Np mrd loader

Showing NP-Card for (25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+ (NP0038227)

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Record Information
Version2.0
Created at2021-06-20 20:58:17 UTC
Updated at2021-06-30 00:10:54 UTC
NP-MRD IDNP0038227
Secondary Accession NumbersNone
Natural Product Identification
Common Name(25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+
Provided ByJEOL DatabaseJEOL Logo
Description(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,13'S,15'R,16'R,18'S)-16'-{[(2R,3R,4R,5R,6R)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]Icosan]-11'-en-10'-one belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative. (25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+ is found in Agave utahensis. (25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+ was first documented in 2009 (Yokosuka, A., et al.). Based on a literature review very few articles have been published on (1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,13'S,15'R,16'R,18'S)-16'-{[(2R,3R,4R,5R,6R)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]Icosan]-11'-en-10'-one.
Structure
Thumb
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0038227 ((25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+)


  Mrv1652306202122583D          

131139  0  0  0  0            999 V2000
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M  END
Download

3D MOL for NP0038227 ((25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+)

     RDKit          3D

131139  0  0  0  0  0  0  0  0999 V2000
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M  END
Download

3D SDF for NP0038227 ((25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+)


  Mrv1652306202122583D          

131139  0  0  0  0            999 V2000
   -2.3888   -6.1397   -6.6866 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0038227

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(O[C@]2([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]([H])(O[C@]3([H])C([H])([H])[C@]4([H])C([H])([H])C([H])([H])[C@]5([H])C(=C([H])C(=O)[C@@]6(C([H])([H])[H])[C@@]5([H])C([H])([H])[C@]5([H])O[C@@]7(OC([H])([H])[C@]([H])(C([H])([H])[H])C([H])([H])C7([H])[H])[C@@]([H])(C([H])([H])[H])[C@]65[H])[C@@]4(C([H])([H])[H])C([H])([H])[C@@]3([H])O[H])O[C@]2([H])C([H])([H])O[H])[C@]([H])(O[C@]2([H])OC([H])([H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])[C@@]([H])(O[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C44H68O19/c1-17-7-8-44(57-15-17)18(2)30-26(63-44)10-22-20-6-5-19-9-25(23(47)12-42(19,3)21(20)11-29(49)43(22,30)4)58-40-36(55)34(53)37(28(14-46)60-40)61-41-38(33(52)32(51)27(13-45)59-41)62-39-35(54)31(50)24(48)16-56-39/h11,17-20,22-28,30-41,45-48,50-55H,5-10,12-16H2,1-4H3/t17-,18+,19+,20-,22+,23-,24-,25-,26+,27-,28-,30+,31+,32-,33+,34-,35-,36-,37+,38-,39+,40-,41+,42+,43-,44-/m1/s1

> <INCHI_KEY>
VRYJBJLYAWJDKR-YRLNELPCSA-N

> <FORMULA>
C44H68O19

> <MOLECULAR_WEIGHT>
901.009

> <EXACT_MASS>
900.43547997

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
131

> <JCHEM_AVERAGE_POLARIZABILITY>
95.56533507408952

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,13'S,15'R,16'R,18'S)-16'-{[(2R,3R,4R,5R,6R)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-11'-en-10'-one

> <ALOGPS_LOGP>
-0.27

> <JCHEM_LOGP>
-1.137308363

> <ALOGPS_LOGS>
-2.82

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.370381934094464

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.88641389454098

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1638264313124793

> <JCHEM_POLAR_SURFACE_AREA>
293.21

> <JCHEM_REFRACTIVITY>
213.57470000000012

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.36e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,13'S,15'R,16'R,18'S)-16'-{[(2R,3R,4R,5R,6R)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-11'-en-10'-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0038227 ((25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+)

