MiMeDB: Showing metabocard for Pseudouridine 5'-phosphate (MMDBc0029604)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:34:07 UTC

Update Date

2024-04-30 19:38:55 UTC

Metabolite ID

MMDBc0029604

Metabolite Identification

Common Name

Pseudouridine 5'-phosphate

Description

Pseudouridine 5'-phosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Pseudouridine 5'-phosphate is an intermediate in pseudouridine degradation pathway. In this pathway, pseudouridine is metabolised to uracil. [BiocycPWY-6019]

Structure

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

HMDB0001271
     RDKit          3D
Pseudouridine 5'-phosphate
 34 35  0  0  0  0  0  0  0  0999 V2000
   -4.4828    2.7658   -1.6486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7232    1.9334   -1.0482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3975    0.7802   -1.6562 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5968   -0.1292   -1.0581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0947    0.1098    0.1974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2197   -0.7730    0.9689 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0032   -0.1245    1.1138 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9928   -0.8725    0.5504 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0262   -0.1033   -0.2117 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6506    0.8063    0.6589 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8066    1.6390   -0.2652 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.3778    1.7292   -1.6941 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2715    0.8035   -0.1508 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9805    3.1780    0.3710 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3264   -1.8664   -0.4060 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1023   -2.9945   -0.5087 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9651   -2.1029    0.3541 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6532   -3.0083    1.3883 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4559    1.3142    0.7911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0374    1.6138    1.9470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2480    2.2030    0.1869 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7793    0.6041   -2.6070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3307   -1.0490   -1.5330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6690   -0.8985    1.9834 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5083   -1.4107    1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7510   -0.8279   -0.6246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5949    0.4513   -1.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1373   -0.1755   -0.1148 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8331    3.1338    1.3565 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1574   -1.4024   -1.3826 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4307   -3.2832    0.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7653   -2.5145   -0.2513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0051   -2.6404    2.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5305    3.1112    0.6136 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  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
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  2  0
 19 21  1  0
 21  2  1  0
 17  6  1  0
  3 22  1  0
  4 23  1  0
  6 24  1  1
  8 25  1  1
  9 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  6
 16 31  1  0
 17 32  1  6
 18 33  1  0
 21 34  1  0
M  END


  Mrv1652304282021312D          

 21 22  0  0  0  0            999 V2000
10000.906010001.5423    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.120010001.5505    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6112 9999.6953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.6591 9998.4594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.898210000.1057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1853 9999.6953    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10003.5096 9998.4594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.5979 9998.9823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.470310000.1078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.7747 9998.9823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9946 9999.6113    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.662010000.0963    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.407110000.8809    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.582110000.8809    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.327210000.0963    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10002.084710000.1083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3702 9999.6958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3702 9998.8707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.0847 9998.4583    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10002.7992 9998.8707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.7992 9999.6958    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  8  2  0  0  0  0
  6  9  1  0  0  0  0
  6 10  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 12  1  0  0  0  0
 11 15  1  0  0  0  0
 13  1  1  1  0  0  0
 14  2  1  1  0  0  0
 15  3  1  6  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 21  1  0  0  0  0
 20 21  1  0  0  0  0
 12 17  1  6  0  0  0
 18  4  2  0  0  0  0
 20  7  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029604

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)C1=CNC(=O)NC1=O

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

> <INCHI_KEY>
MOBMOJGXNHLLIR-GBNDHIKLSA-N

> <FORMULA>
C9H13N2O9P

> <MOLECULAR_WEIGHT>
324.1813

> <EXACT_MASS>
324.035866536

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
26.315367273298467

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.86

> <JCHEM_LOGP>
-3.2237138943333337

> <ALOGPS_LOGS>
-1.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.253241023189858

