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7722    1.4322   -1.7394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8245   -1.5720   -1.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1715   -2.8004   -0.0282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5468   -3.3073   -0.2058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2362   -1.9763    2.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5415   -1.7799    0.7950 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9440   -3.0323   -0.8465 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8436    1.1003    1.8211 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8547    2.7678    0.0252 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
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  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  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 12 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
  7 28  1  0
 28 29  1  0
 28  3  1  0
 26 10  1  0
 21 16  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  4 33  1  0
  5 34  1  0
  5 35  1  0
  7 36  1  0
  9 37  1  0
  9 38  1  0
 10 39  1  0
 12 40  1  0
 14 41  1  0
 14 42  1  0
 15 43  1  0
 15 44  1  0
 17 45  1  0
 18 46  1  0
 19 47  1  0
 20 48  1  0
 21 49  1  0
 22 50  1  0
 23 51  1  0
 24 52  1  0
 25 53  1  0
 26 54  1  0
 27 55  1  0
 28 56  1  0
 29 57  1  0
M  END
Download

3D SDF for HMDB0303758 (Icariside D1)


  Mrv0541 02241209482D          

 29 31  0  0  0  0            999 V2000
   -1.2891   -3.8951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -4.3076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175   -3.8951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175   -3.0701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -2.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -3.0701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -2.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -1.8327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -1.4203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -0.5953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039   -0.1829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175   -0.5953    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -0.1829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754    0.6421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1395    1.0545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1395    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8751    2.2534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0030    3.0687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4199    3.6517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891    1.0545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0039    0.6421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7175    1.0545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6093    1.8795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1923    2.4624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8183    3.1980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5882    3.4936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7175    4.3076    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6051    3.9941    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 13  1  0  0  0  0
 11 12  1  0  0  0  0
 11 22  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 21  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 24  1  0  0  0  0
 18 19  1  0  0  0  0
 18 26  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 29  1  0  0  0  0
 27 28  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0303758

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1(O)COC(OCC2OC(OCCC3=CC=CC=C3)C(O)C(O)C2O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C19H28O10/c20-9-19(25)10-28-18(16(19)24)27-8-12-13(21)14(22)15(23)17(29-12)26-7-6-11-4-2-1-3-5-11/h1-5,12-18,20-25H,6-10H2

> <INCHI_KEY>
GZSQKOFXMZDKPV-UHFFFAOYSA-N

> <FORMULA>
C19H28O10

> <MOLECULAR_WEIGHT>
416.4196

> <EXACT_MASS>
416.168247116

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
42.005174282739894

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-6-(2-phenylethoxy)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-1.19

> <JCHEM_LOGP>
-1.5527774520000004

> <ALOGPS_LOGS>
-1.61

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.318486073980544

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.705149140598072

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423790163389214

> <JCHEM_POLAR_SURFACE_AREA>
158.3

> <JCHEM_REFRACTIVITY>
96.71239999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.02e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-6-(2-phenylethoxy)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0303758 (Icariside D1)

