MiMeDB: Showing metabocard for UDP-N-acetyl-Œ±-D-muramoyl-L-alanyl-Œ≥-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine (MMDBc0032171)

Microbial

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:05:25 UTC

Update Date

2022-08-31 18:31:11 UTC

Metabolite ID

MMDBc0032171

Metabolite Identification

Common Name

UDP-N-acetyl-Œ±-D-muramoyl-L-alanyl-Œ≥-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine

Description

UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine is an intermediate in peptidoglycan biosynthesis I (meso-diaminopimelate containing) in E.coli. It is a substrate for the enzyme phospho-N-acetylmuramoyl-pentapeptide transferase which catalyzes the reaction UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + di-trans,octa-cis-undecaprenyl phosphate -> undecaprenyldiphospho-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP. It is also a product for enzyme D-alanyl-D-alanine-adding enzyme which catalyzes reaction D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimelate + ATP ‚Üí UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + ADP + phosphate + H+ (BioCyc compound: C1).

Structure

MOL SDF PDB SMILES InChI

      
  Mrv1533006031515572D          

 80 82  0  0  0  0            999 V2000
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  1  2  1  0  0  0  0
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M  CHG  6  19  -1  20   1  33  -1  36  -1  55  -1  59  -1
M  END

      
  Mrv1533006031515572D          

 80 82  0  0  0  0            999 V2000
   -1.5793    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   11.0343    0.4462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8548    0.3600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1903   -0.3936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0108   -0.4799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7054   -1.0611    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.8849   -0.9748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4000   -1.6423    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6520    1.3331    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8963    0.9600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7074    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9930    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2785    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9930    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  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
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 16 20  1  0  0  0  0
 12 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
  6 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
  2 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
 38 40  1  0  0  0  0
 40 41  1  0  0  0  0
 40 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  1  0  0  0  0
 43 48  1  0  0  0  0
 48 49  1  0  0  0  0
 47 50  1  0  0  0  0
 50 51  1  0  0  0  0
 45 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  2  0  0  0  0
 53 55  1  0  0  0  0
 53 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  2  0  0  0  0
 57 59  1  0  0  0  0
 57 60  1  0  0  0  0
 60 61  1  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  1  0  0  0  0
 64 65  1  0  0  0  0
 65 66  1  0  0  0  0
 62 66  1  0  0  0  0
 65 67  1  0  0  0  0
 67 68  1  0  0  0  0
 68 69  2  0  0  0  0
 69 70  1  0  0  0  0
 70 71  2  0  0  0  0
 70 72  1  0  0  0  0
 72 73  1  0  0  0  0
 67 73  1  0  0  0  0
 73 74  2  0  0  0  0
 64 75  1  0  0  0  0
 63 76  1  0  0  0  0
 44 77  1  0  0  0  0
 77 78  1  0  0  0  0
 78 79  2  0  0  0  0
 78 80  1  0  0  0  0
M  CHG  6  19  -1  20   1  33  -1  36  -1  55  -1  59  -1
M  END
> <DATABASE_ID>
MMDBc0032171

> <DATABASE_NAME>
MIME

> <SMILES>
CC(NC(=O)C(C)NC(=O)C(CCCC([NH3+])C([O-])=O)NC(=O)CCC(NC(=O)C(C)NC(=O)C(C)OC1C(O)C(CO)OC(OP([O-])(=O)OP([O-])(=O)OCC2OC(C(O)C2O)N2C=CC(=O)NC2=O)C1NC(C)=O)C([O-])=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C41H65N9O28P2/c1-15(32(58)45-17(3)37(62)63)44-35(61)21(8-6-7-20(42)38(64)65)47-25(53)10-9-22(39(66)67)48-33(59)16(2)43-34(60)18(4)74-31-27(46-19(5)52)40(76-23(13-51)29(31)56)77-80(71,72)78-79(69,70)73-14-24-28(55)30(57)36(75-24)50-12-11-26(54)49-41(50)68/h11-12,15-18,20-24,27-31,36,40,51,55-57H,6-10,13-14,42H2,1-5H3,(H,43,60)(H,44,61)(H,45,58)(H,46,52)(H,47,53)(H,48,59)(H,62,63)(H,64,65)(H,66,67)(H,69,70)(H,71,72)(H,49,54,68)/p-4

> <INCHI_KEY>
IMWOXEZVYQDRDF-UHFFFAOYSA-J

> <FORMULA>
C41H61N9O28P2

> <MOLECULAR_WEIGHT>
1189.924

> <EXACT_MASS>
1189.312320676

> <JCHEM_ACCEPTOR_COUNT>
25

> <JCHEM_ATOM_COUNT>
141

> <JCHEM_AVERAGE_POLARIZABILITY>
106.97950445662583

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-azaniumyl-6-[4-carboxylato-4-(2-{2-[(2-{[({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphinato]oxy}-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl)oxy]propanamido}propanamido)butanamido]-6-({1-[(1-carboxylatoethyl)carbamoyl]ethyl}carbamoyl)hexanoate

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-9.625220915211136

> <ALOGPS_LOGS>
-2.85

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
2.1055280381732504

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5175241986754013

> <JCHEM_PKA_STRONGEST_BASIC>
9.304108388719676

> <JCHEM_POLAR_SURFACE_AREA>
588.6000000000001

> <JCHEM_REFRACTIVITY>
294.86700000000013

> <JCHEM_ROTATABLE_BOND_COUNT>
31

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.86e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-ammonio-6-(4-carboxylato-4-{2-[2-({2-[({[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphinato)oxy]-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl}oxy)propanamido]propanamido}butanamido)-6-({1-[(1-carboxylatoethyl)carbamoyl]ethyl}carbamoyl)hexanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-JUN-15         0                                  
HETATM    1  C   UNK     0      -2.948   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.948  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.282  -1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -4.282  -3.080   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0      -5.615  -0.770   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -6.949  -1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -8.283  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -9.616  -1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -10.950  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0     -10.950   0.770   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0     -12.284  -1.540   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0     -13.618  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -13.618   0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -12.284   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -12.284   3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -10.950   3.850   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -10.950   5.390   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0     -12.284   6.160   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -9.616   6.160   0.000  0.00  0.00           O-1
HETATM   20  N   UNK     0      -9.616   3.080   0.000  0.00  0.00           N+1
HETATM   21  C   UNK     0     -14.951  -1.540   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0     -14.951  -3.080   0.000  0.00  0.00           O+0
HETATM   23  N   UNK     0     -16.285  -0.770   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0     -17.619  -1.540   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -17.619  -3.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0     -18.952  -0.770   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0     -18.952   0.770   0.000  0.00  0.00           O+0
HETATM   28  N   UNK     0     -20.286  -1.540   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0     -21.620  -0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -21.620   0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -22.953  -1.540   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0     -24.287  -0.770   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0     -22.953  -3.080   0.000  0.00  0.00           O-1
HETATM   34  C   UNK     0      -6.949  -3.080   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -8.283  -3.850   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -5.615  -3.850   0.000  0.00  0.00           O-1
HETATM   37  N   UNK     0      -1.614  -1.540   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0      -0.281  -0.770   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -0.281   0.770   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       1.053  -1.540   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       1.053  -3.080   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       2.387  -0.770   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0       3.720  -1.540   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       5.054  -0.770   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       6.388  -1.540   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0       6.388  -3.080   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0       5.054  -3.850   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       3.720  -3.080   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0       2.387  -3.850   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0       5.054  -5.390   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       3.720  -6.160   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       7.721  -0.770   0.000  0.00  0.00           O+0
HETATM   53  P   UNK     0       9.055  -1.540   0.000  0.00  0.00           P+0
HETATM   54  O   UNK     0       8.285  -2.874   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       9.825  -0.206   0.000  0.00  0.00           O-1
HETATM   56  O   UNK     0      10.389  -2.310   0.000  0.00  0.00           O+0
HETATM   57  P   UNK     0      11.722  -1.540   0.000  0.00  0.00           P+0
HETATM   58  O   UNK     0      12.492  -2.874   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      10.952  -0.206   0.000  0.00  0.00           O-1
