3D structure for (2R,3R,4R,5R)-4,5-Dihydroxy-2-(hydroxymethyl)-6-oxo-3-piperidinyl beta-D-glucopyranoside (DB04096)

447325
  -OEChem-01012023253D

44 45  0     1  0  0  0  0  0999 V2000
   -0.2358   -0.7567   -0.1329 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5547    0.7392   -0.1251 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5723   -2.8890    0.3057 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2565   -2.2898   -0.7512 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1726    0.2780    0.2096 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6554    2.3974   -0.5484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4449    0.8689   -2.5007 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8291   -0.1948    2.9551 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2517    3.3274    0.4843 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3440   -1.4408   -1.4531 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0844   -1.2072    0.4499 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1233    0.2515    0.3695 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1022   -0.5395    0.3139 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9790   -1.6475   -0.2695 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4571   -1.4064    0.0368 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1585   -0.4358    1.2668 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8653    0.0279   -0.3001 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7318    0.9941   -0.8295 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8835    1.0300    0.3118 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1991    0.6573   -1.1168 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8957    0.5369    2.1831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5956   -0.7625   -0.7514 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2027    2.4614   -0.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5702    0.9579    1.0039 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1074   -0.5877    1.4118 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8254   -1.7307   -1.3526 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6801   -1.6436    1.0837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6581   -1.1857    1.8934 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9094    0.1525   -1.3890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1228    0.8314   -1.7275 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9064    0.9849    1.4091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8716    1.3358   -0.5810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3493   -2.1343    0.7687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4385    1.3140    1.6392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1971    1.0292    2.8668 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1360    2.5851   -1.1937 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1997    2.7675    0.2217 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6265   -3.0043    0.1107 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0657   -2.1156   -1.6886 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1411    0.1827    1.1769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7139    2.6323   -0.4864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8627    0.2748   -3.0047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4539   -0.6152    2.3398 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3701    3.0392    0.1932 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
  2 13  1  0  0  0  0
  2 19  1  0  0  0  0
  3 14  1  0  0  0  0
  3 38  1  0  0  0  0
  4 15  1  0  0  0  0
  4 39  1  0  0  0  0
  5 17  1  0  0  0  0
  5 40  1  0  0  0  0
  6 18  1  0  0  0  0
  6 41  1  0  0  0  0
  7 20  1  0  0  0  0
  7 42  1  0  0  0  0
  8 21  1  0  0  0  0
  8 43  1  0  0  0  0
  9 23  1  0  0  0  0
  9 44  1  0  0  0  0
 10 22  2  0  0  0  0
 11 16  1  0  0  0  0
 11 22  1  0  0  0  0
 11 33  1  0  0  0  0
 12 16  1  0  0  0  0
 12 18  1  0  0  0  0
 12 24  1  0  0  0  0
 13 14  1  0  0  0  0
 13 25  1  0  0  0  0
 14 15  1  0  0  0  0
 14 26  1  0  0  0  0
 15 17  1  0  0  0  0
 15 27  1  0  0  0  0
 16 21  1  0  0  0  0
 16 28  1  0  0  0  0
 17 19  1  0  0  0  0
 17 29  1  0  0  0  0
 18 20  1  0  0  0  0
 18 30  1  0  0  0  0
 19 23  1  0  0  0  0
 19 31  1  0  0  0  0
 20 22  1  0  0  0  0
 20 32  1  0  0  0  0
 21 34  1  0  0  0  0
 21 35  1  0  0  0  0
 23 36  1  0  0  0  0
 23 37  1  0  0  0  0
M  END
> <DATABASE_ID>
DB04096

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

> <ORIGINAL_SOURCE_URL>
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WXSNJJDPPISYEF-ZNLUKOTNSA-N/SDF?record_type=3d

> <SMILES>
[H]N1[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H21NO10/c14-1-3-10(7(18)8(19)11(21)13-3)23-12-9(20)6(17)5(16)4(2-15)22-12/h3-10,12,14-20H,1-2H2,(H,13,21)/t3-,4-,5-,6+,7-,8-,9-,10-,12+/m1/s1

> <INCHI_KEY>
WXSNJJDPPISYEF-ZNLUKOTNSA-N

> <FORMULA>
C12H21NO10

> <MOLECULAR_WEIGHT>
339.2958

> <EXACT_MASS>
339.116545897

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_NEUTRAL_MICROSPECIES_CHARGE>
-0.00013725336822689228

> <JCHEM_AVERAGE_POLARIZABILITY>
30.732472205593726

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R,5R,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}piperidin-2-one

> <ALOGPS_LOGP>
-2.97

> <JCHEM_LOGP>
-5.245269435666668

> <ALOGPS_LOGS>
-0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NEUTRAL_CHARGE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.102679918073987

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.90126446348943

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7920918360416707

> <JCHEM_POLAR_SURFACE_AREA>
189.17

> <JCHEM_REFRACTIVITY>
69.14189999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.94e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3H,5H-pyrrolo[3,2-d]pyrimidin-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

Similar Structures

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

3D structure for (2R,3R,4R,5R)-4,5-Dihydroxy-2-(hydroxymethyl)-6-oxo-3-piperidinyl beta-D-glucopyranoside (DB04096)

Structure for (2R,3R,4R,5R)-4,5-Dihydroxy-2-(hydroxymethyl)-6-oxo-3-piperidinyl beta-D-glucopyranoside (DB04096)