HMDB0303758
     RDKit          3D
Icariside D1
 57 59  0  0  0  0  0  0  0  0999 V2000
    7.5455    0.4569   -1.6405 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5661    1.2490   -1.0460 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9260    0.4200    0.0502 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8304    0.0254    1.0069 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2850   -0.7782   -0.6155 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0657   -0.9227    0.0103 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5732    0.3621    0.2416 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6090    0.2572    1.2276 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3447    0.6588    0.8323 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7649   -0.1537   -0.3049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4900    0.3735   -0.5617 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4909   -0.0778    0.2582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6425    0.6640    0.0419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1295    1.2334    1.2257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3739    2.0130    0.8822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4137    1.1600    0.2967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3647    0.5192    1.0760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3481   -0.2838    0.5562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4040   -0.4700   -0.7993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4633    0.1606   -1.6008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4892    0.9588   -1.0602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7146   -1.5488   -0.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8308   -2.0588    0.5305 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4797   -2.2812    0.2637 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5347   -2.5320    1.6475 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7988   -1.6112   -0.0411 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3801   -2.2870   -1.1411 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7870    1.1374    0.7099 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7370    2.4584    0.3299 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1935   -0.4650   -1.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8166    1.4876   -1.8079 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0661    2.1208   -0.6105 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3430   -0.4538    1.7100 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8972   -1.6820   -0.3668 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1314   -0.6514   -1.6903 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1612    0.7671   -0.6948 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6474    0.7496    1.6825 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4870    1.7023    0.4177 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3706    0.0629   -1.2076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1698   -0.0866    1.3054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3271    0.4787    1.9942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3458    1.9176    1.5882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0723    2.7642    0.0996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7522    2.5801    1.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3219    0.6651    2.1457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0766   -0.7721    1.1781 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1714   -1.0978   -1.2155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5535   -0.0217   -2.6739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7722    1.4322   -1.7394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8245   -1.5720   -1.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1715   -2.8004   -0.0282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5468   -3.3073   -0.2058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2362   -1.9763    2.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5415   -1.7799    0.7950 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9440   -3.0323   -0.8465 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8436    1.1003    1.8211 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8547    2.7678    0.0252 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
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  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  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 12 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
  7 28  1  0
 28 29  1  0
 28  3  1  0
 26 10  1  0
 21 16  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  4 33  1  0
  5 34  1  0
  5 35  1  0
  7 36  1  0
  9 37  1  0
  9 38  1  0
 10 39  1  0
 12 40  1  0
 14 41  1  0
 14 42  1  0
 15 43  1  0
 15 44  1  0
 17 45  1  0
 18 46  1  0
 19 47  1  0
 20 48  1  0
 21 49  1  0
 22 50  1  0
 23 51  1  0
 24 52  1  0
 25 53  1  0
 26 54  1  0
 27 55  1  0
 28 56  1  0
 29 57  1  0
M  END
Download

PDB for HMDB0303758 (Icariside D1)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.406  -7.271   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.741  -8.041   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.073  -7.271   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.073  -5.731   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.741  -4.961   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.406  -5.731   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.074  -4.961   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.074  -3.421   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.406  -2.651   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -2.406  -1.111   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.741  -0.341   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -5.073  -1.111   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -1.074  -0.341   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -1.074   1.199   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.260   1.968   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.260   3.508   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.634   4.206   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.872   5.728   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.784   6.817   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -2.406   3.508   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -2.406   1.968   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.741   1.199   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -5.073   1.968   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       3.004   3.508   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       4.092   4.596   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.394   5.970   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.831   6.521   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       5.073   8.041   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       2.996   7.456   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12   22                                                  
CONECT   12   11                                                            
CONECT   13   10   14                                                       
CONECT   14   13   15   21                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   24                                                  
CONECT   18   17   19   26                                                  
CONECT   19   18                                                            
CONECT   20   21                                                            
CONECT   21   14   20   22                                                  
CONECT   22   11   21   23                                                  
CONECT   23   22                                                            
CONECT   24   17   25                                                       
CONECT   25   24   26                                                       
CONECT   26   18   25   27   29                                             
CONECT   27   26   28                                                       
CONECT   28   27                                                            
CONECT   29   26                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   62    0
END
Download

3D PDB for HMDB0303758 (Icariside D1)

