MiMeDB: Showing metabocard for Uridine 3'-phosphate (MMDBc0057139)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-11-09 19:12:50 UTC

Update Date

2025-10-07 16:09:51 UTC

Metabolite ID

MMDBc0057139

Metabolite Identification

Common Name

Uridine 3'-phosphate

Description

Uridine 3'-phosphate is a nucleotide metabolite belonging to the class of ribonucleotides. Its chemical structure features a ribose sugar with a phosphate group attached at the 3' position, along with a uracil base. In biochemical pathways, uridine 3'-phosphate plays a role in various enzymatic reactions, including those involving ribonucleases, where it has been shown to have lower affinity compared to modified nucleotides like 2'-fluoro-2'-deoxyuridine 3'-phosphate (dU(F)MP) and arabinouridine 3'-phosphate (araUMP) (PMID:15670155 ). Additionally, studies have investigated the alkaline cyclization of uridine 3'-phosphate esters, revealing a stepwise mechanism supported by a Bronsted graph indicating an intermediate (PMID:15280948 ). Furthermore, in the context of ribonuclease A activity, the presence of uridine 3'-phosphate can influence protonation events at the enzyme's active site (PMID:10049337 ). These insights into uridine 3'-phosphate's chemical interactions and structural dynamics contribute to our understanding of its role in nucleotide metabolism and enzymatic functions.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0060282
     RDKit          3D
Uridine 3'-monophosphate
 34 35  0  0  0  0  0  0  0  0999 V2000
    2.5539   -0.4120    2.5784 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0057   -0.1753    1.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3358   -0.0497    1.2925 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9059    0.2055    0.1009 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2744    0.3322   -0.0376 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0536    0.3347   -0.9776 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6884    0.2013   -0.8003 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1598   -0.0502    0.3880 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7537   -0.1971    0.6243 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2234   -1.3507    0.0103 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1274   -1.2059    0.3177 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9941   -2.1260   -0.5281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6709   -3.4559   -0.3344 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4601    0.2285   -0.0144 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2969    0.7975    0.9156 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7007    1.3044    0.1207 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.6072    2.7976   -0.0506 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8018    0.5608   -1.3906 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0468    0.9455    1.0732 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0818    0.8804   -0.0101 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0659    2.0727    0.6811 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7630    1.1971    0.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4751    0.5392   -1.9471 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0384    0.3052   -1.6530 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5235   -0.2700    1.6898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3136   -1.4477    1.3774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8698   -1.8013   -1.5846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0479   -1.9147   -0.2249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2050   -3.8765    0.3691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8942    0.2398   -1.0254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4868   -0.1703   -1.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6115    1.7476    1.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2203    1.0242   -1.0592 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3079    2.7893    0.0827 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
 14 20  1  0
 20 21  1  0
  8  2  1  0
 20  9  1  0
  5 22  1  0
  6 23  1  0
  7 24  1  0
  9 25  1  1
 11 26  1  1
 12 27  1  0
 12 28  1  0
 13 29  1  0
 14 30  1  6
 18 31  1  0
 19 32  1  0
 20 33  1  6
 21 34  1  0
M  END

 
  Mrv1652309191919292D          

 21 22  0  0  0  0            999 V2000
   13.2753  -10.1145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8988   -9.5709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6788   -9.8331    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.9246  -10.6246    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.3805  -11.2466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7508  -10.6322    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.2240  -11.3060    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0130   -9.8522    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.3525   -9.3598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8006   -9.6063    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.4098  -10.1689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2270  -10.9734    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.1972   -9.9228    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.3800   -9.1181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7708   -8.5557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9833   -8.8016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6457  -12.0252    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   14.9018  -12.8051    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4257  -11.7643    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8661  -12.2879    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1656   -8.8744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  3  9  1  0  0  0  0
  8 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 10 16  1  0  0  0  0
  5 17  1  0  0  0  0
  1  2  1  0  0  0  0
 17 18  1  0  0  0  0
  3  2  1  1  0  0  0
 17 19  2  0  0  0  0
  3  4  1  0  0  0  0
 17 20  1  0  0  0  0
  4  5  1  6  0  0  0
 14 21  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057139

