MiMeDB: Showing metabocard for Deoxythymidine diphosphate-L-rhamnose (MMDBc0029827)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:43:20 UTC

Update Date

2022-12-15 22:51:48 UTC

Metabolite ID

MMDBc0029827

Metabolite Identification

Common Name

Deoxythymidine diphosphate-L-rhamnose

Description

Deoxythymidine diphosphate (dTDP)-L-rhamnose is the precursor of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. In gram negative bacteria such as Salmonella enterica, Vibrio cholerae or Escherichia coli 075:K5, L-rhamnose is an important residue in the O-antigen of lipopolysaccharides, which are essential for resistance to serum killing and for colonization. dTDP-L-rhamnose is synthesized from glucose-1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway involving four distinct enzymes. Whereas common sugars such as glucose, fructose and mannose are all D-configured, bacteria commonly utilize the L-configured carbohydrates in pharmacologically active compounds and in their cell-wall structures. The enzymes involved in dTDP-L-rhamnose synthesis are potential targets for the design of new therapeutic agents against bacteria. (PMID 10802738 , 12773151 )

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231220382D          

 35 37  0  0  1  0            999 V2000
   17.2028  -10.1744    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.9172   -8.9369    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.9643   -6.3895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2028  -11.8243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0837   -6.6443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4883  -10.5869    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0593  -13.0619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4883  -13.8869    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0593  -11.4118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.9172   -8.1119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.9172   -9.7619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7903   -9.4599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8903   -4.0974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7422   -8.9369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6153  -10.8889    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0922   -8.9369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2795   -2.9350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7342   -4.9374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.5849   -3.5162    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.2992   -6.3895    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.6318   -6.8742    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.0442   -5.6048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2193   -5.6048    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.7738  -12.6494    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4883  -13.0619    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.7738  -11.8243    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.2028  -12.6494    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4883  -11.4118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6318   -7.6994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9172  -13.0619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9138   -5.0236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0698   -4.1836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4289   -4.3561    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7644   -3.6026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6083   -4.4424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  1 15  2  0  0  0  0
  2 10  1  0  0  0  0
  2 11  1  0  0  0  0
  2 14  1  0  0  0  0
  2 16  2  0  0  0  0
  3 21  1  0  0  0  0
  3 23  1  0  0  0  0
  4 27  1  0  0  0  0
  4 28  1  0  0  0  0
 20  5  1  6  0  0  0
  6 28  1  0  0  0  0
 24  7  1  1  0  0  0
 25  8  1  6  0  0  0
 26  9  1  1  0  0  0
 10 29  1  0  0  0  0
 13 32  2  0  0  0  0
 17 34  2  0  0  0  0
 23 18  1  1  0  0  0
 18 31  1  0  0  0  0
 18 32  1  0  0  0  0
 19 32  1  0  0  0  0
 19 34  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 29  1  1  0  0  0
 22 23  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 25 27  1  0  0  0  0
 26 28  1  0  0  0  0
 27 30  1  1  0  0  0
 31 33  2  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
M  END


  Mrv0541 02231220382D          

 35 37  0  0  1  0            999 V2000
   17.2028  -10.1744    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.9172   -8.9369    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.9643   -6.3895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.2028  -11.8243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0837   -6.6443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4883  -10.5869    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0593  -13.0619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4883  -13.8869    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0593  -11.4118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.9172   -8.1119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.9172   -9.7619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7903   -9.4599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8903   -4.0974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7422   -8.9369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6153  -10.8889    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0922   -8.9369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2795   -2.9350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7342   -4.9374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.5849   -3.5162    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.2992   -6.3895    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.6318   -6.8742    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.0442   -5.6048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2193   -5.6048    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.7738  -12.6494    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4883  -13.0619    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.7738  -11.8243    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.2028  -12.6494    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4883  -11.4118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6318   -7.6994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9172  -13.0619    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9138   -5.0236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0698   -4.1836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4289   -4.3561    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7644   -3.6026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6083   -4.4424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  1 15  2  0  0  0  0
  2 10  1  0  0  0  0
  2 11  1  0  0  0  0
  2 14  1  0  0  0  0
  2 16  2  0  0  0  0
  3 21  1  0  0  0  0
  3 23  1  0  0  0  0
  4 27  1  0  0  0  0
  4 28  1  0  0  0  0
 20  5  1  6  0  0  0
  6 28  1  0  0  0  0
 24  7  1  1  0  0  0
 25  8  1  6  0  0  0
 26  9  1  1  0  0  0
 10 29  1  0  0  0  0
 13 32  2  0  0  0  0
 17 34  2  0  0  0  0
 23 18  1  1  0  0  0
 18 31  1  0  0  0  0
 18 32  1  0  0  0  0
 19 32  1  0  0  0  0
 19 34  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 29  1  1  0  0  0
 22 23  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 25 27  1  0  0  0  0
 26 28  1  0  0  0  0
 27 30  1  1  0  0  0
 31 33  2  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029827