COMPND    HMDB0303758
HETATM    1  O1  UNL     1       7.546   0.457  -1.641  1.00  0.00           O  
HETATM    2  C1  UNL     1       6.566   1.249  -1.046  1.00  0.00           C  
HETATM    3  C2  UNL     1       5.926   0.420   0.050  1.00  0.00           C  
HETATM    4  O2  UNL     1       6.830   0.025   1.007  1.00  0.00           O  
HETATM    5  C3  UNL     1       5.285  -0.778  -0.615  1.00  0.00           C  
HETATM    6  O3  UNL     1       4.066  -0.923   0.010  1.00  0.00           O  
HETATM    7  C4  UNL     1       3.573   0.362   0.242  1.00  0.00           C  
HETATM    8  O4  UNL     1       2.609   0.257   1.228  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.345   0.659   0.832  1.00  0.00           C  
HETATM   10  C6  UNL     1       0.765  -0.154  -0.305  1.00  0.00           C  
HETATM   11  O5  UNL     1      -0.490   0.373  -0.562  1.00  0.00           O  
HETATM   12  C7  UNL     1      -1.491  -0.078   0.258  1.00  0.00           C  
HETATM   13  O6  UNL     1      -2.643   0.664   0.042  1.00  0.00           O  
HETATM   14  C8  UNL     1      -3.129   1.233   1.226  1.00  0.00           C  
HETATM   15  C9  UNL     1      -4.374   2.013   0.882  1.00  0.00           C  
HETATM   16  C10 UNL     1      -5.414   1.160   0.297  1.00  0.00           C  
HETATM   17  C11 UNL     1      -6.365   0.519   1.076  1.00  0.00           C  
HETATM   18  C12 UNL     1      -7.348  -0.284   0.556  1.00  0.00           C  
HETATM   19  C13 UNL     1      -7.404  -0.470  -0.799  1.00  0.00           C  
HETATM   20  C14 UNL     1      -6.463   0.161  -1.601  1.00  0.00           C  
HETATM   21  C15 UNL     1      -5.489   0.959  -1.060  1.00  0.00           C  
HETATM   22  C16 UNL     1      -1.715  -1.549  -0.119  1.00  0.00           C  
HETATM   23  O7  UNL     1      -2.831  -2.059   0.531  1.00  0.00           O  
HETATM   24  C17 UNL     1      -0.480  -2.281   0.264  1.00  0.00           C  
HETATM   25  O8  UNL     1      -0.535  -2.532   1.647  1.00  0.00           O  
HETATM   26  C18 UNL     1       0.799  -1.611  -0.041  1.00  0.00           C  
HETATM   27  O9  UNL     1       1.380  -2.287  -1.141  1.00  0.00           O  
HETATM   28  C19 UNL     1       4.787   1.137   0.710  1.00  0.00           C  
HETATM   29  O10 UNL     1       4.737   2.458   0.330  1.00  0.00           O  
HETATM   30  H1  UNL     1       7.193  -0.465  -1.848  1.00  0.00           H  
HETATM   31  H2  UNL     1       5.817   1.488  -1.808  1.00  0.00           H  
HETATM   32  H3  UNL     1       7.066   2.121  -0.611  1.00  0.00           H  
HETATM   33  H4  UNL     1       6.343  -0.454   1.710  1.00  0.00           H  
HETATM   34  H5  UNL     1       5.897  -1.682  -0.367  1.00  0.00           H  
HETATM   35  H6  UNL     1       5.131  -0.651  -1.690  1.00  0.00           H  
HETATM   36  H7  UNL     1       3.161   0.767  -0.695  1.00  0.00           H  
HETATM   37  H8  UNL     1       0.647   0.750   1.683  1.00  0.00           H  
HETATM   38  H9  UNL     1       1.487   1.702   0.418  1.00  0.00           H  
HETATM   39  H10 UNL     1       1.371   0.063  -1.208  1.00  0.00           H  
HETATM   40  H11 UNL     1      -1.170  -0.087   1.305  1.00  0.00           H  
HETATM   41  H12 UNL     1      -3.327   0.479   1.994  1.00  0.00           H  
HETATM   42  H13 UNL     1      -2.346   1.918   1.588  1.00  0.00           H  
HETATM   43  H14 UNL     1      -4.072   2.764   0.100  1.00  0.00           H  
HETATM   44  H15 UNL     1      -4.752   2.580   1.756  1.00  0.00           H  
HETATM   45  H16 UNL     1      -6.322   0.665   2.146  1.00  0.00           H  
HETATM   46  H17 UNL     1      -8.077  -0.772   1.178  1.00  0.00           H  
HETATM   47  H18 UNL     1      -8.171  -1.098  -1.216  1.00  0.00           H  
HETATM   48  H19 UNL     1      -6.553  -0.022  -2.674  1.00  0.00           H  
HETATM   49  H20 UNL     1      -4.772   1.432  -1.739  1.00  0.00           H  
HETATM   50  H21 UNL     1      -1.825  -1.572  -1.221  1.00  0.00           H  
HETATM   51  H22 UNL     1      -3.171  -2.800  -0.028  1.00  0.00           H  
HETATM   52  H23 UNL     1      -0.547  -3.307  -0.206  1.00  0.00           H  
HETATM   53  H24 UNL     1      -1.236  -1.976   2.071  1.00  0.00           H  
HETATM   54  H25 UNL     1       1.541  -1.780   0.795  1.00  0.00           H  
HETATM   55  H26 UNL     1       1.944  -3.032  -0.847  1.00  0.00           H  
HETATM   56  H27 UNL     1       4.844   1.100   1.821  1.00  0.00           H  
HETATM   57  H28 UNL     1       3.855   2.768   0.025  1.00  0.00           H  
CONECT    1    2   30
CONECT    2    3   31   32
CONECT    3    4    5   28
CONECT    4   33
CONECT    5    6   34   35
CONECT    6    7
CONECT    7    8   28   36
CONECT    8    9
CONECT    9   10   37   38
CONECT   10   11   26   39
CONECT   11   12
CONECT   12   13   22   40
CONECT   13   14
CONECT   14   15   41   42
CONECT   15   16   43   44
CONECT   16   17   17   21
CONECT   17   18   45
CONECT   18   19   19   46
CONECT   19   20   47
CONECT   20   21   21   48
CONECT   21   49
CONECT   22   23   24   50
CONECT   23   51
CONECT   24   25   26   52
CONECT   25   53
CONECT   26   27   54
CONECT   27   55
CONECT   28   29   56
CONECT   29   57
END
Download