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N2O9P/c12-3-4-7(20-21(16,17)18)6(14)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
FOGRQMPFHUHIGU-XVFCMESISA-N

> <FORMULA>
C9H13N2O9P

> <MOLECULAR_WEIGHT>
324.1813

> <EXACT_MASS>
324.035866536

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.55651888785477

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.75

> <JCHEM_LOGP>
-2.1713073686666666

> <ALOGPS_LOGS>
-1.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.894408374166111

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8747321923263796

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9813008545882633

> <JCHEM_POLAR_SURFACE_AREA>
169.35

> <JCHEM_REFRACTIVITY>
63.7602

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.29e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
disodium salt 3'-uridylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060282
     RDKit          3D
Uridine 3'-monophosphate
 34 35  0  0  0  0  0  0  0  0999 V2000
    2.5539   -0.4120    2.5784 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0057   -0.1753    1.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3358   -0.0497    1.2925 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9059    0.2055    0.1009 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2744    0.3322   -0.0376 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0536    0.3347   -0.9776 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6884    0.2013   -0.8003 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1598   -0.0502    0.3880 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7537   -0.1971    0.6243 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2234   -1.3507    0.0103 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1274   -1.2059    0.3177 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9941   -2.1260   -0.5281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6709   -3.4559   -0.3344 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4601    0.2285   -0.0144 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2969    0.7975    0.9156 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7007    1.3044    0.1207 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.6072    2.7976   -0.0506 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8018    0.5608   -1.3906 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0468    0.9455    1.0732 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0818    0.8804   -0.0101 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0659    2.0727    0.6811 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7630    1.1971    0.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4751    0.5392   -1.9471 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0384    0.3052   -1.6530 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5235   -0.2700    1.6898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3136   -1.4477    1.3774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8698   -1.8013   -1.5846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0479   -1.9147   -0.2249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2050   -3.8765    0.3691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8942    0.2398   -1.0254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4868   -0.1703   -1.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6115    1.7476    1.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2203    1.0242   -1.0592 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3079    2.7893    0.0827 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
 14 20  1  0
 20 21  1  0
  8  2  1  0
 20  9  1  0
  5 22  1  0
  6 23  1  0
  7 24  1  0
  9 25  1  1
 11 26  1  1
 12 27  1  0
 12 28  1  0
 13 29  1  0
 14 30  1  6
 18 31  1  0
 19 32  1  0
 20 33  1  6
 21 34  1  0
M  END

HEADER    PROTEIN                                 19-SEP-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-SEP-19         0                                  
HETATM    1  O   UNK     0      24.781 -18.880   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      25.944 -17.866   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.400 -18.355   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.859 -19.833   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      26.844 -20.994   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      29.402 -19.847   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      30.285 -21.105   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      29.891 -18.391   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      28.658 -17.472   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      31.361 -17.932   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      32.498 -18.982   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      32.157 -20.484   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0      33.968 -18.523   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      34.309 -17.020   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      33.172 -15.971   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      31.702 -16.430   0.000  0.00  0.00           C+0
HETATM   17  P   UNK     0      27.339 -22.447   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      27.817 -23.903   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      28.795 -21.960   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      25.883 -22.937   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      35.776 -16.566   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    9    2    4                                                  
CONECT    4    6    3    5                                                  
CONECT    5   17    4                                                       
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8    3                                                       
CONECT   10    8   11   16                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   21                                                  
CONECT   15   14   16                                                       
CONECT   16   15   10                                                       
CONECT   17    5   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17                                                            
CONECT   21   14                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

