NP-MRD: Showing NP-Card for UDP-D-Xylose (NP0044463)

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Record Information

Version

2.0

Created at

2022-02-14 20:57:11 UTC

Updated at

2022-03-10 22:22:47 UTC

NP-MRD ID

NP0044463

Secondary Accession Numbers

None

Natural Product Identification

Common Name

UDP-D-Xylose

Description

UDP-D-Xylose, also known as UDP xylose or UDP-alpha, belongs to the class of organic compounds known as methionine and derivatives. Methionine and derivatives are compounds containing methionine or a derivative thereof resulting from reaction of methionine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. UDP-D-Xylose is an extremely weak basic (essentially neutral) compound (based on its pKa). UDP-D-xylose can be biosynthesized from uridine diphosphate glucuronic acid through its interaction with the enzyme UDP-glucuronic acid decarboxylase 1. In humans, UDP-D-xylose is involved in the metabolic disorder called galactosemia II (galk). UDP-D-Xylose is expected to be in Cannabis as all living plants are known to produce and metabolize it.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306222023502D          

 42 44  0  0  1  0            999 V2000
   -2.4757    3.8205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9908    4.4879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2893    9.8372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0231    6.9486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4608   10.6442    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7615    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2962    3.9067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8477   11.1962    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    7.1786    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0964    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0631   10.9413    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8414    5.9090    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8916   10.1343    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1468    5.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.3264    5.2416    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.7811    3.2393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.2785   10.6864    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  1  0  0  0
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 15  7  2  0  0  0  0
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  9 38  1  1  0  0  0
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 11 40  1  1  0  0  0
 41 12  1  0  0  0  0
 42 13  1  0  0  0  0
M  END

     RDKit          3D

 56 58  0  0  0  0  0  0  0  0999 V2000
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   -8.1576    0.6411   -0.2244 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2625    0.4891    1.1091 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4595    0.9964    1.7531 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3057   -0.1229    1.8389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1457   -0.5948    1.1743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0420   -0.4302   -0.1780 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6949   -0.5405   -0.7597 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8879   -1.4529   -0.1637 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6554   -0.9315   -0.0575 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7612   -1.5175    0.9946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8142   -0.4851    1.1478 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6813   -1.0611    0.6205 P   0  0  1  0  0  5  0  0  0  0  0  0
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   -4.5579    1.8899   -0.9452 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.7242   -0.5504   -1.8247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0913   -1.2597   -1.0725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3211   -1.6131    1.9746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3044   -2.4362    0.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
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  6  4  1  0
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  3  2  1  0
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  9 33  1  0
 33 34  1  0
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 31 32  1  0
 31 11  1  0
 29 22  1  0
  2  8  1  0
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 33 55  1  1
 34 56  1  0
 31 53  1  1
 32 54  1  0
M  END


  Mrv1652306222023502D          

 42 44  0  0  1  0            999 V2000
   -2.4757    3.8205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4669    5.1739    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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  2  1  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  1  0  0  0
  7  1  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  9  1  0  0  0  0
 11  8  1  0  0  0  0
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 15  7  2  0  0  0  0
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 16  2  1  0  0  0  0
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  5 17  1  6  0  0  0
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  9 20  1  6  0  0  0
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 34 32  1  0  0  0  0
  5 35  1  1  0  0  0
  6 36  1  6  0  0  0
  8 37  1  6  0  0  0
  9 38  1  1  0  0  0
 10 39  1  1  0  0  0
 11 40  1  1  0  0  0
 41 12  1  0  0  0  0
 42 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0044463

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(COP(O)(=O)OP(O)(=O)OC2([H])OC[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])O)OC([H])(N2C=CC(O)=NC2=O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/t5-,6-,8+,9-,10-,11-,12?,13?/m1/s1