SMILES for HMDB0303758 (Icariside D1)

OCC1(O)COC(OCC2OC(OCCC3=CC=CC=C3)C(O)C(O)C2O)C1O
Download

INCHI for HMDB0303758 (Icariside D1)

InChI=1S/C19H28O10/c20-9-19(25)10-28-18(16(19)24)27-8-12-13(21)14(22)15(23)17(29-12)26-7-6-11-4-2-1-3-5-11/h1-5,12-18,20-25H,6-10H2
Download
View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC19H28O10
Average Molecular Weight416.4196
Monoisotopic Molecular Weight416.168247116
IUPAC Name2-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-6-(2-phenylethoxy)oxane-3,4,5-triol
Traditional Name2-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-6-(2-phenylethoxy)oxane-3,4,5-triol
CAS Registry NumberNot Available
SMILES
OCC1(O)COC(OCC2OC(OCCC3=CC=CC=C3)C(O)C(O)C2O)C1O
InChI Identifier
InChI=1S/C19H28O10/c20-9-19(25)10-28-18(16(19)24)27-8-12-13(21)14(22)15(23)17(29-12)26-7-6-11-4-2-1-3-5-11/h1-5,12-18,20-25H,6-10H2
InChI KeyGZSQKOFXMZDKPV-UHFFFAOYSA-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
  • Monocyclic benzene moiety
  • Oxane
  • Benzenoid
  • Tertiary alcohol
  • Tetrahydrofuran
  • Secondary alcohol
  • Polyol
  • Oxacycle
  • Acetal
  • Organoheterocyclic compound
  • Primary alcohol
  • Alcohol
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.2ALOGPS
logP-1.6ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)11.71ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area158.3 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity96.71 m³·mol⁻¹ChemAxon
Polarizability42.01 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+197.01832859911
AllCCS[M+H-H2O]+194.70832859911
AllCCS[M+Na]+199.74432859911
AllCCS[M+NH4]+199.13832859911
AllCCS[M-H]-191.81232859911
AllCCS[M+Na-2H]-192.37932859911
AllCCS[M+HCOO]-193.14532859911
DeepCCS[M+H]+188.4730932474
DeepCCS[M-H]-186.07930932474
DeepCCS[M-2H]-220.40330932474
DeepCCS[M+Na]+195.83230932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202210.4598 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.41 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1315.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid207.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid97.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid185.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid67.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid296.1 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid349.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)438.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid707.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid174.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid846.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid224.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid249.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate363.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA272.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water148.8 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 10V, Positive-QTOFsplash10-014j-0639500000-0cf44c3fcbd27d9177982019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 20V, Positive-QTOFsplash10-0ab9-0921000000-cd139961efab667714d62019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 40V, Positive-QTOFsplash10-0a4i-2910000000-dd4582eac3e5e83209632019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 10V, Negative-QTOFsplash10-014j-1947500000-1fb798afd4211551513f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 20V, Negative-QTOFsplash10-015a-1943000000-0b5aef77d72684a2de642019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 40V, Negative-QTOFsplash10-0kgn-5910000000-18c163731afd8f591f5e2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 10V, Negative-QTOFsplash10-014i-0035900000-7a0cc8cdb3144933f4e82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 20V, Negative-QTOFsplash10-01ox-9747000000-d72e97025653ce88db422021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 40V, Negative-QTOFsplash10-0f6x-9400000000-d2f63f78e6f3f00b063d2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 10V, Positive-QTOFsplash10-0avj-0921100000-1f068ae3c8d829e7ab642021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 20V, Positive-QTOFsplash10-0a4i-1923000000-0fb078f5ecc3bf8b53d02021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Icariside D1 40V, Positive-QTOFsplash10-0a4i-4910000000-7284f878bd7bae61b3dc2021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB020703
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound13893574
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