NP-MRD: Showing NP-Card for {[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid (NP0235900)

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Record Information

Version

2.0

Created at

2022-09-06 18:40:03 UTC

Updated at

2022-09-06 18:40:04 UTC

NP-MRD ID

NP0235900

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid

Description

UDP-alpha-D-xylose, also known as UDP xylose or UDP-α-D-xylose, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. {[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid is found in Glycine max. {[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid was first documented in 2002 (PMID: 12481102). UDP-alpha-D-xylose is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 20847005) (PMID: 22008417) (PMID: 23053089) (PMID: 24561591).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306182019102D          

 34 36  0  0  0  0            999 V2000
 9996.7222 9998.4634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5136 9998.4551    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.021310000.3165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.5429 9999.0774    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7358 9999.9025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.450910000.3165    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9994.112110001.5527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.3652 9999.7919    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.038110001.0306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.863710001.0306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.275310000.3185    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10002.9915 9999.9045    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.862610001.0326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.688110001.0326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.4196 9999.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10005.8478 9999.9045    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10005.847810001.5548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.541610001.5537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.827110001.1412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.827110000.3161    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9995.5416 9999.9037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.256110000.3161    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.256110001.1412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.635210000.3965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.9678 9999.9115    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9997.2227 9999.1269    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.0477 9999.1269    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.3026 9999.9115    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10004.419610001.5558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.705110001.1433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.705110000.3182    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10004.4196 9999.9058    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10005.134110000.3182    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10005.134110001.1433    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  6 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 11 14  1  0  0  0  0
 18 19  1  0  0  0  0
 18 23  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 24 25  1  0  0  0  0
 24 28  1  0  0  0  0
 29 34  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 12  1  1  0  0  0
 32 15  1  1  0  0  0
 33 16  1  6  0  0  0
 34 17  1  1  0  0  0
 26  1  1  1  0  0  0
 27  2  1  1  0  0  0
 28  3  1  6  0  0  0
 25 22  1  6  0  0  0
 21  4  2  0  0  0  0
 19  7  2  0  0  0  0
M  END

     RDKit          3D

 56 58  0  0  0  0  0  0  0  0999 V2000
    9.4158   -2.0576    0.6534 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3224   -1.4075    0.5725 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1505   -0.1801    1.1785 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9338    0.4933    1.0610 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9090   -0.0308    0.3619 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6901    0.6586    0.2525 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5574   -0.1197    0.5789 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5484    0.8284    0.4262 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1979    0.1973    0.1708 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8104   -0.6352    1.2167 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7001   -1.2954    0.8530 P   0  0  2  0  0  5  0  0  0  0  0  0
   -1.6904   -1.0452    1.9778 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5258   -2.9495    0.6668 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3556   -0.5912   -0.5426 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8143   -1.3251   -0.9056 P   0  0  1  0  0  5  0  0  0  0  0  0
   -2.7930   -1.6485   -2.4020 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0172   -2.7936   -0.1042 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1373   -0.2953   -0.6667 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7928   -0.5281    0.5193 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8475    0.6212    1.3067 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2410    1.6832    0.4853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6942    1.5340    0.1295 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.9857    2.4853   -0.8479 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0000    0.1772   -0.4406 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.3688   -0.0658   -0.2512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2454   -0.9284    0.2508 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.3096   -2.0546   -0.5649 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9071    1.6210   -0.8328 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9709    2.9799   -0.5889 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2971    1.0884   -1.1367 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1241    2.0455   -1.6739 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1152   -1.2268   -0.2131 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1755   -1.7234   -0.8630 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2760   -1.8977   -0.1166 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9855    0.2192    1.7329 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8369    1.4656    1.5567 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6190    1.5556    0.9025 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4967    1.5506    1.2506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1987   -0.4134   -0.7537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4844    1.0302    0.0066 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0835   -3.1452   -0.0815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8781   -2.7286    0.8733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3586   -1.3405    1.1224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1317    2.6358    1.0711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6725    1.7136   -0.4659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3269    1.7815    1.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2865    2.4262   -1.5490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7531    0.1732   -1.5365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8312    0.7177    0.1525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7331   -1.1547    1.2183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6042   -2.0374   -1.2712 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2138    1.4116   -1.6629 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9384    3.2325    0.3483 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1210    0.2162   -1.8133 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3403    1.9143   -2.6201 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3751   -2.8379   -0.5939 H   0  0  0  0  0  0  0  0  0  0  0  0
 29 28  1  0
 28  8  1  0
  8  9  1  0
  9 10  1  0
 11 10  1  1
 11 13  1  0
 11 12  2  0
 11 14  1  0
 15 14  1  1
 15 17  1  0
 15 16  2  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
  8  7  1  0
  7  6  1  0
  6 30  1  0
 30 31  1  0
  6  5  1  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  2 34  1  0
 34 32  1  0
 32 33  2  0
 30 28  1  0
 32  5  1  0
 26 19  1  0
 29 53  1  0
 28 52  1  6
  8 38  1  1
  9 39  1  0
  9 40  1  0
 13 41  1  0
 17 42  1  0
 19 43  1  1
 21 44  1  0
 21 45  1  0
 22 46  1  1
 23 47  1  0
 24 48  1  6
 25 49  1  0
 26 50  1  1
 27 51  1  0
  6 37  1  1
 30 54  1  6
 31 55  1  0
  4 36  1  0
  3 35  1  0
 34 56  1  0
M  END


