3D structure for Thymidine-5'-diphospho-beta-D-xylose (DB03161)

447462
  -OEChem-11241922213D

58 60  0     1  0  0  0  0  0999 V2000
    2.8524   -2.2735   -1.2642 P   0  0  2  0  0  0  0  0  0  0  0  0
    4.0598    0.2240   -0.2837 P   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7956   -1.5081    0.9192 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3969   -4.2213    2.2034 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7356    3.1925    0.4523 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3625   -1.8005   -0.8482 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6538    0.8348    0.2201 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8832    2.4605    2.3060 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3321    0.6325    2.6733 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7928    3.7294   -0.3560 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6541   -0.8762   -1.3966 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7335   -0.3775    1.4489 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6943   -2.7491   -2.8023 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7286    1.4083   -1.1599 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4950   -3.2783   -0.3530 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9369   -0.3051    0.8138 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3191    2.2923   -2.2724 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8105   -0.6053    0.1448 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5143    0.9471   -0.4105 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3307   -3.8163    0.8378 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2137   -2.7989    0.6528 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5713   -3.0317    0.4787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2244   -1.6312    0.9568 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3407   -2.7787   -0.7658 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1394    2.2593    1.3287 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4351    1.9147    2.0641 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3197    3.5396    0.5117 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6456    1.9352    1.1280 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5836    3.4786   -0.3375 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1167   -0.1724   -0.9780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0635   -0.0428    0.4697 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5510    0.7752   -1.8180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8641    1.4163   -1.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7881    1.2267   -3.0218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2104   -4.7191    0.2318 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6019   -2.9349    1.3717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4848   -3.4035    0.9533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7210   -3.0525   -0.6076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5352   -1.5004    2.0002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4174   -2.5471   -1.5172 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7462   -3.7662   -1.0152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1897    1.4278    0.6976 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5869    2.6472    2.8675 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3643    4.4014    1.1889 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5453    1.8482    1.7482 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7466    4.4425   -0.8326 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4892    2.7389   -1.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5641   -4.6786    2.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1590   -0.6234   -1.1809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6217    3.2080    2.8701 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1709    0.4566    3.1325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4146    1.3670   -0.1962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6471    4.5570   -0.8453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5671    2.2969   -2.9557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8348    0.6974   -3.1249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3689    1.0467   -3.9323 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3033   -2.1275   -3.4525 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6592    1.3124   -1.4548 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1 11  1  0  0  0  0
  1 13  1  0  0  0  0
  1 15  2  0  0  0  0
  2  7  1  0  0  0  0
  2 11  1  0  0  0  0
  2 14  1  0  0  0  0
  2 16  2  0  0  0  0
  3 21  1  0  0  0  0
  3 23  1  0  0  0  0
  4 20  1  0  0  0  0
  4 48  1  0  0  0  0
  5 28  1  0  0  0  0
  5 29  1  0  0  0  0
  6 24  1  0  0  0  0
  7 28  1  0  0  0  0
  8 25  1  0  0  0  0
  8 50  1  0  0  0  0
  9 26  1  0  0  0  0
  9 51  1  0  0  0  0
 10 27  1  0  0  0  0
 10 53  1  0  0  0  0
 12 31  2  0  0  0  0
 13 57  1  0  0  0  0
 14 58  1  0  0  0  0
 17 33  2  0  0  0  0
 18 23  1  0  0  0  0
 18 30  1  0  0  0  0
 18 31  1  0  0  0  0
 19 31  1  0  0  0  0
 19 33  1  0  0  0  0
 19 52  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 20 35  1  0  0  0  0
 21 24  1  0  0  0  0
 21 36  1  0  0  0  0
 22 23  1  0  0  0  0
 22 37  1  0  0  0  0
 22 38  1  0  0  0  0
 23 39  1  0  0  0  0
 24 40  1  0  0  0  0
 24 41  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 25 42  1  0  0  0  0
 26 28  1  0  0  0  0
 26 43  1  0  0  0  0
 27 29  1  0  0  0  0
 27 44  1  0  0  0  0
 28 45  1  0  0  0  0
 29 46  1  0  0  0  0
 29 47  1  0  0  0  0
 30 32  2  0  0  0  0
 30 49  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 54  1  0  0  0  0
 34 55  1  0  0  0  0
 34 56  1  0  0  0  0
M  END
> <DATABASE_ID>
DB03161

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

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

> <SMILES>
[H]N1C(=O)N(C=C(C)C1=O)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C15H24N2O15P2/c1-6-3-17(15(23)16-13(6)22)10-2-7(18)9(30-10)5-29-33(24,25)32-34(26,27)31-14-12(21)11(20)8(19)4-28-14/h3,7-12,14,18-21H,2,4-5H2,1H3,(H,24,25)(H,26,27)(H,16,22,23)/t7-,8+,9+,10+,11-,12+,14+/m0/s1

> <INCHI_KEY>
AJUADKZRQSBUAK-KDGZBOQCSA-N

> <FORMULA>
C15H24N2O15P2

> <MOLECULAR_WEIGHT>
534.303

> <EXACT_MASS>
534.065191132

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_POLARIZABILITY>
44.46022769160744

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[hydroxy({[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy})phosphoryl]oxy}({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid

> <ALOGPS_LOGP>
-1.29

> <JCHEM_LOGP>
-3.070084584333334

> <ALOGPS_LOGS>
-1.67

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.176365422960129

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7326574728244148

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2403442590943885

> <JCHEM_POLAR_SURFACE_AREA>
251.07999999999998

> <JCHEM_REFRACTIVITY>
103.33969999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.13e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1lambda4-thia-2,3,4,5-tetracupratetracyclo[2.1.0.0^{1,3}.0^{2,5}]pentane

> <JCHEM_VEBER_RULE>
0

$$$$

Similar Structures

Viewer powered by 3dmol.js

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

3D structure for Thymidine-5'-diphospho-beta-D-xylose (DB03161)

Structure for Thymidine-5'-diphospho-beta-D-xylose (DB03161)