Showing metabocard for UDP-D-apiose (MMDBc0053892)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-05-16 21:37:45 UTC
Update Date2022-09-01 02:26:39 UTC
Metabolite IDMMDBc0053892
Metabolite Identification
Common NameUDP-D-apiose
DescriptionD-Apiose is a plant-specific branched-chain monosaccharide found in rhamnogalacturonan II (RG-II), apiogalacturonan, and several apioglycosides. Within RG-II, D-apiose serves as the binding site for borate, which leads to the formation of cross-links within the wall. Biochemical studies in duckweed and parsley have established that uridine 5'-diphospho-D-apiose (UDP-D-apiose) is formed from UDP-D-glucuronate by decarboxylation and re-arrangement of the carbon skeleton, leading to ring contraction and branch formation. The enzyme catalyzing this reaction also forms UDP-D-xylose by decarboxylation of UDP-D-glucuronate, and has therefore been named UDP-D-apiose/UDP-D-xylose synthase (PMID: 12969423 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f122002e020>


  Mrv1652306222023392D          

 40 42  0  0  1  0            999 V2000
    6.0822  -14.1496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0822  -13.3246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2651  -10.1501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5737   -4.0041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7932   -5.1022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7802  -10.8176    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3677  -14.5621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9552  -10.8176    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7003  -11.6022    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.4583   -5.1022    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3677  -12.0871    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.7132   -5.8868    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6532  -13.3246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1257   -4.6172    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6532  -14.1496    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3677  -12.9121    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7667   -4.1757    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3677  -15.3871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4703  -10.1501    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9157  -11.8571    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6737   -4.8472    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9388  -12.9121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6778   -4.0041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7471   -8.2441    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0819   -9.2139    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8102   -7.6435    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3175   -6.9723    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5382   -5.8868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9296   -9.3965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0352  -11.6022    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2283   -6.5542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8994   -8.0616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4145   -8.7290    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.5639   -7.3079    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.4057  -10.0825    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1404  -10.9466    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5712  -12.4170    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3292   -4.2873    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1028  -12.4617    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8984   -5.7577    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  6  3  1  1  0  0  0
  7  1  1  0  0  0  0
  8  6  1  0  0  0  0
  9  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 14  4  1  1  0  0  0
 14  5  1  0  0  0  0
 14 10  1  0  0  0  0
 15  7  2  0  0  0  0
 15 13  1  0  0  0  0
 16  2  1  0  0  0  0
 11 16  1  1  0  0  0
 16 13  1  0  0  0  0
 17  4  1  0  0  0  0
 18  7  1  0  0  0  0
  8 19  1  6  0  0  0
  9 20  1  6  0  0  0
 10 21  1  6  0  0  0
 22 13  2  0  0  0  0
 14 23  1  6  0  0  0
 28  5  1  0  0  0  0
 28 12  1  0  0  0  0
 29  3  1  0  0  0  0
 30  6  1  0  0  0  0
 30 11  1  0  0  0  0
 12 31  1  1  0  0  0
 33 24  1  0  0  0  0
 33 25  2  0  0  0  0
 33 29  1  0  0  0  0
 33 32  1  0  0  0  0
 34 26  1  0  0  0  0
 34 27  2  0  0  0  0
 34 31  1  0  0  0  0
 34 32  1  0  0  0  0
  6 35  1  6  0  0  0
  8 36  1  1  0  0  0
  9 37  1  1  0  0  0
 10 38  1  1  0  0  0
 11 39  1  6  0  0  0
 12 40  1  6  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f122002e020>