COMPND    HMDB0060282
HETATM    1  O1  UNL     1       2.554  -0.412   2.578  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.006  -0.175   1.441  1.00  0.00           C  
HETATM    3  N1  UNL     1       4.336  -0.050   1.293  1.00  0.00           N  
HETATM    4  C2  UNL     1       4.906   0.206   0.101  1.00  0.00           C  
HETATM    5  O2  UNL     1       6.274   0.332  -0.038  1.00  0.00           O  
HETATM    6  C3  UNL     1       4.054   0.335  -0.978  1.00  0.00           C  
HETATM    7  C4  UNL     1       2.688   0.201  -0.800  1.00  0.00           C  
HETATM    8  N2  UNL     1       2.160  -0.050   0.388  1.00  0.00           N  
HETATM    9  C5  UNL     1       0.754  -0.197   0.624  1.00  0.00           C  
HETATM   10  O3  UNL     1       0.223  -1.351   0.010  1.00  0.00           O  
HETATM   11  C6  UNL     1      -1.127  -1.206   0.318  1.00  0.00           C  
HETATM   12  C7  UNL     1      -1.994  -2.126  -0.528  1.00  0.00           C  
HETATM   13  O4  UNL     1      -1.671  -3.456  -0.334  1.00  0.00           O  
HETATM   14  C8  UNL     1      -1.460   0.228  -0.014  1.00  0.00           C  
HETATM   15  O5  UNL     1      -2.297   0.797   0.916  1.00  0.00           O  
HETATM   16  P1  UNL     1      -3.701   1.304   0.121  1.00  0.00           P  
HETATM   17  O6  UNL     1      -3.607   2.798  -0.051  1.00  0.00           O  
HETATM   18  O7  UNL     1      -3.802   0.561  -1.391  1.00  0.00           O  
HETATM   19  O8  UNL     1      -5.047   0.945   1.073  1.00  0.00           O  
HETATM   20  C9  UNL     1      -0.082   0.880  -0.010  1.00  0.00           C  
HETATM   21  O9  UNL     1      -0.066   2.073   0.681  1.00  0.00           O  
HETATM   22  H1  UNL     1       6.763   1.197   0.116  1.00  0.00           H  
HETATM   23  H2  UNL     1       4.475   0.539  -1.947  1.00  0.00           H  
HETATM   24  H3  UNL     1       2.038   0.305  -1.653  1.00  0.00           H  
HETATM   25  H4  UNL     1       0.523  -0.270   1.690  1.00  0.00           H  
HETATM   26  H5  UNL     1      -1.314  -1.448   1.377  1.00  0.00           H  
HETATM   27  H6  UNL     1      -1.870  -1.801  -1.585  1.00  0.00           H  
HETATM   28  H7  UNL     1      -3.048  -1.915  -0.225  1.00  0.00           H  
HETATM   29  H8  UNL     1      -2.205  -3.876   0.369  1.00  0.00           H  
HETATM   30  H9  UNL     1      -1.894   0.240  -1.025  1.00  0.00           H  
HETATM   31  H10 UNL     1      -4.487  -0.170  -1.326  1.00  0.00           H  
HETATM   32  H11 UNL     1      -5.611   1.748   1.179  1.00  0.00           H  
HETATM   33  H12 UNL     1       0.220   1.024  -1.059  1.00  0.00           H  
HETATM   34  H13 UNL     1       0.308   2.789   0.083  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    4
CONECT    4    5    6
CONECT    5   22
CONECT    6    7    7   23
CONECT    7    8   24
CONECT    8    9
CONECT    9   10   20   25
CONECT   10   11
CONECT   11   12   14   26
CONECT   12   13   27   28
CONECT   13   29
CONECT   14   15   20   30
CONECT   15   16
CONECT   16   17   17   18   19
CONECT   18   31
CONECT   19   32
CONECT   20   21   33
CONECT   21   34
END

HMDB0060282
     RDKit          3D
Uridine 3'-monophosphate
 34 35  0  0  0  0  0  0  0  0999 V2000
    2.5539   -0.4120    2.5784 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0057   -0.1753    1.4410 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3358   -0.0497    1.2925 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9059    0.2055    0.1009 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2744    0.3322   -0.0376 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0536    0.3347   -0.9776 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6884    0.2013   -0.8003 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1598   -0.0502    0.3880 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7537   -0.1971    0.6243 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2234   -1.3507    0.0103 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1274   -1.2059    0.3177 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9941   -2.1260   -0.5281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6709   -3.4559   -0.3344 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4601    0.2285   -0.0144 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2969    0.7975    0.9156 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7007    1.3044    0.1207 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.6072    2.7976   -0.0506 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8018    0.5608   -1.3906 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0468    0.9455    1.0732 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0818    0.8804   -0.0101 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0659    2.0727    0.6811 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7630    1.1971    0.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4751    0.5392   -1.9471 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0384    0.3052   -1.6530 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5235   -0.2700    1.6898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3136   -1.4477    1.3774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8698   -1.8013   -1.5846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0479   -1.9147   -0.2249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2050   -3.8765    0.3691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8942    0.2398   -1.0254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4868   -0.1703   -1.3260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6115    1.7476    1.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2203    1.0242   -1.0592 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3079    2.7893    0.0827 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
 14 20  1  0
 20 21  1  0
  8  2  1  0
 20  9  1  0
  5 22  1  0
  6 23  1  0
  7 24  1  0
  9 25  1  1
 11 26  1  1
 12 27  1  0
 12 28  1  0
 13 29  1  0
 14 30  1  6
 18 31  1  0
 19 32  1  0
 20 33  1  6
 21 34  1  0
M  END

