MiMeDB: Showing metabocard for 2',3'-Cyclic UMP (MMDBc0029992)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:49:47 UTC

Update Date

2024-04-30 19:43:55 UTC

Metabolite ID

MMDBc0029992

Metabolite Identification

Common Name

2',3'-Cyclic UMP

Description

Uridine 2',3'-cyclic phosphate is a cyclic nucleotide. A cyclic nucleotide is any nucleotide in which the phosphate group is bonded to two of the sugar's hydroxyl groups, forming a cyclical or ring structure. Cyclic phosphates are commonly found at the 3' end of mRNAs and other small RNAs. Uridine 2',3'-cyclic phosphate is a substrate for the enzyme 2',3'-cyclic nucleotide-3'-phosphodiesterase (CNPase, EC 3.1.4.37) which hydrolyses it to Uridine 2'-phosphate. CNPase is a unique RNase in that it only cleaves nucleoside 2',3'-cyclic phosphates and not the RNA internucleotide linkage, like other RNases such as RNase A and RNase T1.

Structure

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

HMDB0011640
     RDKit          3D
Uridine 2',3'-cyclic phosphate
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.3806    0.3374   -0.4090 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1390    0.3769   -0.2247 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3011   -0.4532   -0.9398 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9378   -0.4090   -0.7367 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3626    0.4337    0.1562 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0378    0.5090    0.3945 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4094   -0.5026    1.2448 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4325   -1.2253    0.7054 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0637   -2.6014    0.2411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5879   -3.3090    1.3290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0322   -0.3890   -0.4322 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0426    0.3533    0.1077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6982    1.9579   -0.2889 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.3967    2.7810    0.9350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9304    2.6672   -1.1657 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3153    1.6926   -1.2341 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8969    0.4590   -0.8246 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2157    1.2259    0.8324 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7166    2.0355    1.6840 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5497    1.2070    0.6575 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7549   -1.1384   -1.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3230   -1.0588   -1.3010 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2550    1.4720    0.9110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2091   -1.3599    1.5143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3203   -2.6376   -0.5486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9875   -3.0825   -0.1455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3898   -3.6843    1.7968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4165   -1.0580   -1.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0708    3.5848   -0.8467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3857   -0.0244   -1.7069 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1972    1.8400    1.2018 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 16 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  1  0
 17  6  1  0
 17 11  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  1
  8 24  1  1
  9 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  6
 15 29  1  0
 17 30  1  6
 20 31  1  0
M  END


  Mrv0541 02241201482D          

 20 22  0  0  1  0            999 V2000
    7.3786  -10.0062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.0460   -9.5213    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6335  -10.7908    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7134  -10.0062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4585  -10.7908    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.5518   -9.6330    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.0443   -8.9294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9758   -9.7516    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.3665   -8.4591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2296  -10.1034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6203   -8.8108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1611  -10.9255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7905   -8.5777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5939   -9.7513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4224   -8.9443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7134  -11.5755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0460  -12.0604    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    7.6335  -12.7749    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4585  -12.7749    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3786  -11.5755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  4  6  1  1  0  0  0
  8  7  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  2  0  0  0  0
  6 10  1  0  0  0  0
  6 11  1  0  0  0  0
 12 10  2  0  0  0  0
 13  7  2  0  0  0  0
  1 14  1  1  0  0  0
 15 14  1  0  0  0  0
  5 16  1  6  0  0  0
 18 17  2  0  0  0  0
 19 17  1  0  0  0  0
 20 17  1  0  0  0  0
 16 17  1  0  0  0  0
  3 20  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029992

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@H]([C@@H]2OP(O)(=O)O[C@H]12)N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H11N2O8P/c12-3-4-6-7(19-20(15,16)18-6)8(17-4)11-2-1-5(13)10-9(11)14/h1-2,4,6-8,12H,3H2,(H,15,16)(H,10,13,14)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
HWDMHJDYMFRXOX-XVFCMESISA-N

> <FORMULA>
C9H11N2O8P

> <MOLECULAR_WEIGHT>
306.166

> <EXACT_MASS>
306.02530185

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
24.699985437895975

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxo-tetrahydro-2H-2λ⁵-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-1.30

> <JCHEM_LOGP>
-1.6422703816666666

> <ALOGPS_LOGS>
-1.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.701346058916792