> <INCHI_KEY>
DQQDLYVHOTZLOR-QDHANXEVSA-N

> <FORMULA>
C14H22N2O16P2

> <MOLECULAR_WEIGHT>
536.2758

> <EXACT_MASS>
536.04445569

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
43.529970219666026

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.19

> <JCHEM_LOGP>
-3.9987723323333335

> <ALOGPS_LOGS>
-1.39

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1763411018919383

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7326517523572988

> <JCHEM_PKA_STRONGEST_BASIC>
-3.526611516883185

> <JCHEM_POLAR_SURFACE_AREA>
274.8

> <JCHEM_REFRACTIVITY>
100.81499999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.18e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy([hydroxy([(3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  C   UNK     0      -4.621   7.132   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.716   8.377   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.007  18.363   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.043  12.971   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.327  19.869   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.421  12.495   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.153   7.293   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.182  20.900   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667  13.400   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.913  12.495   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.718  20.424   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.437  11.030   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.398  18.917   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.874   9.945   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -6.779   8.699   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -4.343   9.784   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0       9.791  20.345   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -7.058   6.047   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       7.503  22.406   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -2.667  14.940   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -5.378  12.971   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.573  21.454   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -6.500  11.352   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.352  16.418   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       2.304  13.488   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       2.106  17.255   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       5.119  16.615   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       6.542  17.887   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.363  14.477   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -1.897  11.030   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       3.933  18.442   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       3.293  15.429   0.000  0.00  0.00           O+0
HETATM   33  P   UNK     0       1.828  14.953   0.000  0.00  0.00           P+0
HETATM   34  P   UNK     0       3.613  16.935   0.000  0.00  0.00           P+0
HETATM   35  H   UNK     0       8.647  21.376   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0      -1.180  14.016   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       6.862  19.393   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0      -4.039  14.099   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0      -5.002  11.406   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0       6.038  21.930   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0      -2.738   9.658   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0       4.253  19.948   0.000  0.00  0.00           H+0
CONECT    1    2    7                                                       
CONECT    2    1   16                                                       
CONECT    3    5   28                                                       
CONECT    4    6   29                                                       
CONECT    5    3    8   17   35                                             
CONECT    6    4    9   30   36                                             
CONECT    7    1   15   18                                                  
CONECT    8    5   11   19   37                                             
CONECT    9    6   10   20   38                                             
CONECT   10    9   12   21   39                                             
CONECT   11    8   13   22   40                                             
CONECT   12   10   16   30   41                                             
CONECT   13   11   28   31   42                                             
CONECT   14   15   16   23                                                  
CONECT   15    7   14                                                       
CONECT   16    2   12   14                                                  
CONECT   17    5                                                            
CONECT   18    7                                                            
CONECT   19    8                                                            
CONECT   20    9                                                            
CONECT   21   10                                                            
CONECT   22   11                                                            
CONECT   23   14                                                            
CONECT   24   33                                                            
CONECT   25   33                                                            
CONECT   26   34                                                            
CONECT   27   34                                                            
CONECT   28    3   13                                                       
CONECT   29    4   33                                                       
CONECT   30    6   12                                                       
CONECT   31   13   34                                                       
CONECT   32   33   34                                                       
CONECT   33   24   25   29   32                                             
CONECT   34   26   27   31   32                                             
CONECT   35    5                                                            
CONECT   36    6                                                            
CONECT   37    8                                                            
CONECT   38    9                                                            
CONECT   39   10                                                            
CONECT   40   11                                                            
CONECT   41   12                                                            
CONECT   42   13                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   88    0
END

View in JSmol

Synonyms

Value	Source
alpha-D-Xylopyranosyl ester	HMDB
alpha-delta-Xylopyranosyl ester	HMDB
UDP Xylose	HMDB
UDP-alpha	HMDB
UDP-delta-Xylose	HMDB
Uridine diphosphate xylose	HMDB

Chemical Formula

C₁₄H₂₂N₂O₁₆P₂

Average Mass

536.2758 Da

Monoisotopic Mass

536.04446 Da

IUPAC Name

{[(2R,3S,4R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({[hydroxy({[(3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy})phosphoryl]oxy})phosphinic acid

Traditional Name

[(2R,3S,4R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy([hydroxy([(3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphoryl]oxy)phosphinic acid

CAS Registry Number

3616-06-6

SMILES

[H][C@]1(COP(O)(=O)OP(O)(=O)OC2([H])OC[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])O)OC([H])(N2C=CC(O)=NC2=O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/t5-,6-,8+,9-,10-,11-,12?,13?/m1/s1

InChI Key

DQQDLYVHOTZLOR-QDHANXEVSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Arabidopsis thaliana	Plant	KNApSAcK
Cannabis sativa	CannabisDB	Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as methionine and derivatives. Methionine and derivatives are compounds containing methionine or a derivative thereof resulting from reaction of methionine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Methionine and derivatives

Alternative Parents

Substituents

Methionine or derivatives
N-acyl-l-alpha-amino acid
N-formyl-alpha-amino acid
N-formyl-alpha amino acid or derivatives
Thia fatty acid
Fatty acid
Fatty acyl
Carboxamide group
Secondary carboxylic acid amide
Dialkylthioether
Sulfenyl compound
Thioether
Monocarboxylic acid or derivatives
Carboxylic acid
Hydrocarbon derivative
Organic oxide
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

proteinogenic amino acid (CHEBI:16552 )
L-methionine derivative (CHEBI:16552 )
N-formyl amino acid (CHEBI:16552 )
Other amino acids (C03145 )

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	-1.2	ALOGPS
logP	-4	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	274.8 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	100.82 m³·mol⁻¹	ChemAxon
Polarizability	43.53 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon