NP-MRD: Showing NP-Card for 1,4-D-xylobiose (NP0002920)

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Record Information

Version

1.0

Created at

2020-11-23 19:43:38 UTC

Updated at

2021-08-12 19:52:31 UTC

NP-MRD ID

NP0002920

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1,4-D-xylobiose

Provided By

BMRB

Description

It was first documented in 2008 (PMID: 17984079). Based on a literature review very few articles have been published on (2R,3R,4R,5R)-5-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxane-2,3,4-triol.

Structure

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


     RDKit          2D

 37 38  0  0  0  0  0  0  0  0999 V2000
   -4.8529   -1.3213    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4466   -0.7996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2047    0.4948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3597    1.4518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4627    1.7985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9628    1.8078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2047    0.5134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0497   -0.4436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3566    0.0782    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6263   -1.3974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0390   -1.9016    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1820   -0.9303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9401   -2.2247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9124    0.5452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4124    0.5545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4997    1.0495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2416    2.3532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9466   -0.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1979   -2.2690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1042   -2.8001    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1770   -2.2751    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3477   -0.4765    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7660    0.9300    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8754    2.3027    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2115    3.2773    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1886    1.6168    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8750    1.1936    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3750   -2.8762    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2874   -1.5703    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5884   -0.4086    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4401   -2.2154    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1637    2.0240    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1543    1.8582    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5641    1.8247    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4836    3.6475    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7400   -1.3957    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0429   -3.2261    0.0000 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
 12 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  7 18  1  0
 18 19  1  0
 18  2  1  0
 16  9  1  0
  1 20  1  0
  2 21  1  6
  3 22  1  1
  4 23  1  0
  5 24  1  1
  5 25  1  0
  7 26  1  6
  9 27  1  6
 10 28  1  1
 10 29  1  0
 12 30  1  1
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  1
 17 35  1  0
 18 36  1  1
 19 37  1  0
M  END

NP0002920
     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
    4.2666    1.6757    0.6756 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4264    0.7855    0.0104 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6435   -0.6110    0.5362 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7881   -1.1104   -0.1251 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4609   -1.4972    0.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6891   -0.9044   -0.7749 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0223    0.2167   -0.3389 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1017   -0.1336    0.6349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1761    0.1409    0.2161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8548    1.1732    1.0923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0007    1.6020    0.4124 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9283    0.5959    0.2772 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.9597    1.0937   -0.5390 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3967   -0.6385   -0.3992 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.3718   -1.6343   -0.2743 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0687   -1.0756    0.1467 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4962   -1.9548   -0.7843 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0045    1.2574    0.1681 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8843    2.4357   -0.5905 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8169    2.5416    0.7071 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6482    0.7540   -1.0855 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8856   -0.6235    1.6046 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1202   -1.8683    0.3916 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8351   -2.4650   -0.2315 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8688   -1.7749    1.0944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4833    0.6396   -1.2307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1449    0.5792   -0.8097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1747    2.0545    1.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0808    0.8055    2.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3921    0.3089    1.2642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5755    1.2089   -1.4463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2567   -0.4293   -1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0807   -2.4699   -0.6918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1550   -1.5359    1.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8575   -2.8604   -0.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7890    1.5132    1.2411 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2366    2.2048   -1.5085 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
 12 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  7 18  1  0
 18 19  1  0
 18  2  1  0
 16  9  1  0
  1 20  1  0
  2 21  1  6
  3 22  1  1
  4 23  1  0
  5 24  1  0
  5 25  1  0
  7 26  1  6
  9 27  1  6
 10 28  1  0
 10 29  1  0
 12 30  1  1
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  1
 17 35  1  0
 18 36  1  1
 19 37  1  0
M  END


     RDKit          2D

 37 38  0  0  0  0  0  0  0  0999 V2000
   -4.8529   -1.3213    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4466   -0.7996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2047    0.4948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3597    1.4518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4627    1.7985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9628    1.8078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2047    0.5134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0497   -0.4436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3566    0.0782    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6263   -1.3974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0390   -1.9016    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1820   -0.9303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9401   -2.2247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9124    0.5452    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4124    0.5545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4997    1.0495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2416    2.3532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9466   -0.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1979   -2.2690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1042   -2.8001    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1770   -2.2751    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3477   -0.4765    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7660    0.9300    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8754    2.3027    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2115    3.2773    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1886    1.6168    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8750    1.1936    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3750   -2.8762    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2874   -1.5703    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5884   -0.4086    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4401   -2.2154    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1637    2.0240    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1543    1.8582    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5641    1.8247    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4836    3.6475    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7400   -1.3957    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0429   -3.2261    0.0000 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
 12 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  7 18  1  0
 18 19  1  0
 18  2  1  0
 16  9  1  0
  1 20  1  0
  2 21  1  6
  3 22  1  1
  4 23  1  0
  5 24  1  1
  5 25  1  0
  7 26  1  6
  9 27  1  6
 10 28  1  1
 10 29  1  0
 12 30  1  1
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  1
 17 35  1  0
 18 36  1  1
 19 37  1  0
M  END
> <DATABASE_ID>
NP0002920

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O9/c11-3-1-18-10(8(15)5(3)12)19-4-2-17-9(16)7(14)6(4)13/h3-16H,1-2H2/t3-,4-,5+,6+,7-,8-,9-,10+/m1/s1

> <INCHI_KEY>
LGQKSQQRKHFMLI-SJYYZXOBSA-N

> <FORMULA>
C10H18O9

> <MOLECULAR_WEIGHT>
282.2445

> <EXACT_MASS>
282.095082174

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
25.797609691039042

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5R)-2-{[(3R,4R,5R,6R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxane-3,4,5-triol

> <ALOGPS_LOGP>
-3.02

> <JCHEM_LOGP>
-3.442704979666666

> <ALOGPS_LOGS>
0.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.204983173397084

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.266268780829055

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265806595271325

> <JCHEM_POLAR_SURFACE_AREA>
149.07

> <JCHEM_REFRACTIVITY>
56.4117

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5R)-2-{[(3R,4R,5R,6R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

NP0002920
     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
    4.2666    1.6757    0.6756 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4264    0.7855    0.0104 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6435   -0.6110    0.5362 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7881   -1.1104   -0.1251 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4609   -1.4972    0.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6891   -0.9044   -0.7749 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0223    0.2167   -0.3389 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1017   -0.1336    0.6349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1761    0.1409    0.2161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8548    1.1732    1.0923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0007    1.6020    0.4124 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9283    0.5959    0.2772 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.9597    1.0937   -0.5390 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3967   -0.6385   -0.3992 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.3718   -1.6343   -0.2743 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0687   -1.0756    0.1467 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4962   -1.9548   -0.7843 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0045    1.2574    0.1681 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8843    2.4357   -0.5905 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8169    2.5416    0.7071 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6482    0.7540   -1.0855 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8856   -0.6235    1.6046 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1202   -1.8683    0.3916 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8351   -2.4650   -0.2315 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8688   -1.7749    1.0944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4833    0.6396   -1.2307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1449    0.5792   -0.8097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1747    2.0545    1.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0808    0.8055    2.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3921    0.3089    1.2642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5755    1.2089   -1.4463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2567   -0.4293   -1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0807   -2.4699   -0.6918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1550   -1.5359    1.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8575   -2.8604   -0.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7890    1.5132    1.2411 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2366    2.2048   -1.5085 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
 12 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  7 18  1  0
 18 19  1  0
 18  2  1  0
 16  9  1  0
  1 20  1  0
  2 21  1  6
  3 22  1  1
  4 23  1  0
  5 24  1  0
  5 25  1  0
  7 26  1  6
  9 27  1  6
 10 28  1  0
 10 29  1  0
 12 30  1  1
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  1
 17 35  1  0
 18 36  1  1
 19 37  1  0
M  END

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3   18                                                       
CONECT    2    4   17                                                       
CONECT    3    1    5   11   20                                             
CONECT    4    2    6   19   21                                             
CONECT    5    3    8   12   22                                             
CONECT    6    4    7   13   23                                             
CONECT    7    6    9   14   24                                             
CONECT    8    5   10   15   25                                             
CONECT    9    7   16   17   26                                             
CONECT   10    8   18   19   27                                             
CONECT   11    3                                                            
CONECT   12    5                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    8                                                            
CONECT   16    9                                                            
CONECT   17    2    9                                                       
CONECT   18    1   10                                                       
CONECT   19    4   10                                                       
CONECT   20    3                                                            
CONECT   21    4                                                            
CONECT   22    5                                                            
CONECT   23    6                                                            
CONECT   24    7                                                            
CONECT   25    8                                                            
CONECT   26    9                                                            
CONECT   27   10                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END

COMPND    NP0002920
HETATM    1  O1  UNL     1       4.267   1.676   0.676  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.426   0.786   0.010  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.643  -0.611   0.536  1.00  0.00           C  
HETATM    4  O2  UNL     1       4.788  -1.110  -0.125  1.00  0.00           O  
HETATM    5  C3  UNL     1       2.461  -1.497   0.197  1.00  0.00           C  
HETATM    6  O3  UNL     1       1.689  -0.904  -0.775  1.00  0.00           O  
HETATM    7  C4  UNL     1       1.022   0.217  -0.339  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.102  -0.134   0.635  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.176   0.141   0.216  1.00  0.00           C  
HETATM   10  C6  UNL     1      -1.855   1.173   1.092  1.00  0.00           C  
HETATM   11  O5  UNL     1      -3.001   1.602   0.412  1.00  0.00           O  
HETATM   12  C7  UNL     1      -3.928   0.596   0.277  1.00  0.00           C  
HETATM   13  O6  UNL     1      -4.960   1.094  -0.539  1.00  0.00           O  
HETATM   14  C8  UNL     1      -3.397  -0.638  -0.399  1.00  0.00           C  
HETATM   15  O7  UNL     1      -4.372  -1.634  -0.274  1.00  0.00           O  
HETATM   16  C9  UNL     1      -2.069  -1.076   0.147  1.00  0.00           C  
HETATM   17  O8  UNL     1      -1.496  -1.955  -0.784  1.00  0.00           O  
HETATM   18  C10 UNL     1       2.005   1.257   0.168  1.00  0.00           C  
HETATM   19  O9  UNL     1       1.884   2.436  -0.591  1.00  0.00           O  
HETATM   20  H1  UNL     1       3.817   2.542   0.707  1.00  0.00           H  
HETATM   21  H2  UNL     1       3.648   0.754  -1.085  1.00  0.00           H  
HETATM   22  H3  UNL     1       3.886  -0.624   1.605  1.00  0.00           H  
HETATM   23  H4  UNL     1       5.120  -1.868   0.392  1.00  0.00           H  
HETATM   24  H5  UNL     1       2.835  -2.465  -0.232  1.00  0.00           H  
HETATM   25  H6  UNL     1       1.869  -1.775   1.094  1.00  0.00           H  
HETATM   26  H7  UNL     1       0.483   0.640  -1.231  1.00  0.00           H  
HETATM   27  H8  UNL     1      -1.145   0.579  -0.810  1.00  0.00           H  
HETATM   28  H9  UNL     1      -1.175   2.055   1.136  1.00  0.00           H  
HETATM   29  H10 UNL     1      -2.081   0.806   2.099  1.00  0.00           H  
HETATM   30  H11 UNL     1      -4.392   0.309   1.264  1.00  0.00           H  
HETATM   31  H12 UNL     1      -4.575   1.209  -1.446  1.00  0.00           H  
HETATM   32  H13 UNL     1      -3.257  -0.429  -1.480  1.00  0.00           H  
HETATM   33  H14 UNL     1      -4.081  -2.470  -0.692  1.00  0.00           H  
HETATM   34  H15 UNL     1      -2.155  -1.536   1.139  1.00  0.00           H  
HETATM   35  H16 UNL     1      -1.858  -2.860  -0.730  1.00  0.00           H  
HETATM   36  H17 UNL     1       1.789   1.513   1.241  1.00  0.00           H  
HETATM   37  H18 UNL     1       2.237   2.205  -1.508  1.00  0.00           H  
CONECT    1    2   20
CONECT    2    3   18   21
CONECT    3    4    5   22
CONECT    4   23
CONECT    5    6   24   25
CONECT    6    7
CONECT    7    8   18   26
CONECT    8    9
CONECT    9   10   16   27
CONECT   10   11   28   29
CONECT   11   12
CONECT   12   13   14   30
CONECT   13   31
CONECT   14   15   16   32
CONECT   15   33
CONECT   16   17   34
CONECT   17   35
CONECT   18   19   36
CONECT   19   37
END