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7621871169083843

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9813280853111124

> <JCHEM_POLAR_SURFACE_AREA>
134.63000000000002

> <JCHEM_REFRACTIVITY>
59.6595

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.08e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2',3'-cyclic ump

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0011640
     RDKit          3D
Uridine 2',3'-cyclic phosphate
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.3806    0.3374   -0.4090 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1390    0.3769   -0.2247 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3011   -0.4532   -0.9398 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9378   -0.4090   -0.7367 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3626    0.4337    0.1562 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0378    0.5090    0.3945 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4094   -0.5026    1.2448 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4325   -1.2253    0.7054 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0637   -2.6014    0.2411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5879   -3.3090    1.3290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0322   -0.3890   -0.4322 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0426    0.3533    0.1077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6982    1.9579   -0.2889 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.3967    2.7810    0.9350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9304    2.6672   -1.1657 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3153    1.6926   -1.2341 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8969    0.4590   -0.8246 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2157    1.2259    0.8324 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7166    2.0355    1.6840 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5497    1.2070    0.6575 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7549   -1.1384   -1.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3230   -1.0588   -1.3010 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2550    1.4720    0.9110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2091   -1.3599    1.5143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3203   -2.6376   -0.5486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9875   -3.0825   -0.1455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3898   -3.6843    1.7968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4165   -1.0580   -1.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0708    3.5848   -0.8467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3857   -0.0244   -1.7069 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1972    1.8400    1.2018 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 16 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  1  0
 17  6  1  0
 17 11  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  1
  8 24  1  1
  9 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  6
 15 29  1  0
 17 30  1  6
 20 31  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      13.773 -18.678   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      15.019 -17.773   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      14.249 -20.143   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.265 -18.678   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.789 -20.143   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      17.830 -17.982   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      20.616 -16.668   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      20.488 -18.203   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      19.351 -15.790   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.095 -18.860   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.958 -16.447   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      18.967 -20.394   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      22.009 -16.012   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      12.309 -18.202   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      11.988 -16.696   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      16.265 -21.608   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0      15.019 -22.513   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      14.249 -23.846   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      15.789 -23.846   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      13.773 -21.608   0.000  0.00  0.00           O+0
CONECT    1    2    3   14                                                  
CONECT    2    1    4                                                       
CONECT    3    1    5   20                                                  
CONECT    4    2    5    6                                                  
CONECT    5    3    4   16                                                  
CONECT    6    4   10   11                                                  
CONECT    7    8    9   13                                                  
CONECT    8    7   10                                                       
CONECT    9    7   11                                                       
CONECT   10    8    6   12                                                  
CONECT   11    9    6                                                       
CONECT   12   10                                                            
CONECT   13    7                                                            
CONECT   14    1   15                                                       
CONECT   15   14                                                            
CONECT   16    5   17                                                       
CONECT   17   18   19   20   16                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17    3                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

COMPND    HMDB0011640
HETATM    1  O1  UNL     1       5.381   0.337  -0.409  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.139   0.377  -0.225  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.301  -0.453  -0.940  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.938  -0.409  -0.737  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.363   0.434   0.156  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.038   0.509   0.394  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.409  -0.503   1.245  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.432  -1.225   0.705  1.00  0.00           C  
HETATM    9  C6  UNL     1      -1.064  -2.601   0.241  1.00  0.00           C  
HETATM   10  O3  UNL     1      -0.588  -3.309   1.329  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.032  -0.389  -0.432  1.00  0.00           C  
HETATM   12  O4  UNL     1      -3.043   0.353   0.108  1.00  0.00           O  
HETATM   13  P1  UNL     1      -2.698   1.958  -0.289  1.00  0.00           P  
HETATM   14  O5  UNL     1      -2.397   2.781   0.935  1.00  0.00           O  
HETATM   15  O6  UNL     1      -3.930   2.667  -1.166  1.00  0.00           O  
HETATM   16  O7  UNL     1      -1.315   1.693  -1.234  1.00  0.00           O  
HETATM   17  C8  UNL     1      -0.897   0.459  -0.825  1.00  0.00           C  
HETATM   18  C9  UNL     1       2.216   1.226   0.832  1.00  0.00           C  
HETATM   19  O8  UNL     1       1.717   2.036   1.684  1.00  0.00           O  
HETATM   20  N2  UNL     1       3.550   1.207   0.658  1.00  0.00           N  
HETATM   21  H1  UNL     1       3.755  -1.138  -1.664  1.00  0.00           H  
HETATM   22  H2  UNL     1       1.323  -1.059  -1.301  1.00  0.00           H  
HETATM   23  H3  UNL     1      -0.255   1.472   0.911  1.00  0.00           H  
HETATM   24  H4  UNL     1      -2.209  -1.360   1.514  1.00  0.00           H  
HETATM   25  H5  UNL     1      -0.320  -2.638  -0.549  1.00  0.00           H  
HETATM   26  H6  UNL     1      -1.988  -3.082  -0.146  1.00  0.00           H  
HETATM   27  H7  UNL     1      -1.390  -3.684   1.797  1.00  0.00           H  
HETATM   28  H8  UNL     1      -2.416  -1.058  -1.243  1.00  0.00           H  
HETATM   29  H9  UNL     1      -4.071   3.585  -0.847  1.00  0.00           H  
HETATM   30  H10 UNL     1      -0.386  -0.024  -1.707  1.00  0.00           H  
HETATM   31  H11 UNL     1       4.197   1.840   1.202  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   20
CONECT    3    4    4   21
CONECT    4    5   22
CONECT    5    6   18
CONECT    6    7   17   23
CONECT    7    8
CONECT    8    9   11   24
CONECT    9   10   25   26
CONECT   10   27
CONECT   11   12   17   28
CONECT   12   13
CONECT   13   14   14   15   16
CONECT   15   29
CONECT   16   17
CONECT   17   30
CONECT   18   19   19   20
CONECT   20   31
END

HMDB0011640
     RDKit          3D
Uridine 2',3'-cyclic phosphate
 31 33  0  0  0  0  0  0  0  0999 V2000
    5.3806    0.3374   -0.4090 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1390    0.3769   -0.2247 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3011   -0.4532   -0.9398 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9378   -0.4090   -0.7367 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3626    0.4337    0.1562 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0378    0.5090    0.3945 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4094   -0.5026    1.2448 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4325   -1.2253    0.7054 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0637   -2.6014    0.2411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5879   -3.3090    1.3290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0322   -0.3890   -0.4322 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0426    0.3533    0.1077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6982    1.9579   -0.2889 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.3967    2.7810    0.9350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9304    2.6672   -1.1657 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3153    1.6926   -1.2341 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8969    0.4590   -0.8246 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2157    1.2259    0.8324 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7166    2.0355    1.6840 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5497    1.2070    0.6575 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7549   -1.1384   -1.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3230   -1.0588   -1.3010 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2550    1.4720    0.9110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2091   -1.3599    1.5143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3203   -2.6376   -0.5486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9875   -3.0825   -0.1455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3898   -3.6843    1.7968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4165   -1.0580   -1.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0708    3.5848   -0.8467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3857   -0.0244   -1.7069 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1972    1.8400    1.2018 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 13 16  1  0
 16 17  1  0
  5 18  1  0
 18 19  2  0
 18 20  1  0
 20  2  1  0
 17  6  1  0
 17 11  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  1
  8 24  1  1
  9 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  6
 15 29  1  0
 17 30  1  6
 20 31  1  0
M  END

Synonyms

Value	Source
CUMP	ChEBI
Uridine 2',3'-cyclophosphate	ChEBI
Uridine, cyclic 2',3'-(hydrogen phosphate)	ChEBI
Uridine 2',3'-cyclophosphoric acid	Generator
Uridine, cyclic 2',3'-(hydrogen phosphoric acid)	Generator
Uridine 2',3'-cyclic phosphoric acid	Generator
1-(2,3-O-Phosphinico-a-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
1-(2,3-O-Phosphinico-alpha-delta-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione	HMDB
2',3'-CUMP	HMDB
Uridine 2',3'-cyclic monophosphate	HMDB
Uridine 2',3'-cyclophosphate, monosodium salt	MeSH

Molecular Formula

C₉H₁₁N₂O₈P

Average Mass

306.166

Monoisotopic Mass

306.02530185

IUPAC Name

1-[(3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxo-tetrahydro-2H-2λ⁵-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

2',3'-cyclic ump

CAS Registry Number

40632-52-8

SMILES

OC[C@H]1O[C@H]([C@@H]2OP(O)(=O)O[C@H]12)N1C=CC(=O)NC1=O

InChI Identifier

InChI=1S/C9H11N2O8P/c12-3-4-6-7(19-20(15,16)18-6)8(17-4)11-2-1-5(13)10-9(11)14/h1-2,4,6-8,12H,3H2,(H,15,16)(H,10,13,14)/t4-,6-,7-,8-/m1/s1

InChI Key

HWDMHJDYMFRXOX-XVFCMESISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2',3'-cyclic pyrimidine nucleotides. These are pyrimidine nucleotides in which the oxygen atoms linked to the C2 and C3 carbon atoms of the ribose moiety are both bonded the same phosphorus atom of the phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Cyclic pyrimidine nucleotides

Direct Parent

2',3'-cyclic pyrimidine nucleotides

Alternative Parents

Substituents

2',3'-cyclic pyrimidine ribonucleotide
Ribonucleoside 3'-phosphate
Pyrimidone
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Pyrimidine
1,3_dioxaphospholane
Heteroaromatic compound
Tetrahydrofuran
Vinylogous amide
Urea
Lactam
Organoheterocyclic compound
Azacycle
Oxacycle
Alcohol
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

2',3'-cyclic pyrimidine nucleotide (CHEBI:28637 )
2',3'-Cyclic nucleotides (C02355 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	20.8 g/L	ALOGPS
logP	-1.3	ALOGPS
logP	-1.6	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	1.76	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	134.63 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	59.66 m³·mol⁻¹	ChemAxon
Polarizability	24.7 Å³	ChemAxon
Number of Rings	3	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	splash10-00di-3930000000-eeef1c59101eac345740	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00di-4970000000-ba43e7e87e9b1da0ce7c	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-1901000000-0d360d67bf767c95b2c9	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-5900000000-a9897f40443893ba5342	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08fu-9400000000-239eade290faab347bc0	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0bt9-5497000000-784d39c6cdcea534b626	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ox-9440000000-c6d0dde6755d0f4cdb28	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-0c839a884da572f801c3	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0009000000-296e5af1cfc5c172dc29	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-3389000000-ed033e9972509ec4ffa0	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-002f-7390000000-0be4168504ae9e2d5691	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-002b-0901000000-13423eb865c91fd69b03	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0bta-1905000000-eac4b0d63e2e24bf36d4	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3950000000-bfe76f46f1ed6470e081	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces
Placenta

Tissue Locations

Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0193538	2',3'-cyclic-nucleotide 3'-phosphodiesterase	Enzyme	P09543	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0004108	2',3'-Cyclic UMP	3'-UMP	Not Available	VMH	12225906
MMDBr0004109	2',3'-Cyclic UMP	3'-UMP	2',3'-cyclic nucleotide 3' phosphodiesterase	VMH; KEGG	30371894
MMDBr0007227	2',3'-Cyclic UMP	3'-UMP	Not Available	VMH	30371894

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	Proteobacteria	91	Human feces; Human sputum; Pig ; Human ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	169	Human feces; Human ; Human sputum; Human saliva; Human urine; Human supragingival plaque; Pig ; Cattle ; Human subgingival plaque	Metabolic reconstruction
Bacteria	Bacteroidetes	113	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque	Metabolic reconstruction
Bacteria	Actinobacteria	25	Human feces; Human ; Human supragingival plaque	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	3	Human feces; Human	Metabolic reconstruction

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Placenta	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	27543620

External Links

HMDB ID

HMDB0011640

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028337

KNApSAcK ID

Not Available

Chemspider ID

388781

KEGG Compound ID

C02355

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439715

PDB ID

Not Available

ChEBI ID

28637

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for 2',3'-Cyclic UMP (MMDBc0029992)

MOL for #<Metabolite:0x00007fdb054b1b70>

3D MOL for #<Metabolite:0x00007fdb054b1b70>

3D SDF for #<Metabolite:0x00007fdb054b1b70>

3D-SDF for #<Metabolite:0x00007fdb054b1b70>

PDB for #<Metabolite:0x00007fdb054b1b70>

3D PDB for #<Metabolite:0x00007fdb054b1b70>

SMILES for #<Metabolite:0x00007fdb054b1b70>

INCHI for #<Metabolite:0x00007fdb054b1b70>

Structure for #<Metabolite:0x00007fdb054b1b70>

3D Structure for #<Metabolite:0x00007fdb054b1b70>