HMDB0012301
     RDKit          3D
UDP-D-apiose
 56 58  0  0  0  0  0  0  0  0999 V2000
    9.9131    0.3532    0.6038 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7065    0.0554    0.4042 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8779    0.9867   -0.1791 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5520    0.6272   -0.3857 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0668   -0.5659   -0.0442 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7073   -0.9035   -0.2682 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0272   -0.0055   -1.0636 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6832   -0.1682   -0.8668 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9499    1.1563   -0.6526 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5901    0.8188   -0.4665 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3320    2.2147   -0.2175 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.1135    2.4876   -1.4791 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6652    3.5501    0.0758 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4441    1.9991    1.0446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4383    0.6943    0.6294 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.3004   -0.3272    1.7588 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9747   -0.0068   -0.8299 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0520    1.1325    0.5528 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7908    0.3569   -0.3304 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.4395    1.1286   -1.2825 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3832    0.2261   -1.8173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0075   -0.4026   -0.5767 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.3915   -1.7180   -0.7997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2224    0.4336   -0.1796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7750   -0.0936    0.9867 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9345   -0.2560    0.4507 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.5212   -1.4752    0.9824 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4874   -0.9745    0.3954 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2702   -2.2995    0.0657 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8716   -0.8836    1.0068 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1601   -1.9361    1.8444 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8893   -1.4592    0.5226 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5199   -2.6163    0.8803 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1953   -1.1445    0.7415 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.2696    1.9543   -0.4565 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9177    1.3648   -0.8419 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5849   -1.9195   -0.6942 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1656   -0.6511   -1.7330 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3566    1.6729    0.2281 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0072    1.7333   -1.5865 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8153    3.6949    1.0589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3946   -0.8009   -0.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1543   -0.4162   -0.8218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1189    0.8101   -2.3913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9050   -0.5247   -2.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6368   -2.3365   -0.7465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0087    0.3476   -0.9674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9365    1.4882   -0.0841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2611    0.2553    1.7513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2052    0.4525    1.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5585   -1.5998    0.8395 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7054   -0.5561    1.0545 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4785   -2.6371    0.5913 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9318    0.1109    1.5059 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1127   -1.5702    2.7849 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8215   -1.8572    1.1859 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  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  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  6
 22 24  1  0
 24 25  1  0
 22 26  1  0
 26 27  1  0
  8 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
  5 32  1  0
 32 33  2  0
 32 34  1  0
 34  2  1  0
 30  6  1  0
 26 19  1  0
  3 35  1  0
  4 36  1  0
  6 37  1  6
  8 38  1  6
  9 39  1  0
  9 40  1  0
 13 41  1  0
 17 42  1  0
 19 43  1  6
 21 44  1  0
 21 45  1  0
 23 46  1  0
 24 47  1  0
 24 48  1  0
 25 49  1  0
 26 50  1  1
 27 51  1  0
 28 52  1  1
 29 53  1  0
 30 54  1  1
 31 55  1  0
 34 56  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f122002e020>


  Mrv1652306222023392D          

 40 42  0  0  1  0            999 V2000
    6.0822  -14.1496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0822  -13.3246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2651  -10.1501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5737   -4.0041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7932   -5.1022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7802  -10.8176    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3677  -14.5621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9552  -10.8176    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7003  -11.6022    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.4583   -5.1022    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3677  -12.0871    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.7132   -5.8868    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6532  -13.3246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1257   -4.6172    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6532  -14.1496    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3677  -12.9121    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7667   -4.1757    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3677  -15.3871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4703  -10.1501    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9157  -11.8571    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6737   -4.8472    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9388  -12.9121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6778   -4.0041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7471   -8.2441    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0819   -9.2139    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8102   -7.6435    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3175   -6.9723    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5382   -5.8868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9296   -9.3965    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0352  -11.6022    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2283   -6.5542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8994   -8.0616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4145   -8.7290    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.5639   -7.3079    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.4057  -10.0825    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1404  -10.9466    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5712  -12.4170    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3292   -4.2873    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1028  -12.4617    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8984   -5.7577    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  6  3  1  1  0  0  0
  7  1  1  0  0  0  0
  8  6  1  0  0  0  0
  9  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 14  4  1  1  0  0  0
 14  5  1  0  0  0  0
 14 10  1  0  0  0  0
 15  7  2  0  0  0  0
 15 13  1  0  0  0  0
 16  2  1  0  0  0  0
 11 16  1  1  0  0  0
 16 13  1  0  0  0  0
 17  4  1  0  0  0  0
 18  7  1  0  0  0  0
  8 19  1  6  0  0  0
  9 20  1  6  0  0  0
 10 21  1  6  0  0  0
 22 13  2  0  0  0  0
 14 23  1  6  0  0  0
 28  5  1  0  0  0  0
 28 12  1  0  0  0  0
 29  3  1  0  0  0  0
 30  6  1  0  0  0  0
 30 11  1  0  0  0  0
 12 31  1  1  0  0  0
 33 24  1  0  0  0  0
 33 25  2  0  0  0  0
 33 29  1  0  0  0  0
 33 32  1  0  0  0  0
 34 26  1  0  0  0  0
 34 27  2  0  0  0  0
 34 31  1  0  0  0  0
 34 32  1  0  0  0  0
  6 35  1  6  0  0  0
  8 36  1  1  0  0  0
  9 37  1  1  0  0  0
 10 38  1  1  0  0  0
 11 39  1  6  0  0  0
 12 40  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0053892

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C14H22N2O16P2/c17-4-14(23)5-28-12(10(14)21)31-34(26,27)32-33(24,25)29-3-6-8(19)9(20)11(30-6)16-2-1-7(18)15-13(16)22/h1-2,6,8-12,17,19-21,23H,3-5H2,(H,24,25)(H,26,27)(H,15,18,22)/t6-,8-,9-,10+,11-,12+,14-/m1/s1

> <INCHI_KEY>
SYVORCSTSYHSPN-VPPDZDBCSA-N

> <FORMULA>
C14H22N2O16P2

> <MOLECULAR_WEIGHT>
536.2758

> <EXACT_MASS>
536.04445569

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
43.56549424457794

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.70

> <JCHEM_LOGP>
-4.134770688666666

> <ALOGPS_LOGS>
-1.44

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.176305059512126

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.732592905895912

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423949844966748

> <JCHEM_POLAR_SURFACE_AREA>
274.8

> <JCHEM_REFRACTIVITY>
101.03439999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.95e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f122002e020>

HMDB0012301
     RDKit          3D
UDP-D-apiose
 56 58  0  0  0  0  0  0  0  0999 V2000
    9.9131    0.3532    0.6038 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7065    0.0554    0.4042 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8779    0.9867   -0.1791 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5520    0.6272   -0.3857 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0668   -0.5659   -0.0442 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7073   -0.9035   -0.2682 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0272   -0.0055   -1.0636 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6832   -0.1682   -0.8668 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9499    1.1563   -0.6526 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5901    0.8188   -0.4665 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3320    2.2147   -0.2175 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.1135    2.4876   -1.4791 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6652    3.5501    0.0758 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4441    1.9991    1.0446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4383    0.6943    0.6294 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.3004   -0.3272    1.7588 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9747   -0.0068   -0.8299 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0520    1.1325    0.5528 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7908    0.3569   -0.3304 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.4395    1.1286   -1.2825 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3832    0.2261   -1.8173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0075   -0.4026   -0.5767 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.3915   -1.7180   -0.7997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2224    0.4336   -0.1796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7750   -0.0936    0.9867 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9345   -0.2560    0.4507 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.5212   -1.4752    0.9824 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4874   -0.9745    0.3954 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2702   -2.2995    0.0657 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8716   -0.8836    1.0068 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1601   -1.9361    1.8444 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8893   -1.4592    0.5226 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5199   -2.6163    0.8803 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1953   -1.1445    0.7415 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.2696    1.9543   -0.4565 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9177    1.3648   -0.8419 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5849   -1.9195   -0.6942 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1656   -0.6511   -1.7330 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3566    1.6729    0.2281 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0072    1.7333   -1.5865 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8153    3.6949    1.0589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3946   -0.8009   -0.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1543   -0.4162   -0.8218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1189    0.8101   -2.3913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9050   -0.5247   -2.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6368   -2.3365   -0.7465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0087    0.3476   -0.9674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9365    1.4882   -0.0841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2611    0.2553    1.7513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2052    0.4525    1.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5585   -1.5998    0.8395 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7054   -0.5561    1.0545 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4785   -2.6371    0.5913 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9318    0.1109    1.5059 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1127   -1.5702    2.7849 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8215   -1.8572    1.1859 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  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  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  6
 22 24  1  0
 24 25  1  0
 22 26  1  0
 26 27  1  0
  8 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
  5 32  1  0
 32 33  2  0
 32 34  1  0
 34  2  1  0
 30  6  1  0
 26 19  1  0
  3 35  1  0
  4 36  1  0
  6 37  1  6
  8 38  1  6
  9 39  1  0
  9 40  1  0
 13 41  1  0
 17 42  1  0
 19 43  1  6
 21 44  1  0
 21 45  1  0
 23 46  1  0
 24 47  1  0
 24 48  1  0
 25 49  1  0
 26 50  1  1
 27 51  1  0
 28 52  1  1
 29 53  1  0
 30 54  1  1
 31 55  1  0
 34 56  1  0
M  END
Download

PDB for #<Metabolite:0x00007f122002e020>

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      11.353 -26.413   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.353 -24.873   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.695 -18.947   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.271  -7.474   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.547  -9.524   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.790 -20.193   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.020 -27.183   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.250 -20.193   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.774 -21.657   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.055  -9.524   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.020 -22.563   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.531 -10.989   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.686 -24.873   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.301  -8.619   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       8.686 -26.413   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      10.020 -24.103   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      10.765  -7.795   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      10.020 -28.723   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       8.345 -18.947   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       7.309 -22.133   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      10.591  -9.048   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       7.352 -24.103   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      14.332  -7.474   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      10.728 -15.389   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      13.220 -17.199   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      10.846 -14.268   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      13.659 -13.015   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      14.071 -10.989   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      11.069 -17.540   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      11.266 -21.657   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      11.626 -12.235   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      12.879 -15.048   0.000  0.00  0.00           O+0
HETATM   33  P   UNK     0      11.974 -16.294   0.000  0.00  0.00           P+0
HETATM   34  P   UNK     0      12.253 -13.641   0.000  0.00  0.00           P+0
HETATM   35  H   UNK     0      10.091 -18.821   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0       7.729 -20.434   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       8.533 -23.178   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0      11.815  -8.003   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0      11.392 -23.262   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0      11.010 -10.748   0.000  0.00  0.00           H+0
CONECT    1    2    7                                                       
CONECT    2    1   16                                                       
CONECT    3    6   29                                                       
CONECT    4   14   17                                                       
CONECT    5   14   28                                                       
CONECT    6    3    8   30   35                                             
CONECT    7    1   15   18                                                  
CONECT    8    6    9   19   36                                             
CONECT    9    8   11   20   37                                             
CONECT   10   12   14   21   38                                             
CONECT   11    9   16   30   39                                             
CONECT   12   10   28   31   40                                             
CONECT   13   15   16   22                                                  
CONECT   14    4    5   10   23                                             
CONECT   15    7   13                                                       
CONECT   16    2   11   13                                                  
CONECT   17    4                                                            
CONECT   18    7                                                            
CONECT   19    8                                                            
CONECT   20    9                                                            
CONECT   21   10                                                            
CONECT   22   13                                                            
CONECT   23   14                                                            
CONECT   24   33                                                            
CONECT   25   33                                                            
CONECT   26   34                                                            
CONECT   27   34                                                            
CONECT   28    5   12                                                       
CONECT   29    3   33                                                       
CONECT   30    6   11                                                       
CONECT   31   12   34                                                       
CONECT   32   33   34                                                       
CONECT   33   24   25   29   32                                             
CONECT   34   26   27   31   32                                             
CONECT   35    6                                                            
CONECT   36    8                                                            
CONECT   37    9                                                            
CONECT   38   10                                                            
CONECT   39   11                                                            
CONECT   40   12                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   84    0
END
Download