NP0002920
     RDKit          3D

37 38  0  0  0  0  0  0  0  0999 V2000
    4.2666    1.6757    0.6756 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4264    0.7855    0.0104 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6435   -0.6110    0.5362 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7881   -1.1104   -0.1251 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4609   -1.4972    0.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6891   -0.9044   -0.7749 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0223    0.2167   -0.3389 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1017   -0.1336    0.6349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1761    0.1409    0.2161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8548    1.1732    1.0923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0007    1.6020    0.4124 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9283    0.5959    0.2772 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.9597    1.0937   -0.5390 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3967   -0.6385   -0.3992 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.3718   -1.6343   -0.2743 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0687   -1.0756    0.1467 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4962   -1.9548   -0.7843 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0045    1.2574    0.1681 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8843    2.4357   -0.5905 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8169    2.5416    0.7071 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6482    0.7540   -1.0855 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8856   -0.6235    1.6046 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1202   -1.8683    0.3916 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8351   -2.4650   -0.2315 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8688   -1.7749    1.0944 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4833    0.6396   -1.2307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1449    0.5792   -0.8097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1747    2.0545    1.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0808    0.8055    2.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3921    0.3089    1.2642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5755    1.2089   -1.4463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2567   -0.4293   -1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0807   -2.4699   -0.6918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1550   -1.5359    1.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8575   -2.8604   -0.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7890    1.5132    1.2411 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2366    2.2048   -1.5085 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
 12 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  7 18  1  0
 18 19  1  0
 18  2  1  0
 16  9  1  0
  1 20  1  0
  2 21  1  6
  3 22  1  1
  4 23  1  0
  5 24  1  0
  5 25  1  0
  7 26  1  6
  9 27  1  6
 10 28  1  0
 10 29  1  0
 12 30  1  1
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  1
 17 35  1  0
 18 36  1  1
 19 37  1  0
M  END

View in JSmol

Synonyms

Value	Source
beta-D-Xylose OF xylobiose	MeSH

Chemical Formula

C₁₀H₁₈O₉

Average Mass

282.2445 Da

Monoisotopic Mass

282.09508 Da

IUPAC Name

(2S,3R,4S,5R)-2-{[(3R,4R,5R,6R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxane-3,4,5-triol

Traditional Name

(2S,3R,4S,5R)-2-{[(3R,4R,5R,6R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)CO[C@@]([H])(O[C@]2([H])CO[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])O)[C@]([H])(O)[C@@]1([H])O

InChI Identifier

InChI=1S/C10H18O9/c11-3-1-18-10(8(15)5(3)12)19-4-2-17-9(16)7(14)6(4)13/h3-16H,1-2H2/t3-,4-,5+,6+,7-,8-,9-,10+/m1/s1

InChI Key

LGQKSQQRKHFMLI-SJYYZXOBSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, 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
Pinus sylvestris	KNApSAcK Database	22123792

Chemical Taxonomy

Description

This compound 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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

O-glycosyl compound
Disaccharide
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

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	-3	ALOGPS
logP	-3.4	ChemAxon
logS	0.35	ALOGPS
pKa (Strongest Acidic)	11.27	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	149.07 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	56.41 m³·mol⁻¹	ChemAxon
Polarizability	25.8 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4451529

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]

Showing NP-Card for 1,4-D-xylobiose (NP0002920)

MOL for NP0002920 (1,4-D-xylobiose)

3D MOL for NP0002920 (1,4-D-xylobiose)

3D SDF for NP0002920 (1,4-D-xylobiose)

3D-SDF for NP0002920 (1,4-D-xylobiose)

PDB for NP0002920 (1,4-D-xylobiose)

3D PDB for NP0002920 (1,4-D-xylobiose)

SMILES for NP0002920 (1,4-D-xylobiose)

INCHI for NP0002920 (1,4-D-xylobiose)

Structure for NP0002920 (1,4-D-xylobiose)

3D Structure for NP0002920 (1,4-D-xylobiose)