     RDKit          3D

131139  0  0  0  0  0  0  0  0999 V2000
   -2.3888   -6.1397   -6.6866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5405   -6.2119   -5.4240 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0769   -5.3157   -4.3019 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7435   -6.1148   -3.0254 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9465   -5.1929   -2.1063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4763   -3.8305   -2.5307 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8033   -2.5660   -1.9803 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0160   -2.4979   -0.4581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5772   -1.1707    0.1480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2816   -0.0034   -0.5530 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9639    1.3193    0.1546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7391    2.4965   -0.4469 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2775    3.6620    0.2539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1542    4.7873    0.1699 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7707    5.6441   -0.9052 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5271    6.3585   -0.7512 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6454    5.5944   -1.3797 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3980    5.3948   -2.7740 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2405    6.8375    0.6864 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6157    5.9257    1.3873 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7401    6.5552    2.0123 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8057    6.5742    1.0711 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0298    7.0856    1.6165 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0773    7.1704    0.4942 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5235    5.8845    0.0654 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4877    6.2019    2.7811 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7083    6.6868    3.3463 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4035    6.1784    3.8618 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8443    5.2954    4.9067 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0643    5.7268    3.2717 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0169    5.9688    4.2325 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6727    4.8242    5.0153 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6395    4.4262    4.6174 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1294    3.3187    5.3681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2330    3.6647    6.8530 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6645    2.5431    7.6250 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1404    4.1064    7.3612 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0515    4.5552    8.7220 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6992    5.2373    6.4994 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0430    5.5366    6.9284 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5538    6.9031    1.4609 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3402    7.3843    2.8023 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2016    5.5159    1.5329 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5589    5.6858    1.9937 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5111    2.5828   -1.9681 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3911    3.5395   -2.5616 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7819    1.2432   -2.6649 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9820    0.0444   -2.0806 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5205    0.2734   -2.3903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3625   -1.3227   -2.7048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1027   -1.4373   -3.8327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3186   -2.7469   -4.5285 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1058   -2.8165   -5.4668 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4551   -3.9115   -4.0719 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0605   -3.7286   -4.7008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0185   -7.2769   -3.4161 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4739   -7.5928   -4.7464 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4725   -8.5278   -5.4319 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4697   -9.9095   -4.7820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8953  -10.4598   -4.6995 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9291  -11.7938   -3.9618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8097   -9.4342   -4.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7754   -8.1831   -4.7142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4359   -6.3926   -6.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3636   -5.1285   -7.1057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0125   -6.8268   -7.4507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5174   -5.9312   -5.6891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1701   -5.2291   -4.3706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6684   -6.4336   -2.5275 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1331   -5.2941   -2.2599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1516   -5.4136   -1.0541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5317   -3.7918   -2.2051 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2765   -2.6180   -2.1653 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.8300   -1.1721    1.2155 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5121   -1.0687    0.0887 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3639   -0.1695   -0.4315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2190    1.2432    1.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1133    1.5277    0.1375 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.6897    7.2563   -1.3617 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7870    4.6116   -0.9235 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5717    6.1695   -1.2895 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1821    4.9449   -3.1334 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2306    7.8272    0.6380 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4862    7.5812    2.3116 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8504    8.1123    1.9630 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for NP0038227 ((25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+)