HETATM   60  O   UNK     0      13.056  -0.770   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0      14.390  -1.540   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      15.723  -0.770   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      15.884   0.761   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      17.391   1.082   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      18.161  -0.252   0.000  0.00  0.00           C+0
HETATM   66  O   UNK     0      17.130  -1.396   0.000  0.00  0.00           O+0
HETATM   67  N   UNK     0      19.692  -0.413   0.000  0.00  0.00           N+0
HETATM   68  C   UNK     0      20.597   0.833   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      22.129   0.672   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      22.755  -0.735   0.000  0.00  0.00           C+0
HETATM   71  O   UNK     0      24.287  -0.896   0.000  0.00  0.00           O+0
HETATM   72  N   UNK     0      21.850  -1.981   0.000  0.00  0.00           N+0
HETATM   73  C   UNK     0      20.318  -1.820   0.000  0.00  0.00           C+0
HETATM   74  O   UNK     0      19.413  -3.066   0.000  0.00  0.00           O+0
HETATM   75  O   UNK     0      18.017   2.488   0.000  0.00  0.00           O+0
HETATM   76  O   UNK     0      14.740   1.792   0.000  0.00  0.00           O+0
HETATM   77  N   UNK     0       5.054   0.770   0.000  0.00  0.00           N+0
HETATM   78  C   UNK     0       3.720   1.540   0.000  0.00  0.00           C+0
HETATM   79  O   UNK     0       2.387   0.770   0.000  0.00  0.00           O+0
HETATM   80  C   UNK     0       3.720   3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   37                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   34                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   21                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   16                                                            
CONECT   21   12   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34    6   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
CONECT   37    2   38                                                       
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41   42                                                  
CONECT   41   40                                                            
CONECT   42   40   43                                                       
CONECT   43   42   44   48                                                  
CONECT   44   43   45   77                                                  
CONECT   45   44   46   52                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48   50                                                  
CONECT   48   47   43   49                                                  
CONECT   49   48                                                            
CONECT   50   47   51                                                       
CONECT   51   50                                                            
CONECT   52   45   53                                                       
CONECT   53   52   54   55   56                                             
CONECT   54   53                                                            
CONECT   55   53                                                            
CONECT   56   53   57                                                       
CONECT   57   56   58   59   60                                             
CONECT   58   57                                                            
CONECT   59   57                                                            
CONECT   60   57   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63   66                                                  
CONECT   63   62   64   76                                                  
CONECT   64   63   65   75                                                  
CONECT   65   64   66   67                                                  
CONECT   66   65   62                                                       
CONECT   67   65   68   73                                                  
CONECT   68   67   69                                                       
CONECT   69   68   70                                                       
CONECT   70   69   71   72                                                  
CONECT   71   70                                                            
CONECT   72   70   73                                                       
CONECT   73   72   67   74                                                  
CONECT   74   73                                                            
CONECT   75   64                                                            
CONECT   76   63                                                            
CONECT   77   44   78                                                       
CONECT   78   77   79   80                                                  
CONECT   79   78                                                            
CONECT   80   78                                                            
MASTER        0    0    0    0    0    0    0    0   80    0  164    0
END

Synonyms

Not Available

Molecular Formula

C₄₁H₆₁N₉O₂₈P₂

Average Mass

1189.924

Monoisotopic Mass

1189.312320676

IUPAC Name

2-azaniumyl-6-[4-carboxylato-4-(2-{2-[(2-{[({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphinato]oxy}-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl)oxy]propanamido}propanamido)butanamido]-6-({1-[(1-carboxylatoethyl)carbamoyl]ethyl}carbamoyl)hexanoate

Traditional Name

2-ammonio-6-(4-carboxylato-4-{2-[2-({2-[({[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphinato)oxy]-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl}oxy)propanamido]propanamido}butanamido)-6-({1-[(1-carboxylatoethyl)carbamoyl]ethyl}carbamoyl)hexanoate