  Mrv1652306182019102D          

 34 36  0  0  0  0            999 V2000
 9996.7222 9998.4634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5136 9998.4551    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.021310000.3165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.5429 9999.0774    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7358 9999.9025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.450910000.3165    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9994.112110001.5527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.3652 9999.7919    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.038110001.0306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.863710001.0306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.275310000.3185    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10002.9915 9999.9045    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.862610001.0326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.688110001.0326    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.4196 9999.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10005.8478 9999.9045    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10005.847810001.5548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.541610001.5537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.827110001.1412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9994.827110000.3161    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9995.5416 9999.9037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.256110000.3161    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.256110001.1412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.635210000.3965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.9678 9999.9115    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9997.2227 9999.1269    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.0477 9999.1269    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.3026 9999.9115    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10004.419610001.5558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.705110001.1433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.705110000.3182    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10004.4196 9999.9058    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10005.134110000.3182    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10005.134110001.1433    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  6 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 11 14  1  0  0  0  0
 18 19  1  0  0  0  0
 18 23  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 24 25  1  0  0  0  0
 24 28  1  0  0  0  0
 29 34  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 12  1  1  0  0  0
 32 15  1  1  0  0  0
 33 16  1  6  0  0  0
 34 17  1  1  0  0  0
 26  1  1  1  0  0  0
 27  2  1  1  0  0  0
 28  3  1  6  0  0  0
 25 22  1  6  0  0  0
 21  4  2  0  0  0  0
 19  7  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0235900

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2O)O[C@H]([C@@H]1O)N1C=CC(=O)NC1=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-OCIMBMBZSA-N

