NP-MRD: Showing NP-Card for {2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium (NP0316069)

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Record Information

Version

2.0

Created at

2022-09-11 15:01:29 UTC

Updated at

2022-09-11 15:01:30 UTC

NP-MRD ID

NP0316069

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium

Description

(2-{[({[(2S,3S,4R,5S)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy)(hydroxy)phosphoryl]oxy}ethyl)trimethylazanium belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. {2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium is found in Arabidopsis thaliana. Based on a literature review very few articles have been published on (2-{[({[(2S,3S,4R,5S)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy)(hydroxy)phosphoryl]oxy}ethyl)trimethylazanium.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112217012D          

 31 32  0  0  1  0            999 V2000
   -2.1434    5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -2.9684    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    2.7770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 20 26  1  0  0  0  0
 26 27  1  0  0  0  0
 19 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 17 30  1  0  0  0  0
 30 31  1  6  0  0  0
M  CHG  2   2   1  14  -1
M  END

     RDKit          3D

 57 58  0  0  0  0  0  0  0  0999 V2000
    7.0386    4.6036    1.8956 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4155    3.6462    1.7652 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7020    2.6729    1.2855 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3737    2.8411    0.9091 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6275    1.8010    0.4015 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2084    0.5870    0.2685 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4757   -0.5097   -0.2492 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4388   -0.9290    0.6023 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7638   -1.8247   -0.2215 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5115   -2.3615    0.4003 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5903   -1.3694    0.7120 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7764   -2.0788    1.4052 P   0  0  2  0  0  5  0  0  0  0  0  0
   -1.8220   -0.9779    1.5763 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3876   -2.7548    2.9129 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.3863   -3.2879    0.3991 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3207   -2.5908   -0.8245 P   0  0  1  0  0  5  0  0  0  0  0  0
   -1.5743   -2.7626   -2.1442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7706   -3.4479   -0.9780 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5750   -0.9817   -0.4584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9370   -0.6466   -0.4494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0524    0.8319   -0.1065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4143    1.2721   -0.0728 N   0  0  0  0  0  4  0  0  0  0  0  0
   -6.0087    0.9584    1.2328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2460    0.5818   -1.0541 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5661    2.6829   -0.3150 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5084   -0.9778   -1.4465 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4803   -0.0955   -1.1400 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8469   -0.2843   -1.5939 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7550    1.0202   -1.9790 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4928    0.4262    0.6330 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1543   -0.7963    0.5233 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2320    1.4505    1.1342 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9563    3.8354    1.0364 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6032    2.0091    0.1319 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1450   -1.3875   -0.3496 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3883   -2.6724   -0.5359 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7777   -2.8829    1.3216 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0638   -3.0795   -0.3027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1492   -3.6604   -0.0687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2851   -0.7516   -1.4990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5176   -1.2527    0.2514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5996    1.0438    0.8966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5104    1.4470   -0.8384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9297    1.5481    1.4115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2609    1.1380    2.0583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2906   -0.1213    1.1741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5050   -0.4368   -0.7075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1983    1.1461   -1.1869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7592    0.5653   -2.0570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5177    3.0021    0.1506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7476    3.2923    0.1213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6416    2.8329   -1.4209 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2649   -1.5974   -2.3351 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8048    0.5326   -0.4503 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3910   -0.8356   -2.4143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5631    1.0450   -2.9506 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1763   -1.4581    1.2940 H   0  0  0  0  0  0  0  0  0  0  0  0
 23 22  1  0
 22 24  1  0
 22 25  1  0
 22 21  1  0
 21 20  1  0
 20 19  1  0
 16 19  1  1
 16 18  1  0
 16 17  2  0
 16 15  1  0
 15 12  1  0
 12 14  1  1
 12 13  2  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7 28  1  0
 28 29  1  0
 28 26  1  0
 26 27  1  0
  7  6  1  0
  6  5  1  0
  5  4  2  0
  4  3  1  0
  3  2  2  0
  3 32  1  0
 32 30  2  0
 30 31  1  0
 26  9  1  0
 30  6  1  0
 23 44  1  0
 23 45  1  0
 23 46  1  0
 24 47  1  0
 24 48  1  0
 24 49  1  0
 25 50  1  0
 25 51  1  0
 25 52  1  0
 21 42  1  0
 21 43  1  0
 20 40  1  0
 20 41  1  0
 18 39  1  0
 10 37  1  0
 10 38  1  0
  9 36  1  6
  7 35  1  6
 28 55  1  6
 29 56  1  0
 26 53  1  6
 27 54  1  0
  5 34  1  0
  4 33  1  0
  2  1  1  0
 31 57  1  0
M  CHG  2  14  -1  22   1
M  END