3D PDB for #<Metabolite:0x00007f122002e020>

COMPND    HMDB0012301
HETATM    1  O1  UNL     1       9.913   0.353   0.604  1.00  0.00           O  
HETATM    2  C1  UNL     1       8.707   0.055   0.404  1.00  0.00           C  
HETATM    3  C2  UNL     1       7.878   0.987  -0.179  1.00  0.00           C  
HETATM    4  C3  UNL     1       6.552   0.627  -0.386  1.00  0.00           C  
HETATM    5  N1  UNL     1       6.067  -0.566  -0.044  1.00  0.00           N  
HETATM    6  C4  UNL     1       4.707  -0.904  -0.268  1.00  0.00           C  
HETATM    7  O2  UNL     1       4.027  -0.006  -1.064  1.00  0.00           O  
HETATM    8  C5  UNL     1       2.683  -0.168  -0.867  1.00  0.00           C  
HETATM    9  C6  UNL     1       1.950   1.156  -0.653  1.00  0.00           C  
HETATM   10  O3  UNL     1       0.590   0.819  -0.466  1.00  0.00           O  
HETATM   11  P1  UNL     1      -0.332   2.215  -0.218  1.00  0.00           P  
HETATM   12  O4  UNL     1      -1.114   2.488  -1.479  1.00  0.00           O  
HETATM   13  O5  UNL     1       0.665   3.550   0.076  1.00  0.00           O  
HETATM   14  O6  UNL     1      -1.444   1.999   1.045  1.00  0.00           O  
HETATM   15  P2  UNL     1      -2.438   0.694   0.629  1.00  0.00           P  
HETATM   16  O7  UNL     1      -2.300  -0.327   1.759  1.00  0.00           O  
HETATM   17  O8  UNL     1      -1.975  -0.007  -0.830  1.00  0.00           O  
HETATM   18  O9  UNL     1      -4.052   1.132   0.553  1.00  0.00           O  
HETATM   19  C7  UNL     1      -4.791   0.357  -0.330  1.00  0.00           C  
HETATM   20  O10 UNL     1      -5.440   1.129  -1.283  1.00  0.00           O  
HETATM   21  C8  UNL     1      -6.383   0.226  -1.817  1.00  0.00           C  
HETATM   22  C9  UNL     1      -7.007  -0.403  -0.577  1.00  0.00           C  
HETATM   23  O11 UNL     1      -7.391  -1.718  -0.800  1.00  0.00           O  
HETATM   24  C10 UNL     1      -8.222   0.434  -0.180  1.00  0.00           C  
HETATM   25  O12 UNL     1      -8.775  -0.094   0.987  1.00  0.00           O  
HETATM   26  C11 UNL     1      -5.934  -0.256   0.451  1.00  0.00           C  
HETATM   27  O13 UNL     1      -5.521  -1.475   0.982  1.00  0.00           O  
HETATM   28  C12 UNL     1       2.487  -0.975   0.395  1.00  0.00           C  
HETATM   29  O14 UNL     1       2.270  -2.300   0.066  1.00  0.00           O  
HETATM   30  C13 UNL     1       3.872  -0.884   1.007  1.00  0.00           C  
HETATM   31  O15 UNL     1       4.160  -1.936   1.844  1.00  0.00           O  
HETATM   32  C14 UNL     1       6.889  -1.459   0.523  1.00  0.00           C  
HETATM   33  O16 UNL     1       6.520  -2.616   0.880  1.00  0.00           O  
HETATM   34  N2  UNL     1       8.195  -1.144   0.742  1.00  0.00           N  
HETATM   35  H1  UNL     1       8.270   1.954  -0.457  1.00  0.00           H  
HETATM   36  H2  UNL     1       5.918   1.365  -0.842  1.00  0.00           H  
HETATM   37  H3  UNL     1       4.585  -1.920  -0.694  1.00  0.00           H  
HETATM   38  H4  UNL     1       2.166  -0.651  -1.733  1.00  0.00           H  
HETATM   39  H5  UNL     1       2.357   1.673   0.228  1.00  0.00           H  
HETATM   40  H6  UNL     1       2.007   1.733  -1.587  1.00  0.00           H  
HETATM   41  H7  UNL     1       0.815   3.695   1.059  1.00  0.00           H  
HETATM   42  H8  UNL     1      -1.395  -0.801  -0.703  1.00  0.00           H  
HETATM   43  H9  UNL     1      -4.154  -0.416  -0.822  1.00  0.00           H  
HETATM   44  H10 UNL     1      -7.119   0.810  -2.391  1.00  0.00           H  
HETATM   45  H11 UNL     1      -5.905  -0.525  -2.470  1.00  0.00           H  
HETATM   46  H12 UNL     1      -6.637  -2.336  -0.746  1.00  0.00           H  
HETATM   47  H13 UNL     1      -9.009   0.348  -0.967  1.00  0.00           H  
HETATM   48  H14 UNL     1      -7.936   1.488  -0.084  1.00  0.00           H  
HETATM   49  H15 UNL     1      -8.261   0.255   1.751  1.00  0.00           H  
HETATM   50  H16 UNL     1      -6.205   0.452   1.269  1.00  0.00           H  
HETATM   51  H17 UNL     1      -4.558  -1.600   0.839  1.00  0.00           H  
HETATM   52  H18 UNL     1       1.705  -0.556   1.054  1.00  0.00           H  
HETATM   53  H19 UNL     1       1.479  -2.637   0.591  1.00  0.00           H  
HETATM   54  H20 UNL     1       3.932   0.111   1.506  1.00  0.00           H  
HETATM   55  H21 UNL     1       4.113  -1.570   2.785  1.00  0.00           H  
HETATM   56  H22 UNL     1       8.822  -1.857   1.186  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   34
CONECT    3    4    4   35
CONECT    4    5   36
CONECT    5    6   32
CONECT    6    7   30   37
CONECT    7    8
CONECT    8    9   28   38
CONECT    9   10   39   40
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   41
CONECT   14   15
CONECT   15   16   16   17   18
CONECT   17   42
CONECT   18   19
CONECT   19   20   26   43
CONECT   20   21
CONECT   21   22   44   45
CONECT   22   23   24   26
CONECT   23   46
CONECT   24   25   47   48
CONECT   25   49
CONECT   26   27   50
CONECT   27   51
CONECT   28   29   30   52
CONECT   29   53
CONECT   30   31   54
CONECT   31   55
CONECT   32   33   33   34
CONECT   34   56
END
Download