> <FORMULA>
C14H22N2O16P2

> <MOLECULAR_WEIGHT>
536.2758

> <EXACT_MASS>
536.04445569

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
42.57496737890108

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.30

> <JCHEM_LOGP>
-4.366273136666667

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1763571365257834

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7326523511854144

> <JCHEM_PKA_STRONGEST_BASIC>
-3.526611516883185

> <JCHEM_POLAR_SURFACE_AREA>
271.31

> <JCHEM_REFRACTIVITY>
100.49329999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.36e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
udp-xylose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 18-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-JUN-20         0                                  
HETATM    1  O   UNK     0    8660.5488663.798   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8663.8928663.783   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8664.8408667.257   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8658.3478664.944   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8666.1738666.485   0.000  0.00  0.00           O+0
HETATM    6  P   UNK     0    8667.5088667.257   0.000  0.00  0.00           P+0
HETATM    7  O   UNK     0    8655.6768669.565   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0    8669.2158666.278   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8666.7388668.590   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8668.2798668.590   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0    8670.9148667.261   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0    8672.2518666.488   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8670.1448668.594   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8671.6848668.594   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0    8674.9178664.952   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0    8677.5838666.488   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0    8677.5838669.569   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0    8658.3448669.567   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8657.0118668.797   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0    8657.0118667.257   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0    8658.3448666.487   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0    8659.6788667.257   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0    8659.6788668.797   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0    8662.2528667.407   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0    8661.0078666.501   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8661.4828665.037   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8663.0228665.037   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8663.4988666.501   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0    8674.9178669.571   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0    8673.5838668.801   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0    8673.5838667.261   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0    8674.9178666.491   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0    8676.2508667.261   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0    8676.2508668.801   0.000  0.00  0.00           C+0
CONECT    1   26                                                            
CONECT    2   27                                                            
CONECT    3    5   28                                                       
CONECT    4   21                                                            
CONECT    5    3    6                                                       
CONECT    6    5    8    9   10                                             
CONECT    7   19                                                            
CONECT    8    6   11                                                       
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11    8   12   13   14                                             
CONECT   12   11   31                                                       
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15   32                                                            
CONECT   16   33                                                            
CONECT   17   34                                                            
CONECT   18   19   23                                                       
CONECT   19   18   20    7                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22    4                                                  
CONECT   22   21   23   25                                                  
CONECT   23   18   22                                                       
CONECT   24   25   28                                                       
CONECT   25   26   24   22                                                  
CONECT   26   25   27    1                                                  
CONECT   27   26   28    2                                                  
CONECT   28   27   24    3                                                  
CONECT   29   34   30                                                       
CONECT   30   29   31                                                       
CONECT   31   32   30   12                                                  
CONECT   32   31   33   15                                                  
CONECT   33   32   34   16                                                  
CONECT   34   29   33   17                                                  
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Value	Source
UDP Xylose	ChEBI
UDP-D-Xylose	ChEBI
UDP-Xylose	ChEBI
UDPxylose	ChEBI
Uridine 5'-(trihydrogen diphosphate), p'-alpha-D-xylopyranosyl ester	ChEBI
Uridine diphosphate xylose	ChEBI
URIDINE-5'-diphosphATE-xylopyranose	ChEBI
Uridine 5'-(trihydrogen diphosphate), p'-a-D-xylopyranosyl ester	Generator
Uridine 5'-(trihydrogen diphosphate), p'-α-D-xylopyranosyl ester	Generator
Uridine 5'-(trihydrogen diphosphoric acid), p'-a-D-xylopyranosyl ester	Generator
Uridine 5'-(trihydrogen diphosphoric acid), p'-alpha-D-xylopyranosyl ester	Generator
Uridine 5'-(trihydrogen diphosphoric acid), p'-α-D-xylopyranosyl ester	Generator
Uridine diphosphoric acid xylose	Generator
URIDINE-5'-diphosphoric acid-xylopyranose	Generator
UDP-a-D-Xylose	Generator
UDP-Α-D-xylose	Generator
Diphosphate xylose, uridine	MeSH
Xylose, uridine diphosphate	MeSH
Xylose, UDP	MeSH
UDP alpha-D-xylose	HMDB
UDP α-D-xylose	HMDB
UDP-alpha-D-xylopyranose	HMDB
UDP-α-D-xylopyranose	HMDB
Uridine 5'-(trihydrogen diphosphate) mono-D-xylopyranosyl ester	HMDB
Uridine 5'-(trihydrogen pyrophosphate) mono-D-xylopyranosyl ester	HMDB
Uridine 5’-(trihydrogen diphosphate) mono-D-xylopyranosyl ester	HMDB
Uridine 5’-(trihydrogen pyrophosphate) mono-D-xylopyranosyl ester	HMDB
Uridine diphosphate D-xylose	HMDB
Uridine diphospho-alpha-D-xylopyranose	HMDB
Uridine diphospho-α-D-xylopyranose	HMDB
Uridine diphosphoxylose	HMDB