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2291145458274322

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648940885134036

> <JCHEM_POLAR_SURFACE_AREA>
174.64999999999998

> <JCHEM_REFRACTIVITY>
63.3139

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.51e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pseudouridine 5'-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001271
     RDKit          3D
Pseudouridine 5'-phosphate
 34 35  0  0  0  0  0  0  0  0999 V2000
   -4.4828    2.7658   -1.6486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7232    1.9334   -1.0482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3975    0.7802   -1.6562 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5968   -0.1292   -1.0581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0947    0.1098    0.1974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2197   -0.7730    0.9689 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0032   -0.1245    1.1138 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9928   -0.8725    0.5504 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0262   -0.1033   -0.2117 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6506    0.8063    0.6589 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8066    1.6390   -0.2652 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.3778    1.7292   -1.6941 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2715    0.8035   -0.1508 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9805    3.1780    0.3710 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3264   -1.8664   -0.4060 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1023   -2.9945   -0.5087 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9651   -2.1029    0.3541 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6532   -3.0083    1.3883 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4559    1.3142    0.7911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0374    1.6138    1.9470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2480    2.2030    0.1869 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7793    0.6041   -2.6070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3307   -1.0490   -1.5330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6690   -0.8985    1.9834 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5083   -1.4107    1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7510   -0.8279   -0.6246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5949    0.4513   -1.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1373   -0.1755   -0.1148 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8331    3.1338    1.3565 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1574   -1.4024   -1.3826 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4307   -3.2832    0.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7653   -2.5145   -0.2513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0051   -2.6404    2.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5305    3.1112    0.6136 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  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
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  2  0
 19 21  1  0
 21  2  1  0
 17  6  1  0
  3 22  1  0
  4 23  1  0
  6 24  1  1
  8 25  1  1
  9 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  6
 16 31  1  0
 17 32  1  6
 18 33  1  0
 21 34  1  0
M  END

HEADER    PROTEIN                                 28-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-20         0                                  
HETATM    1  O   UNK     0    8668.3588669.546   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8665.0248669.561   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8664.0748666.098   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8667.8978663.791   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8662.7438666.864   0.000  0.00  0.00           O+0
HETATM    6  P   UNK     0    8661.4138666.098   0.000  0.00  0.00           P+0
HETATM    7  O   UNK     0    8673.2188663.791   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0    8662.1838664.767   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8660.0788666.868   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8660.6468664.767   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8666.6578665.941   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0    8667.9028666.846   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8667.4278668.311   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8665.8878668.311   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8665.4118666.846   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8670.5588666.869   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8669.2248666.099   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8669.2248664.559   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0    8670.5588663.789   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0    8671.8928664.559   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0    8671.8928666.099   0.000  0.00  0.00           N+0
CONECT    1   13                                                            
CONECT    2   14                                                            
CONECT    3    5   15                                                       
CONECT    4   18                                                            
CONECT    5    3    6                                                       
CONECT    6    5    8    9   10                                             
CONECT    7   20                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11   12   15                                                       
CONECT   12   13   11   17                                                  
CONECT   13   12   14    1                                                  
CONECT   14   13   15    2                                                  
CONECT   15   14   11    3                                                  
CONECT   16   17   21                                                       
CONECT   17   16   18   12                                                  
CONECT   18   17   19    4                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21    7                                                  
CONECT   21   16   20                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