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0      -2.389  -6.140  -6.687  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.541  -6.212  -5.424  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.077  -5.316  -4.302  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.744  -6.115  -3.025  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.947  -5.193  -2.106  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.476  -3.830  -2.531  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.803  -2.566  -1.980  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.016  -2.498  -0.458  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.577  -1.171   0.148  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.282  -0.003  -0.553  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.964   1.319   0.155  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.739   2.497  -0.447  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.278   3.662   0.254  0.00  0.00           O+0
HETATM   14  C   UNK     0      -2.154   4.787   0.170  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.771   5.644  -0.905  0.00  0.00           O+0
HETATM   16  C   UNK     0      -0.527   6.359  -0.751  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.645   5.594  -1.380  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.398   5.395  -2.774  0.00  0.00           O+0
HETATM   19  C   UNK     0      -0.241   6.838   0.686  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.616   5.926   1.387  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.740   6.555   2.012  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.806   6.574   1.071  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.030   7.086   1.617  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.077   7.170   0.494  0.00  0.00           C+0
HETATM   25  O   UNK     0       5.524   5.885   0.065  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.488   6.202   2.781  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.708   6.687   3.346  0.00  0.00           O+0
HETATM   28  C   UNK     0       3.404   6.178   3.862  0.00  0.00           C+0
HETATM   29  O   UNK     0       3.844   5.295   4.907  0.00  0.00           O+0
HETATM   30  C   UNK     0       2.064   5.727   3.272  0.00  0.00           C+0
HETATM   31  O   UNK     0       1.017   5.969   4.232  0.00  0.00           O+0
HETATM   32  C   UNK     0       0.673   4.824   5.015  0.00  0.00           C+0
HETATM   33  O   UNK     0      -0.640   4.426   4.617  0.00  0.00           O+0
HETATM   34  C   UNK     0      -1.129   3.319   5.368  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.233   3.665   6.853  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.665   2.543   7.625  0.00  0.00           O+0
HETATM   37  C   UNK     0       0.140   4.106   7.361  0.00  0.00           C+0
HETATM   38  O   UNK     0       0.052   4.555   8.722  0.00  0.00           O+0
HETATM   39  C   UNK     0       0.699   5.237   6.499  0.00  0.00           C+0
HETATM   40  O   UNK     0       2.043   5.537   6.928  0.00  0.00           O+0
HETATM   41  C   UNK     0      -1.554   6.903   1.461  0.00  0.00           C+0
HETATM   42  O   UNK     0      -1.340   7.384   2.802  0.00  0.00           O+0
HETATM   43  C   UNK     0      -2.202   5.516   1.533  0.00  0.00           C+0
HETATM   44  O   UNK     0      -3.559   5.686   1.994  0.00  0.00           O+0
HETATM   45  C   UNK     0      -1.511   2.583  -1.968  0.00  0.00           C+0
HETATM   46  O   UNK     0      -2.391   3.539  -2.562  0.00  0.00           O+0
HETATM   47  C   UNK     0      -1.782   1.243  -2.665  0.00  0.00           C+0
HETATM   48  C   UNK     0      -0.982   0.044  -2.081  0.00  0.00           C+0
HETATM   49  C   UNK     0       0.521   0.273  -2.390  0.00  0.00           C+0
HETATM   50  C   UNK     0      -1.363  -1.323  -2.705  0.00  0.00           C+0
HETATM   51  C   UNK     0      -2.103  -1.437  -3.833  0.00  0.00           C+0
HETATM   52  C   UNK     0      -2.319  -2.747  -4.529  0.00  0.00           C+0
HETATM   53  O   UNK     0      -3.106  -2.817  -5.467  0.00  0.00           O+0
HETATM   54  C   UNK     0      -1.455  -3.912  -4.072  0.00  0.00           C+0
HETATM   55  C   UNK     0      -0.061  -3.729  -4.701  0.00  0.00           C+0
HETATM   56  O   UNK     0      -1.018  -7.277  -3.416  0.00  0.00           O+0
HETATM   57  C   UNK     0      -1.474  -7.593  -4.746  0.00  0.00           C+0
HETATM   58  C   UNK     0      -0.473  -8.528  -5.432  0.00  0.00           C+0
HETATM   59  C   UNK     0      -0.470  -9.909  -4.782  0.00  0.00           C+0
HETATM   60  C   UNK     0      -1.895 -10.460  -4.699  0.00  0.00           C+0
HETATM   61  C   UNK     0      -1.929 -11.794  -3.962  0.00  0.00           C+0
HETATM   62  C   UNK     0      -2.810  -9.434  -4.029  0.00  0.00           C+0
HETATM   63  O   UNK     0      -2.775  -8.183  -4.714  0.00  0.00           O+0
HETATM   64  H   UNK     0      -3.436  -6.393  -6.491  0.00  0.00           H+0
HETATM   65  H   UNK     0      -2.364  -5.128  -7.106  0.00  0.00           H+0
HETATM   66  H   UNK     0      -2.013  -6.827  -7.451  0.00  0.00           H+0
HETATM   67  H   UNK     0      -0.517  -5.931  -5.689  0.00  0.00           H+0
HETATM   68  H   UNK     0      -3.170  -5.229  -4.371  0.00  0.00           H+0
HETATM   69  H   UNK     0      -2.668  -6.434  -2.527  0.00  0.00           H+0
HETATM   70  H   UNK     0       0.133  -5.294  -2.260  0.00  0.00           H+0
HETATM   71  H   UNK     0      -1.152  -5.414  -1.054  0.00  0.00           H+0
HETATM   72  H   UNK     0      -2.532  -3.792  -2.205  0.00  0.00           H+0
HETATM   73  H   UNK     0       0.277  -2.618  -2.165  0.00  0.00           H+0
HETATM   74  H   UNK     0      -2.076  -2.655  -0.220  0.00  0.00           H+0
HETATM   75  H   UNK     0      -0.464  -3.309   0.031  0.00  0.00           H+0
HETATM   76  H   UNK     0      -0.830  -1.172   1.216  0.00  0.00           H+0
HETATM   77  H   UNK     0       0.512  -1.069   0.089  0.00  0.00           H+0
HETATM   78  H   UNK     0      -2.364  -0.170  -0.432  0.00  0.00           H+0
HETATM   79  H   UNK     0      -1.219   1.243   1.220  0.00  0.00           H+0
HETATM   80  H   UNK     0       0.113   1.528   0.138  0.00  0.00           H+0
HETATM   81  H   UNK     0      -2.807   2.353  -0.234  0.00  0.00           H+0
HETATM   82  H   UNK     0      -3.171   4.444  -0.057  0.00  0.00           H+0
HETATM   83  H   UNK     0      -0.690   7.256  -1.362  0.00  0.00           H+0
HETATM   84  H   UNK     0       0.787   4.612  -0.924  0.00  0.00           H+0
HETATM   85  H   UNK     0       1.572   6.170  -1.290  0.00  0.00           H+0
HETATM   86  H   UNK     0       1.182   4.945  -3.133  0.00  0.00           H+0
HETATM   87  H   UNK     0       0.231   7.827   0.638  0.00  0.00           H+0
HETATM   88  H   UNK     0       1.486   7.581   2.312  0.00  0.00           H+0
HETATM   89  H   UNK     0       3.850   8.112   1.963  0.00  0.00           H+0
HETATM   90  H   UNK     0       5.952   7.748   0.812  0.00  0.00           H+0
HETATM   91  H   UNK     0       4.643   7.664  -0.381  0.00  0.00           H+0
HETATM   92  H   UNK     0       6.193   5.591   0.710  0.00  0.00           H+0
HETATM   93  H   UNK     0       4.672   5.174   2.444  0.00  0.00           H+0
HETATM   94  H   UNK     0       5.812   6.192   4.186  0.00  0.00           H+0
HETATM   95  H   UNK     0       3.312   7.170   4.324  0.00  0.00           H+0
HETATM   96  H   UNK     0       3.271   5.474   5.688  0.00  0.00           H+0
HETATM   97  H   UNK     0       2.097   4.663   3.002  0.00  0.00           H+0
HETATM   98  H   UNK     0       1.375   3.998   4.846  0.00  0.00           H+0
HETATM   99  H   UNK     0      -2.119   3.055   4.979  0.00  0.00           H+0
HETATM  100  H   UNK     0      -0.490   2.442   5.203  0.00  0.00           H+0
HETATM  101  H   UNK     0      -1.955   4.475   7.012  0.00  0.00           H+0
HETATM  102  H   UNK     0      -2.574   2.328   7.347  0.00  0.00           H+0
HETATM  103  H   UNK     0       0.837   3.259   7.376  0.00  0.00           H+0
HETATM  104  H   UNK     0      -0.446   3.854   9.191  0.00  0.00           H+0
HETATM  105  H   UNK     0       0.115   6.154   6.649  0.00  0.00           H+0
HETATM  106  H   UNK     0       1.966   5.644   7.901  0.00  0.00           H+0
HETATM  107  H   UNK     0      -2.237   7.619   0.988  0.00  0.00           H+0
HETATM  108  H   UNK     0      -0.757   6.733   3.248  0.00  0.00           H+0
HETATM  109  H   UNK     0      -1.723   4.896   2.298  0.00  0.00           H+0
HETATM  110  H   UNK     0      -3.502   6.305   2.747  0.00  0.00           H+0
HETATM  111  H   UNK     0      -0.491   2.916  -2.181  0.00  0.00           H+0
HETATM  112  H   UNK     0      -2.026   4.425  -2.341  0.00  0.00           H+0
HETATM  113  H   UNK     0      -2.861   1.037  -2.606  0.00  0.00           H+0
HETATM  114  H   UNK     0      -1.567   1.369  -3.735  0.00  0.00           H+0
HETATM  115  H   UNK     0       1.158  -0.534  -2.017  0.00  0.00           H+0
HETATM  116  H   UNK     0       0.687   0.335  -3.473  0.00  0.00           H+0
HETATM  117  H   UNK     0       0.905   1.199  -1.954  0.00  0.00           H+0
HETATM  118  H   UNK     0      -2.534  -0.595  -4.362  0.00  0.00           H+0
HETATM  119  H   UNK     0       0.387  -2.758  -4.465  0.00  0.00           H+0
HETATM  120  H   UNK     0      -0.122  -3.762  -5.795  0.00  0.00           H+0
HETATM  121  H   UNK     0       0.646  -4.497  -4.371  0.00  0.00           H+0
HETATM  122  H   UNK     0      -0.738  -8.648  -6.489  0.00  0.00           H+0
HETATM  123  H   UNK     0       0.541  -8.113  -5.383  0.00  0.00           H+0
HETATM  124  H   UNK     0      -0.032  -9.841  -3.778  0.00  0.00           H+0
HETATM  125  H   UNK     0       0.167 -10.588  -5.361  0.00  0.00           H+0
HETATM  126  H   UNK     0      -2.252 -10.618  -5.726  0.00  0.00           H+0
HETATM  127  H   UNK     0      -1.580 -11.687  -2.929  0.00  0.00           H+0
HETATM  128  H   UNK     0      -1.290 -12.530  -4.461  0.00  0.00           H+0
HETATM  129  H   UNK     0      -2.947 -12.197  -3.935  0.00  0.00           H+0
HETATM  130  H   UNK     0      -2.548  -9.284  -2.975  0.00  0.00           H+0