  Mrv1652309112217012D          

 31 32  0  0  1  0            999 V2000
   -2.1434    5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -2.9684    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    2.7770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  2  0  0  0  0
 20 26  1  0  0  0  0
 26 27  1  0  0  0  0
 19 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 17 30  1  0  0  0  0
 30 31  1  6  0  0  0
M  CHG  2   2   1  14  -1
M  END
> <DATABASE_ID>
NP0316069

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[N+](C)(C)CCOP(O)(=O)OP([O-])(=O)OC[C@@H]1O[C@@H]([C@H](O)[C@@H]1O)N1C=CC(=N)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H26N4O11P2/c1-18(2,3)6-7-26-30(22,23)29-31(24,25)27-8-9-11(19)12(20)13(28-9)17-5-4-10(15)16-14(17)21/h4-5,9,11-13,19-20H,6-8H2,1-3H3,(H3-,15,16,21,22,23,24,25)/t9-,11+,12+,13-/m0/s1

> <INCHI_KEY>
RZZPDXZPRHQOCG-SQNXGDPESA-N

> <FORMULA>
C14H26N4O11P2

> <MOLECULAR_WEIGHT>
488.327

> <EXACT_MASS>
488.107331669

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
57

> <JCHEM_AVERAGE_POLARIZABILITY>
43.02850890457089

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2-{[({[(2S,3S,4R,5S)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methyl phosphono}oxy)(hydroxy)phosphoryl]oxy}ethyl)trimethylazanium

> <JCHEM_LOGP>
-4.996356827316207

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.3349972254559304

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5488183805172646

> <JCHEM_PKA_STRONGEST_BASIC>
1.7658215061225624

> <JCHEM_POLAR_SURFACE_AREA>
214.48999999999998

> <JCHEM_REFRACTIVITY>
124.99640000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
{2-[({[(2S,3S,4R,5S)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphono}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -4.001  10.010   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -4.001   8.470   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0      -5.541   8.470   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.461   8.470   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0      -1.334   3.850   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0      -2.104   2.516   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -0.564   5.184   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   3.080   0.000  0.00  0.00           O+0
HETATM   12  P   UNK     0       0.000   1.540   0.000  0.00  0.00           P+0
HETATM   13  O   UNK     0      -1.540   1.540   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.540   1.540   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.580  -3.215   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       3.009  -5.926   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       4.540  -5.765   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.446  -7.011   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.819  -8.417   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       5.724  -9.663   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0       3.288  -8.578   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       2.382  -7.333   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       0.851  -7.494   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -0.342  -5.926   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.377  -2.739   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8   12                                                       
CONECT   12   11   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   30                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   28                                                  
CONECT   20   19   21   26                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   20   27                                                  
CONECT   27   26                                                            
CONECT   28   19   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   17   31                                                  
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₂₆N₄O₁₁P₂

Average Mass

488.3270 Da

Monoisotopic Mass

488.10733 Da

IUPAC Name

(2-{[({[(2S,3S,4R,5S)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methyl phosphono}oxy)(hydroxy)phosphoryl]oxy}ethyl)trimethylazanium

Traditional Name

{2-[({[(2S,3S,4R,5S)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphono}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium

CAS Registry Number

Not Available

SMILES

C[N+](C)(C)CCOP(O)(=O)OP([O-])(=O)OC[C@@H]1O[C@@H]([C@H](O)[C@@H]1O)N1C=CC(=N)N=C1O

InChI Identifier

InChI=1S/C14H26N4O11P2/c1-18(2,3)6-7-26-30(22,23)29-31(24,25)27-8-9-11(19)12(20)13(28-9)17-5-4-10(15)16-14(17)21/h4-5,9,11-13,19-20H,6-8H2,1-3H3,(H3-,15,16,21,22,23,24,25)/t9-,11+,12+,13-/m0/s1

InChI Key

RZZPDXZPRHQOCG-SQNXGDPESA-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
Arabidopsis thaliana	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-5-phosphate
Pentose phosphate
Phosphocholine
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
Hydroxypyrimidine
Monoalkyl phosphate
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Tetraalkylammonium salt
Heteroaromatic compound
Tetrahydrofuran
Quaternary ammonium salt
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic salt
Organic zwitterion
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	-5	ChemAxon
pKa (Strongest Acidic)	2.55	ChemAxon
pKa (Strongest Basic)	1.77	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	214.49 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	125 m³·mol⁻¹	ChemAxon
Polarizability	43.03 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

163193627

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for {2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium (NP0316069)

MOL for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)

3D MOL for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)

3D SDF for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)

3D-SDF for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)

PDB for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)

3D PDB for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)

SMILES for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)

INCHI for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)

Structure for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)

3D Structure for NP0316069 ({2-[({[(2s,3s,4r,5s)-3,4-dihydroxy-5-(2-hydroxy-4-iminopyrimidin-1-yl)oxolan-2-yl]methyl phosphonato}oxy(hydroxy)phosphoryl)oxy]ethyl}trimethylazanium)