NP-MRD: Showing NP-Card for 2'-deoxy-5-hydroxymethyl-cdp (NP0227219)

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Record Information

Version

2.0

Created at

2022-09-06 06:28:43 UTC

Updated at

2022-09-06 06:28:43 UTC

NP-MRD ID

NP0227219

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2'-deoxy-5-hydroxymethyl-cdp

Description

2'-Deoxy-5-hydroxymethyl-CDP belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. 2'-Deoxy-5-hydroxymethyl-CDP is possibly neutral. 2'-deoxy-5-hydroxymethyl-cdp is found in Apis cerana. A pyrimidine 2'-deoxyribonucleoside 5'-diphosphate that is 2'-deoxycytidine 5'-diphosphate (CDP) substituted by a hydroxymethyl group at position 5.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652307022001392D          

 26 27  0  0  1  0            999 V2000
   -4.0981   -0.0946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2755   -0.0944    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2755    0.7249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2818   -0.9151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4279   -0.0946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9563    0.1300    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4891   -1.1571    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6774    0.5503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2464    0.5503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8248   -0.6780    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2359   -1.9423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6774    1.3773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2464    1.3773    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5350    0.1370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1661   -1.1571    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4102   -1.9423    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9563    1.7877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3875    1.7877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6181   -0.8970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0752   -2.6052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9563    2.6052    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0981    1.3822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7852   -0.1000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053   -0.0944    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    0.7249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6116   -0.9151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  2  1  1  0  0  0  0
  7  6  1  1  0  0  0
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
  7 11  1  0  0  0  0
  8 12  2  0  0  0  0
  9 13  1  0  0  0  0
  9 14  2  0  0  0  0
 10 15  1  0  0  0  0
 11 16  1  0  0  0  0
 12 17  1  0  0  0  0
 12 18  1  0  0  0  0
 15 19  1  1  0  0  0
 16 20  1  6  0  0  0
 17 21  1  0  0  0  0
 18 22  1  0  0  0  0
 19 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24  5  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 13 17  2  0  0  0  0
 15 16  1  0  0  0  0
  5  2  1  0  0  0  0
M  END

     RDKit          3D

 43 44  0  0  0  0  0  0  0  0999 V2000
   -6.4729   -0.9096    1.5133 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1511   -0.8550    1.0182 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1748   -1.6642    1.4960 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9341   -1.5649    0.9835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0641   -2.3400    1.4630 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6012   -0.7020    0.0156 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2589   -0.6725   -0.4615 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8995    0.6431   -1.1243 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6101    0.5419   -1.1602 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9731    0.0644   -2.4243 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8741   -0.5568   -0.1650 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0647   -0.2619    0.7189 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1711   -0.1392   -0.1088 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5886    0.1936    0.7441 P   0  0  2  0  0  5  0  0  0  0  0  0
    5.2022   -1.0685    1.3126 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2963    1.2463    2.0224 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6991    0.8390   -0.3576 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1763    0.0221   -0.3145 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.0025   -1.4253   -0.7138 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2233    0.8339   -1.3752 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8621    0.0821    1.2259 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3067   -0.7005    0.5790 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5661    0.1229   -0.4816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8413    0.0439    0.0222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9084    0.9234   -0.4951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3932    1.7498   -1.4877 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1771   -1.5157    1.0631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7286   -0.3345    2.3339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9930   -1.4965   -1.1504 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3489    0.7588   -2.1229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1625    1.4555   -0.4236 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1017    1.4903   -0.9028 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1256   -0.9237   -2.4180 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0320   -1.5354   -0.6816 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2205   -1.1355    1.3609 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8694    0.6598    1.3024 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0966    0.7043    2.8263 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7675    1.0956   -2.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5780    0.9049    1.6597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3060    0.8240   -1.2646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7512    0.3673   -0.9485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2936    1.5791    0.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2015    2.6556   -1.1739 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 14 13  1  6
 14 16  1  0
 14 15  2  0
 14 17  1  0
 17 18  1  0
 18 20  1  0
 18 21  1  0
 18 19  2  0
 11 22  1  0
 24  2  1  0
 22  7  1  0
  1 27  1  0
  1 28  1  0
 23 40  1  0
 25 41  1  0
 25 42  1  0
 26 43  1  0
  7 29  1  6
  8 30  1  0
  8 31  1  0
  9 32  1  1
 10 33  1  0
 11 34  1  6
 12 35  1  0
 12 36  1  0
 16 37  1  0
 20 38  1  0
 21 39  1  0
M  END


  Mrv1652307022001392D          

 26 27  0  0  1  0            999 V2000
   -4.0981   -0.0946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2755   -0.0944    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2755    0.7249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2818   -0.9151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4279   -0.0946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9563    0.1300    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4891   -1.1571    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6774    0.5503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2464    0.5503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8248   -0.6780    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2359   -1.9423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6774    1.3773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2464    1.3773    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5350    0.1370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1661   -1.1571    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4102   -1.9423    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9563    1.7877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3875    1.7877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6181   -0.8970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0752   -2.6052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9563    2.6052    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0981    1.3822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7852   -0.1000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053   -0.0944    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    0.7249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6116   -0.9151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  2  1  1  0  0  0  0
  7  6  1  1  0  0  0
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
  7 11  1  0  0  0  0
  8 12  2  0  0  0  0
  9 13  1  0  0  0  0
  9 14  2  0  0  0  0
 10 15  1  0  0  0  0
 11 16  1  0  0  0  0
 12 17  1  0  0  0  0
 12 18  1  0  0  0  0
 15 19  1  1  0  0  0
 16 20  1  6  0  0  0
 17 21  1  0  0  0  0
 18 22  1  0  0  0  0
 19 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24  5  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 13 17  2  0  0  0  0
 15 16  1  0  0  0  0
  5  2  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0227219