CAS Registry Number

Not Available

SMILES

CC(NC(=O)C(C)NC(=O)C(CCCC([NH3+])C([O-])=O)NC(=O)CCC(NC(=O)C(C)NC(=O)C(C)OC1C(O)C(CO)OC(OP([O-])(=O)OP([O-])(=O)OCC2OC(C(O)C2O)N2C=CC(=O)NC2=O)C1NC(C)=O)C([O-])=O)C([O-])=O

InChI Identifier

InChI=1S/C41H65N9O28P2/c1-15(32(58)45-17(3)37(62)63)44-35(61)21(8-6-7-20(42)38(64)65)47-25(53)10-9-22(39(66)67)48-33(59)16(2)43-34(60)18(4)74-31-27(46-19(5)52)40(76-23(13-51)29(31)56)77-80(71,72)78-79(69,70)73-14-24-28(55)30(57)36(75-24)50-12-11-26(54)49-41(50)68/h11-12,15-18,20-24,27-31,36,40,51,55-57H,6-10,13-14,42H2,1-5H3,(H,43,60)(H,44,61)(H,45,58)(H,46,52)(H,47,53)(H,48,59)(H,62,63)(H,64,65)(H,66,67)(H,69,70)(H,71,72)(H,49,54,68)/p-4

InChI Key

IMWOXEZVYQDRDF-UHFFFAOYSA-J

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine nucleotide sugars

Direct Parent

Pyrimidine nucleotide sugars

Alternative Parents

Substituents

Pyrimidine nucleotide sugar
Pyrimidine ribonucleoside diphosphate
Alpha peptide
Pentose-5-phosphate
Pentose phosphate
N-acyl-alpha-hexosamine
N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
Alanine or derivatives
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
Alpha-amino acid or derivatives
Alpha-amino acid
Tricarboxylic acid or derivatives
Monoalkyl phosphate
Pyrimidone
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Amino acid
Secondary alcohol
Amino acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.86 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-9.6	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	1.52	ChemAxon
pKa (Strongest Basic)	9.3	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	25	ChemAxon
Hydrogen Donor Count	12	ChemAxon
Polar Surface Area	588.6 Å²	ChemAxon
Rotatable Bond Count	31	ChemAxon
Refractivity	294.87 m³·mol⁻¹	ChemAxon
Polarizability	106.98 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0f6x-2940000000-8b57a6ddd508848b307c	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-9740000000-e916809296850c7fc402	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000f-9200000000-3ae64b09ac9cb99d44d6	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-9730000000-ed2b9134718d45200a14	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0f76-9220000000-d1de6e789f13a1fe3104	2015-09-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-000x-9300000000-aee82f584bf1d0e5eec1	2015-09-16	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	790.2
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	369.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	550.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	618.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	387.1
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	154.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	2519.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	697.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	561.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	190.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	337.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	151.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	117.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	563.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	370.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	130.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	369.9
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1932.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1027.2

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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
MMDBr0018543	D-Alanyl-D-alanine	UDP-N-acetyl-Œ±-D-muramoyl-L-alanyl-Œ≥-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase	Ligation	PathBank	31602464
MMDBr0018544	UDP-N-acetyl-Œ±-D-muramoyl-L-alanyl-Œ≥-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine	Uridine 5'-monophosphate	Phospho-N-acetylmuramoyl-pentapeptide-transferase	Transfer of phospho-N-acetylmuramoyl-pentapeptide	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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for UDP-N-acetyl-Œ±-D-muramoyl-L-alanyl-Œ≥-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine (MMDBc0032171)

MOL for #<Metabolite:0x00007f9ab5217120>

3D MOL for #<Metabolite:0x00007f9ab5217120>

3D SDF for #<Metabolite:0x00007f9ab5217120>

3D-SDF for #<Metabolite:0x00007f9ab5217120>

PDB for #<Metabolite:0x00007f9ab5217120>

3D PDB for #<Metabolite:0x00007f9ab5217120>

SMILES for #<Metabolite:0x00007f9ab5217120>

INCHI for #<Metabolite:0x00007f9ab5217120>

Structure for #<Metabolite:0x00007f9ab5217120>

3D Structure for #<Metabolite:0x00007f9ab5217120>