COMPND    HMDB0001271
HETATM    1  O1  UNL     1      -4.483   2.766  -1.649  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.723   1.933  -1.048  1.00  0.00           C  
HETATM    3  N1  UNL     1      -3.398   0.780  -1.656  1.00  0.00           N  
HETATM    4  C2  UNL     1      -2.597  -0.129  -1.058  1.00  0.00           C  
HETATM    5  C3  UNL     1      -2.095   0.110   0.197  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.220  -0.773   0.969  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.003  -0.124   1.114  1.00  0.00           O  
HETATM    8  C5  UNL     1       0.993  -0.873   0.550  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.026  -0.103  -0.212  1.00  0.00           C  
HETATM   10  O3  UNL     1       2.651   0.806   0.659  1.00  0.00           O  
HETATM   11  P1  UNL     1       3.807   1.639  -0.265  1.00  0.00           P  
HETATM   12  O4  UNL     1       3.378   1.729  -1.694  1.00  0.00           O  
HETATM   13  O5  UNL     1       5.271   0.803  -0.151  1.00  0.00           O  
HETATM   14  O6  UNL     1       3.980   3.178   0.371  1.00  0.00           O  
HETATM   15  C7  UNL     1       0.326  -1.866  -0.406  1.00  0.00           C  
HETATM   16  O7  UNL     1       1.102  -2.995  -0.509  1.00  0.00           O  
HETATM   17  C8  UNL     1      -0.965  -2.103   0.354  1.00  0.00           C  
HETATM   18  O8  UNL     1      -0.653  -3.008   1.388  1.00  0.00           O  
HETATM   19  C9  UNL     1      -2.456   1.314   0.791  1.00  0.00           C  
HETATM   20  O9  UNL     1      -2.037   1.614   1.947  1.00  0.00           O  
HETATM   21  N2  UNL     1      -3.248   2.203   0.187  1.00  0.00           N  
HETATM   22  H1  UNL     1      -3.779   0.604  -2.607  1.00  0.00           H  
HETATM   23  H2  UNL     1      -2.331  -1.049  -1.533  1.00  0.00           H  
HETATM   24  H3  UNL     1      -1.669  -0.898   1.983  1.00  0.00           H  
HETATM   25  H4  UNL     1       1.508  -1.411   1.374  1.00  0.00           H  
HETATM   26  H5  UNL     1       2.751  -0.828  -0.625  1.00  0.00           H  
HETATM   27  H6  UNL     1       1.595   0.451  -1.074  1.00  0.00           H  
HETATM   28  H7  UNL     1       5.137  -0.176  -0.115  1.00  0.00           H  
HETATM   29  H8  UNL     1       3.833   3.134   1.356  1.00  0.00           H  
HETATM   30  H9  UNL     1       0.157  -1.402  -1.383  1.00  0.00           H  
HETATM   31  H10 UNL     1       1.431  -3.283   0.377  1.00  0.00           H  
HETATM   32  H11 UNL     1      -1.765  -2.515  -0.251  1.00  0.00           H  
HETATM   33  H12 UNL     1       0.005  -2.640   2.002  1.00  0.00           H  
HETATM   34  H13 UNL     1      -3.531   3.111   0.614  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   21
CONECT    3    4   22
CONECT    4    5    5   23
CONECT    5    6   19
CONECT    6    7   17   24
CONECT    7    8
CONECT    8    9   15   25
CONECT    9   10   26   27
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   28
CONECT   14   29
CONECT   15   16   17   30
CONECT   16   31
CONECT   17   18   32
CONECT   18   33
CONECT   19   20   20   21
CONECT   21   34
END

HMDB0001271
     RDKit          3D
Pseudouridine 5'-phosphate
 34 35  0  0  0  0  0  0  0  0999 V2000
   -4.4828    2.7658   -1.6486 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7232    1.9334   -1.0482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3975    0.7802   -1.6562 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5968   -0.1292   -1.0581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0947    0.1098    0.1974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2197   -0.7730    0.9689 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0032   -0.1245    1.1138 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9928   -0.8725    0.5504 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0262   -0.1033   -0.2117 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6506    0.8063    0.6589 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8066    1.6390   -0.2652 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.3778    1.7292   -1.6941 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2715    0.8035   -0.1508 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9805    3.1780    0.3710 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3264   -1.8664   -0.4060 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1023   -2.9945   -0.5087 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9651   -2.1029    0.3541 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6532   -3.0083    1.3883 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4559    1.3142    0.7911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0374    1.6138    1.9470 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2480    2.2030    0.1869 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7793    0.6041   -2.6070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3307   -1.0490   -1.5330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6690   -0.8985    1.9834 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5083   -1.4107    1.3743 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7510   -0.8279   -0.6246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5949    0.4513   -1.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1373   -0.1755   -0.1148 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8331    3.1338    1.3565 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1574   -1.4024   -1.3826 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4307   -3.2832    0.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7653   -2.5145   -0.2513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0051   -2.6404    2.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5305    3.1112    0.6136 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  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
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
  5 19  1  0
 19 20  2  0
 19 21  1  0
 21  2  1  0
 17  6  1  0
  3 22  1  0
  4 23  1  0
  6 24  1  1
  8 25  1  1
  9 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  6
 16 31  1  0
 17 32  1  6
 18 33  1  0
 21 34  1  0
M  END