HETATM  131  H   UNK     0      -3.846  -9.787  -4.054  0.00  0.00           H+0
CONECT    1    2   64   65   66                                             
CONECT    2   57    3    1   67                                             
CONECT    3   54    4    2   68                                             
CONECT    4    5    3   56   69                                             
CONECT    5    6    4   70   71                                             
CONECT    6    7   54    5   72                                             
CONECT    7    8   50    6   73                                             
CONECT    8    9    7   74   75                                             
CONECT    9   10    8   76   77                                             
CONECT   10    9   11   48   78                                             
CONECT   11   12   10   79   80                                             
CONECT   12   11   45   13   81                                             
CONECT   13   12   14                                                       
CONECT   14   43   15   13   82                                             
CONECT   15   16   14                                                       
CONECT   16   19   15   17   83                                             
CONECT   17   18   16   84   85                                             
CONECT   18   17   86                                                       
CONECT   19   41   16   20   87                                             
CONECT   20   21   19                                                       
CONECT   21   22   20   30   88                                             
CONECT   22   23   21                                                       
CONECT   23   26   22   24   89                                             
CONECT   24   25   23   90   91                                             
CONECT   25   24   92                                                       
CONECT   26   28   23   27   93                                             
CONECT   27   26   94                                                       
CONECT   28   26   30   29   95                                             
CONECT   29   28   96                                                       
CONECT   30   31   21   28   97                                             
CONECT   31   30   32                                                       
CONECT   32   31   39   33   98                                             
CONECT   33   34   32                                                       
CONECT   34   35   33   99  100                                             
CONECT   35   37   34   36  101                                             
CONECT   36   35  102                                                       
CONECT   37   39   35   38  103                                             
CONECT   38   37  104                                                       
CONECT   39   32   37   40  105                                             
CONECT   40   39  106                                                       
CONECT   41   43   19   42  107                                             
CONECT   42   41  108                                                       
CONECT   43   14   41   44  109                                             
CONECT   44   43  110                                                       
CONECT   45   12   47   46  111                                             
CONECT   46   45  112                                                       
CONECT   47   48   45  113  114                                             
CONECT   48   50   47   10   49                                             
CONECT   49   48  115  116  117                                             
CONECT   50   48    7   51                                                  
CONECT   51   50   52  118                                                  
CONECT   52   54   51   53                                                  
CONECT   53   52                                                            
CONECT   54   52    6    3   55                                             
CONECT   55   54  119  120  121                                             
CONECT   56    4   57                                                       
CONECT   57   58   63    2   56                                             
CONECT   58   57   59  122  123                                             
CONECT   59   58   60  124  125                                             
CONECT   60   59   62   61  126                                             
CONECT   61   60  127  128  129                                             
CONECT   62   60   63  130  131                                             
CONECT   63   62   57                                                       
CONECT   64    1                                                            
CONECT   65    1                                                            
CONECT   66    1                                                            