Chemical Formula

C₁₄H₂₂N₂O₁₆P₂

Average Mass

536.2758 Da

Monoisotopic Mass

536.04446 Da

IUPAC Name

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

Traditional Name

udp-xylose

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2O)O[C@H]([C@@H]1O)N1C=CC(=O)NC1=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-OCIMBMBZSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Glycine max	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside diphosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside diphosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Organic pyrophosphate
Monoalkyl phosphate
Pyrimidone
Hydroxypyrimidine
Hydropyrimidine
Monosaccharide
Alkyl phosphate
Organic phosphoric acid derivative
Pyrimidine
Oxane
Phosphoric acid ester
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Polyol
Organoheterocyclic compound
Azacycle
Oxacycle
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Organic nitrogen compound
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

UDP-sugar (CHEBI:16082 )

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	-1.3	ALOGPS
logP	-4.4	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	271.31 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	100.49 m³·mol⁻¹	ChemAxon
Polarizability	42.57 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

External Links

HMDB ID

HMDB0001018

DrugBank ID

DB01713

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB005661

KNApSAcK ID

Not Available

Chemspider ID

18152

KEGG Compound ID

C00190

BioCyc ID

UDP-D-XYLOSE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5948

PubChem Compound

19235

PDB ID

Not Available

ChEBI ID

16082

Good Scents ID

Not Available

References

General References

Harper AD, Bar-Peled M: Biosynthesis of UDP-xylose. Cloning and characterization of a novel Arabidopsis gene family, UXS, encoding soluble and putative membrane-bound UDP-glucuronic acid decarboxylase isoforms. Plant Physiol. 2002 Dec;130(4):2188-98. doi: 10.1104/pp.009654. [PubMed:12481102 ]
Gu X, Lee SG, Bar-Peled M: Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose 4-epimerase. Microbiology (Reading). 2011 Jan;157(Pt 1):260-269. doi: 10.1099/mic.0.040758-0. Epub 2010 Sep 16. [PubMed:20847005 ]
Rosenberger AF, Hangelmann L, Hofinger A, Wilson IB: UDP-xylose and UDP-galactose synthesis in Trichomonas vaginalis. Mol Biochem Parasitol. 2012 Jan;181(1):53-6. doi: 10.1016/j.molbiopara.2011.10.001. Epub 2011 Oct 8. [PubMed:22008417 ]
Pandey RP, Malla S, Simkhada D, Kim BG, Sohng JK: Production of 3-O-xylosyl quercetin in Escherichia coli. Appl Microbiol Biotechnol. 2013 Mar;97(5):1889-901. doi: 10.1007/s00253-012-4438-9. Epub 2012 Oct 5. [PubMed:23053089 ]
Han SH, Kim BG, Yoon JA, Chong Y, Ahn JH: Synthesis of flavonoid O-pentosides by Escherichia coli through engineering of nucleotide sugar pathways and glycosyltransferase. Appl Environ Microbiol. 2014 May;80(9):2754-62. doi: 10.1128/AEM.03797-13. Epub 2014 Feb 21. [PubMed:24561591 ]
LOTUS database [Link]

Showing NP-Card for {[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid (NP0235900)

MOL for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)

3D MOL for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)

3D SDF for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)

3D-SDF for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)

PDB for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)

3D PDB for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)

SMILES for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)

INCHI for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)

Structure for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)

3D Structure for NP0235900 ({[(2r,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy([(2r,3r,4s,5r)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphinic acid)