Synonyms

Value	Source
(1S)-1,4-Anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol	ChEBI
5-(5-O-Phosphono-beta-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione	ChEBI
5-(5-O-Phosphono-b-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione	Generator
5-(5-O-Phosphono-β-D-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione	Generator
Pseudouridine 5'-phosphoric acid	Generator
Pseudouridylic acid	MeSH, HMDB
5-(5-O-Phosphono-beta-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
5-(5-O-Phosphono-β-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
Pseudouridine 5'-phosphate	HMDB
Pseudouridine 5’-phosphate	HMDB
Pseudouridine monophosphate	HMDB

Molecular Formula

C₉H₁₃N₂O₉P

Average Mass

324.1813

Monoisotopic Mass

324.035866536

IUPAC Name

{[(2R,3S,4R,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

pseudouridine 5'-phosphate

CAS Registry Number

1157-60-4

SMILES

O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)C1=CNC(=O)NC1=O

InChI Identifier

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

InChI Key

MOBMOJGXNHLLIR-GBNDHIKLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
C-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Tetrahydrofuran
Vinylogous amide
Heteroaromatic compound
Secondary alcohol
Urea
1,2-diol
Lactam
Dialkyl ether
Azacycle
Ether
Organoheterocyclic compound
Oxacycle
Organonitrogen compound
Alcohol
Organic oxide
Organopnictogen compound
Hydrocarbon derivative
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

C-nucleoside phosphate (CHEBI:18116 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	7.51 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-3.2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	174.65 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	63.31 m³·mol⁻¹	ChemAxon
Polarizability	26.32 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018836	Pseudouridine	Pseudouridine 5'-phosphate	Pseudouridine kinase	Phosphorylation	PathBank	31602464
MMDBr0018837	Pseudouridine 5'-phosphate	Uracil	Pseudouridine-5'-phosphate glycosidase	Transfer of a glycosyl group	PathBank	31602464

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
Bacteria/Eubacteria	Proteobacteria	19	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig	Unknown
Bacteria/Eubacteria	Tenericutes	2
Bacteria/Eubacteria	Firmicutes	10	Human feces; Human
Bacteria/Eubacteria	Spirochaetes	1	Pig
Bacteria/Eubacteria	Chloroflexi	3
Bacteria/Eubacteria	Actinobacteria	7	Human ; Human feces
Bacteria/Eubacteria	Deinococcus-thermus	2
Bacteria/Eubacteria	Thermotogae	9
Bacteria/Eubacteria	Gemmatimonadetes	1
Bacteria/Eubacteria	Acidobacteria	1
Eukaryota/Fungi	Ascomycota	3	Human feces; Human saliva	Unknown

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 Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0001271

DrugBank ID

DB03829

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022525

KNApSAcK ID

Not Available

Chemspider ID

388535

KEGG Compound ID

C01168

BioCyc ID

PSEUDOURIDINE-5-P

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439424

PDB ID

Not Available

ChEBI ID

18116

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Charette M, Gray MW: Pseudouridine in RNA: what, where, how, and why. IUBMB Life. 2000 May;49(5):341-51. doi: 10.1080/152165400410182. [PubMed:10902565 ]
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Drager A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO: Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. [PubMed:29457794 ]

Showing metabocard for Pseudouridine 5'-phosphate (MMDBc0029604)

MOL for #<Metabolite:0x00007f91ed636600>

3D MOL for #<Metabolite:0x00007f91ed636600>

3D SDF for #<Metabolite:0x00007f91ed636600>

3D-SDF for #<Metabolite:0x00007f91ed636600>

PDB for #<Metabolite:0x00007f91ed636600>

3D PDB for #<Metabolite:0x00007f91ed636600>

SMILES for #<Metabolite:0x00007f91ed636600>

INCHI for #<Metabolite:0x00007f91ed636600>

Structure for #<Metabolite:0x00007f91ed636600>

3D Structure for #<Metabolite:0x00007f91ed636600>