CONECT   67    2                                                            
CONECT   68    3                                                            
CONECT   69    4                                                            
CONECT   70    5                                                            
CONECT   71    5                                                            
CONECT   72    6                                                            
CONECT   73    7                                                            
CONECT   74    8                                                            
CONECT   75    8                                                            
CONECT   76    9                                                            
CONECT   77    9                                                            
CONECT   78   10                                                            
CONECT   79   11                                                            
CONECT   80   11                                                            
CONECT   81   12                                                            
CONECT   82   14                                                            
CONECT   83   16                                                            
CONECT   84   17                                                            
CONECT   85   17                                                            
CONECT   86   18                                                            
CONECT   87   19                                                            
CONECT   88   21                                                            
CONECT   89   23                                                            
CONECT   90   24                                                            
CONECT   91   24                                                            
CONECT   92   25                                                            
CONECT   93   26                                                            
CONECT   94   27                                                            
CONECT   95   28                                                            
CONECT   96   29                                                            
CONECT   97   30                                                            
CONECT   98   32                                                            
CONECT   99   34                                                            
CONECT  100   34                                                            
CONECT  101   35                                                            
CONECT  102   36                                                            
CONECT  103   37                                                            
CONECT  104   38                                                            
CONECT  105   39                                                            
CONECT  106   40                                                            
CONECT  107   41                                                            
CONECT  108   42                                                            
CONECT  109   43                                                            
CONECT  110   44                                                            
CONECT  111   45                                                            
CONECT  112   46                                                            
CONECT  113   47                                                            
CONECT  114   47                                                            
CONECT  115   49                                                            
CONECT  116   49                                                            
CONECT  117   49                                                            
CONECT  118   51                                                            
CONECT  119   55                                                            
CONECT  120   55                                                            
CONECT  121   55                                                            
CONECT  122   58                                                            
CONECT  123   58                                                            
CONECT  124   59                                                            
CONECT  125   59                                                            
CONECT  126   60                                                            
CONECT  127   61                                                            
CONECT  128   61                                                            
CONECT  129   61                                                            
CONECT  130   62                                                            
CONECT  131   62                                                            
MASTER        0    0    0    0    0    0    0    0  131    0  278    0
END
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3D PDB for NP0038227 ((25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+)

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SMILES for NP0038227 ((25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+)
[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(O[C@]2([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]([H])(O[C@]3([H])C([H])([H])[C@]4([H])C([H])([H])C([H])([H])[C@]5([H])C(=C([H])C(=O)[C@@]6(C([H])([H])[H])[C@@]5([H])C([H])([H])[C@]5([H])O[C@@]7(OC([H])([H])[C@]([H])(C([H])([H])[H])C([H])([H])C7([H])[H])[C@@]([H])(C([H])([H])[H])[C@]65[H])[C@@]4(C([H])([H])[H])C([H])([H])[C@@]3([H])O[H])O[C@]2([H])C([H])([H])O[H])[C@]([H])(O[C@]2([H])OC([H])([H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])[C@@]([H])(O[H])[C@]1([H])O[H]
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INCHI for NP0038227 ((25R)-2alpha-hydroxy-beta[O-beta-D-xylopyranosyl-(1-2)-O-beta-D-glucopyra+)
InChI=1S/C44H68O19/c1-17-7-8-44(57-15-17)18(2)30-26(63-44)10-22-20-6-5-19-9-25(23(47)12-42(19,3)21(20)11-29(49)43(22,30)4)58-40-36(55)34(53)37(28(14-46)60-40)61-41-38(33(52)32(51)27(13-45)59-41)62-39-35(54)31(50)24(48)16-56-39/h11,17-20,22-28,30-41,45-48,50-55H,5-10,12-16H2,1-4H3/t17-,18+,19+,20-,22+,23-,24-,25-,26+,27-,28-,30+,31+,32-,33+,34-,35-,36-,37+,38-,39+,40-,41+,42+,43-,44-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC44H68O19
Average Mass901.0090 Da
Monoisotopic Mass900.43548 Da
IUPAC Name(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,13'S,15'R,16'R,18'S)-16'-{[(2R,3R,4R,5R,6R)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-11'-en-10'-one
Traditional Name(1'S,2R,2'S,4'S,5R,7'S,8'R,9'S,13'S,15'R,16'R,18'S)-16'-{[(2R,3R,4R,5R,6R)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15'-hydroxy-5,7',9',13'-tetramethyl-5'-oxaspiro[oxane-2,6'-pentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan]-11'-en-10'-one
CAS Registry NumberNot Available
SMILES
[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(O[C@]2([H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@]([H])(O[C@]3([H])C([H])([H])[C@]4([H])C([H])([H])C([H])([H])[C@]5([H])C(=C([H])C(=O)[C@@]6(C([H])([H])[H])[C@@]5([H])C([H])([H])[C@]5([H])O[C@@]7(OC([H])([H])[C@]([H])(C([H])([H])[H])C([H])([H])C7([H])[H])[C@@]([H])(C([H])([H])[H])[C@]65[H])[C@@]4(C([H])([H])[H])C([H])([H])[C@@]3([H])O[H])O[C@]2([H])C([H])([H])O[H])[C@]([H])(O[C@]2([H])OC([H])([H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])[C@@]([H])(O[H])[C@]1([H])O[H]
InChI Identifier
InChI=1S/C44H68O19/c1-17-7-8-44(57-15-17)18(2)30-26(63-44)10-22-20-6-5-19-9-25(23(47)12-42(19,3)21(20)11-29(49)43(22,30)4)58-40-36(55)34(53)37(28(14-46)60-40)61-41-38(33(52)32(51)27(13-45)59-41)62-39-35(54)31(50)24(48)16-56-39/h11,17-20,22-28,30-41,45-48,50-55H,5-10,12-16H2,1-4H3/t17-,18+,19+,20-,22+,23-,24-,25-,26+,27-,28-,30+,31+,32-,33+,34-,35-,36-,37+,38-,39+,40-,41+,42+,43-,44-/m1/s1
InChI KeyVRYJBJLYAWJDKR-YRLNELPCSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, C5D5N, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Agave utahensisJEOL database
    • Yokosuka, A., et al, Phytochemistry 70, 807 (2009)
Chemical Taxonomy
Description Belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassSteroids and steroid derivatives  
Sub ClassSteroidal glycosides  
Direct ParentSteroidal saponins  
Alternative Parents
Substituents
  • Steroidal saponin
    • 

  • Triterpenoid
    • 

  • Spirostane skeleton
    • 

  • Oligosaccharide
    • 

  • 2-hydroxysteroid
    • 

  • Hydroxysteroid
    • 

  • 12-oxosteroid
    • 

  • Oxosteroid
    • 

  • Glycosyl compound
    • 

  • O-glycosyl compound
    • 

  • Cyclohexenone
    • 

  • Ketal
    • 

  • Oxane
    • 

  • Tetrahydrofuran
    • 

  • Cyclic alcohol
    • 

  • Secondary alcohol
    • 

  • Ketone
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Acetal
    • 

  • Alcohol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.27ALOGPS
logP-1.1ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)11.89ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area293.21 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity213.57 m³·mol⁻¹ChemAxon
Polarizability95.57 ųChemAxon
Number of Rings9ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44139498  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Yokosuka, A., et al. (2009). Yokosuka, A., et al, Phytochemistry 70, 807 (2009). Phytochem..