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC(=O)N(C=C1CO)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C10H17N3O11P2/c11-9-5(3-14)2-13(10(16)12-9)8-1-6(15)7(23-8)4-22-26(20,21)24-25(17,18)19/h2,6-8,14-15H,1,3-4H2,(H,20,21)(H2,11,12,16)(H2,17,18,19)/t6-,7+,8+/m0/s1

> <INCHI_KEY>
RQKDPSTWKKMBPM-XLPZGREQSA-N

> <FORMULA>
C10H17N3O11P2

> <MOLECULAR_WEIGHT>
417.204

> <EXACT_MASS>
417.033832375

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
33.498197408179045

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.46

> <JCHEM_LOGP>
-3.3274643989999992

> <ALOGPS_LOGS>
-1.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2104375554874314

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7726007153762566

> <JCHEM_PKA_STRONGEST_BASIC>
-0.9193237572261864

> <JCHEM_POLAR_SURFACE_AREA>
221.66999999999996

> <JCHEM_REFRACTIVITY>
80.9117

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.13e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2'-deoxy-5-hydroxymethyl-cdp

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-JUL-20         0                                  
HETATM    1  O   UNK     0      -7.650  -0.177   0.000  0.00  0.00           O+0
HETATM    2  P   UNK     0      -6.114  -0.176   0.000  0.00  0.00           P+0
HETATM    3  O   UNK     0      -6.114   1.353   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -6.126  -1.708   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -4.532  -0.177   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       3.652   0.243   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       2.780  -2.160   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.998   1.027   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.327   1.027   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.540  -1.266   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.307  -3.626   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.998   2.571   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       2.327   2.571   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       0.999   0.256   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.310  -2.160   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.766  -3.626   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.652   3.337   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.323   3.337   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.154  -1.674   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.140  -4.863   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0       3.652   4.863   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0       7.650   2.580   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -1.466  -0.187   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0      -2.996  -0.176   0.000  0.00  0.00           P+0
HETATM   25  O   UNK     0      -2.996   1.353   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -3.008  -1.708   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    3    4    1    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5   24    2                                                       
CONECT    6    7    8    9                                                  
CONECT    7    6   10   11                                                  
CONECT    8    6   12                                                       
CONECT    9    6   13   14                                                  
CONECT   10    7   15                                                       
CONECT   11    7   16                                                       
CONECT   12    8   17   18                                                  
CONECT   13    9   17                                                       
CONECT   14    9                                                            
CONECT   15   10   19   16                                                  
CONECT   16   11   20   15                                                  
CONECT   17   12   21   13                                                  
CONECT   18   12   22                                                       
CONECT   19   15   23                                                       
CONECT   20   16                                                            
CONECT   21   17                                                            
CONECT   22   18                                                            
CONECT   23   19   24                                                       
CONECT   24   23    5   25   26                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

View in JSmol

Synonyms

Value	Source
2'-Deoxy-5-hydroxymethylcytidine 5'-diphosphate	ChEBI
2'-Deoxy-5-hydroxymethylcytidine-5'-diphosphate	ChEBI
Diphosphoric acid mono-(5-hydroxymethyl-2'-deoxy-cytidin-5'-yl ester)	ChEBI
2'-Deoxy-5-hydroxymethylcytidine 5'-diphosphoric acid	Generator
2'-Deoxy-5-hydroxymethylcytidine-5'-diphosphoric acid	Generator
Diphosphate mono-(5-hydroxymethyl-2'-deoxy-cytidin-5'-yl ester)	Generator

Chemical Formula

C₁₀H₁₇N₃O₁₁P₂

Average Mass

417.2040 Da

Monoisotopic Mass

417.03383 Da

IUPAC Name

[({[(2R,3S,5R)-5-[4-amino-5-(hydroxymethyl)-2-oxo-1,2-dihydropyrimidin-1-yl]-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

2'-deoxy-5-hydroxymethyl-cdp

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1CO)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1

InChI Identifier

InChI=1S/C10H17N3O11P2/c11-9-5(3-14)2-13(10(16)12-9)8-1-6(15)7(23-8)4-22-26(20,21)24-25(17,18)19/h2,6-8,14-15H,1,3-4H2,(H,20,21)(H2,11,12,16)(H2,17,18,19)/t6-,7+,8+/m0/s1

InChI Key

RQKDPSTWKKMBPM-XLPZGREQSA-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
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organic oxoanionic compounds

Sub Class

Organic pyrophosphates

Direct Parent

Organic pyrophosphates

Alternative Parents

Substituents

Organic pyrophosphate
Aminopyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Imidolactam
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Primary amine
Primary alcohol
Alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Amine
Organic nitrogen compound
Aromatic alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside 5'-diphosphate (CHEBI:835 )

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	-1.5	ALOGPS
logP	-3.3	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	-0.92	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	221.67 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	80.91 m³·mol⁻¹	ChemAxon
Polarizability	33.5 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

391351

KEGG Compound ID

C11038

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443051

PDB ID

Not Available

ChEBI ID

835

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2'-deoxy-5-hydroxymethyl-cdp (NP0227219)

MOL for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)

3D MOL for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)

3D SDF for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)

3D-SDF for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)

PDB for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)

3D PDB for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)

SMILES for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)

INCHI for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)

Structure for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)

3D Structure for NP0227219 (2'-deoxy-5-hydroxymethyl-cdp)