SMILES for #<Metabolite:0x00007f122002e020>

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

INCHI for #<Metabolite:0x00007f122002e020>

InChI=1S/C14H22N2O16P2/c17-4-14(23)5-28-12(10(14)21)31-34(26,27)32-33(24,25)29-3-6-8(19)9(20)11(30-6)16-2-1-7(18)15-13(16)22/h1-2,6,8-12,17,19-21,23H,3-5H2,(H,24,25)(H,26,27)(H,15,18,22)/t6-,8-,9-,10+,11-,12+,14-/m1/s1
Download
Synonyms
ValueSource
UDP-ApioseMeSH
Uridine 5'-(alpha-D-apio-D-furanosyl pyrophosphate)MeSH
[({[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}(hydroxy)phosphoryl)oxy]({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinateGenerator
Molecular FormulaC14H22N2O16P2
Average Mass536.2758
Monoisotopic Mass536.04445569
IUPAC Name[({[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}(hydroxy)phosphoryl)oxy]({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid
Traditional Name{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy(hydroxy)phosphoryl}oxy([(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@]1(COP(O)(=O)OP(O)(=O)O[C@]2([H])OC[C@](O)(CO)[C@@]2([H])O)O[C@@]([H])(N2C=CC(O)=NC2=O)[C@]([H])(O)[C@]1([H])O
InChI Identifier
InChI=1S/C14H22N2O16P2/c17-4-14(23)5-28-12(10(14)21)31-34(26,27)32-33(24,25)29-3-6-8(19)9(20)11(30-6)16-2-1-7(18)15-13(16)22/h1-2,6,8-12,17,19-21,23H,3-5H2,(H,24,25)(H,26,27)(H,15,18,22)/t6-,8-,9-,10+,11-,12+,14-/m1/s1
InChI KeySYVORCSTSYHSPN-VPPDZDBCSA-N