Synonyms

Value	Source
Uridine 3'-phosphate	ChEBI
Uridine 3'-phosphoric acid	Generator
Uridine 3'-monophosphoric acid	Generator
3'-Uridylic acid	HMDB
3'-UMP	HMDB
3’-UMP	HMDB
Uridine 3'-(dihydrogen phosphate)	HMDB
Uridine 3’-(dihydrogen phosphate)	HMDB
Uridine 3’-monophosphate	HMDB
Uridine 3’-phosphate	HMDB
Uridine 3’-phosphoric acid	HMDB
Uridine 3'-monophosphate	ChEBI, KEGG

Molecular Formula

C₉H₁₃N₂O₉P

Average Mass

324.1813

Monoisotopic Mass

324.035866536

IUPAC Name

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

Traditional Name

disodium salt 3'-uridylic acid

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C9H13N2O9P/c12-3-4-7(20-21(16,17)18)6(14)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

InChI Key

FOGRQMPFHUHIGU-XVFCMESISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ribonucleoside 3'-phosphates. These are ribonucleosides that contain a phosphate group attached to the C-3 carbon of the ribose or deoxyribose moiety. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Ribonucleoside 3'-phosphates

Sub Class

Not Available

Direct Parent

Ribonucleoside 3'-phosphates

Alternative Parents

Substituents

Ribonucleoside 3'-phosphate
Pentose phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Hydroxypyrimidine
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Azacycle
Alcohol
Primary alcohol
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organopnictogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine ribonucleoside 3'-monophosphate (CHEBI:28895 )
uridine phosphate (CHEBI:28895 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	12.9 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.2	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	0.87	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	169.35 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	63.76 m³·mol⁻¹	ChemAxon
Polarizability	26.56 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9700000000-234bd44f3d34906cbece	2017-09-20	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0002-9421320000-9c4cf530cc9624248dad	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1901000000-307223cc9d7e5ca2c6ee	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-4900000000-62b17f2d271511410cf4	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-9800000000-50f9fd6d43d9e5e16311	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03mi-7944000000-2b222aece47b6e9a695c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01tc-9311000000-cca262c231169b234379	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-82620f8bebfb8aa3568d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03fr-0957000000-a7d0f49263bb2b8e1973	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5914000000-d2595f9fec12f45442c7	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-4900000000-bf51097d1da03b19fd1c	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0009000000-a27b730787a7cecdb7c6	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9010000000-031f5fae06b2768c7c4d	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-08ff6e231aab99a21c75	2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Placenta

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0026012	Uridine 3'-phosphate	Uridine	5'/3'-nucleotidase SurE	Hydrolysis of nucleotide	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Placenta	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597

External Links

HMDB ID

HMDB0060282

DrugBank ID

DB02714

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

91753

KEGG Compound ID

C01368

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101543

PDB ID

Not Available

ChEBI ID

28895

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Uridine 3'-phosphate (MMDBc0057139)

MOL for #<Metabolite:0x00007fade0666828>

3D MOL for #<Metabolite:0x00007fade0666828>

3D SDF for #<Metabolite:0x00007fade0666828>

3D-SDF for #<Metabolite:0x00007fade0666828>

PDB for #<Metabolite:0x00007fade0666828>

3D PDB for #<Metabolite:0x00007fade0666828>

SMILES for #<Metabolite:0x00007fade0666828>

INCHI for #<Metabolite:0x00007fade0666828>

Structure for #<Metabolite:0x00007fade0666828>

3D Structure for #<Metabolite:0x00007fade0666828>