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@@H]1OC(OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N2C=C(C)C(=O)NC2=O)[C@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,11-,12+,13+,15?/m0/s1

> <INCHI_KEY>
ZOSQFDVXNQFKBY-CZRCVJRHSA-N

> <FORMULA>
C16H26N2O15P2

> <MOLECULAR_WEIGHT>
548.3296

> <EXACT_MASS>
548.080841196

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
46.26313925404746

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy}({[(3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphinic acid

> <ALOGPS_LOGP>
-1.09

> <JCHEM_LOGP>
-2.653509559666667

> <ALOGPS_LOGS>
-1.68

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1563386971717415

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7326140016891394

> <JCHEM_PKA_STRONGEST_BASIC>
-3.240344259094388

> <JCHEM_POLAR_SURFACE_AREA>
251.07999999999998

> <JCHEM_REFRACTIVITY>
107.75849999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.16e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dtdp-L-rhamnose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  P   UNK     0      32.112 -18.992   0.000  0.00  0.00           P+0
HETATM    2  P   UNK     0      33.445 -16.682   0.000  0.00  0.00           P+0
HETATM    3  O   UNK     0      33.533 -11.927   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      32.112 -22.072   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      37.490 -12.403   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      30.778 -19.762   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      28.111 -24.382   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      30.778 -25.922   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      28.111 -21.302   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      33.445 -15.142   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      33.445 -18.222   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      31.342 -17.658   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      35.262  -7.648   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      34.985 -16.682   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      32.882 -20.326   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      31.905 -16.682   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      30.388  -5.479   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0      33.104  -9.216   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0      32.825  -6.564   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      36.025 -11.927   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      34.779 -12.832   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      35.549 -10.462   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      34.009 -10.462   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      29.444 -23.612   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      30.778 -24.382   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      29.444 -22.072   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      32.112 -23.612   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      30.778 -21.302   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      34.779 -14.372   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      33.445 -24.382   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      31.572  -9.377   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      33.730  -7.809   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      30.667  -8.131   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      31.294  -6.725   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      29.135  -8.292   0.000  0.00  0.00           C+0
CONECT    1    6   11   12   15                                             
CONECT    2   10   11   14   16                                             
CONECT    3   21   23                                                       
CONECT    4   27   28                                                       
CONECT    5   20                                                            
CONECT    6    1   28                                                       
CONECT    7   24                                                            
CONECT    8   25                                                            
CONECT    9   26                                                            
CONECT   10    2   29                                                       
CONECT   11    1    2                                                       
CONECT   12    1                                                            
CONECT   13   32                                                            
CONECT   14    2                                                            
CONECT   15    1                                                            
CONECT   16    2                                                            
CONECT   17   34                                                            
CONECT   18   23   31   32                                                  
CONECT   19   32   34                                                       
CONECT   20    5   21   22                                                  
CONECT   21    3   20   29                                                  
CONECT   22   20   23                                                       
CONECT   23    3   18   22                                                  
CONECT   24    7   25   26                                                  
CONECT   25    8   24   27                                                  
CONECT   26    9   24   28                                                  
CONECT   27    4   25   30                                                  
CONECT   28    4    6   26                                                  
CONECT   29   10   21                                                       
CONECT   30   27                                                            
CONECT   31   18   33                                                       
CONECT   32   13   18   19                                                  
CONECT   33   31   34   35                                                  
CONECT   34   17   19   33                                                  
CONECT   35   33                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

Synonyms

Value	Source
Thymidine 5'-(trihydrogen diphosphate), p'-(6-deoxy-beta-L-mannopyranosyl) ester	ChEBI
Thymidine diphosphate rhamnose	ChEBI
Thymidine diphosphate-L-rhamnose	ChEBI
Thymidine 5'-(trihydrogen diphosphate), p'-(6-deoxy-b-L-mannopyranosyl) ester	Generator
Thymidine 5'-(trihydrogen diphosphate), p'-(6-deoxy-β-L-mannopyranosyl) ester	Generator
Thymidine 5'-(trihydrogen diphosphoric acid), p'-(6-deoxy-b-L-mannopyranosyl) ester	Generator
Thymidine 5'-(trihydrogen diphosphoric acid), p'-(6-deoxy-beta-L-mannopyranosyl) ester	Generator
Thymidine 5'-(trihydrogen diphosphoric acid), p'-(6-deoxy-β-L-mannopyranosyl) ester	Generator
Thymidine diphosphoric acid rhamnose	Generator
Thymidine diphosphoric acid-L-rhamnose	Generator
Deoxythymidine diphosphoric acid-L-rhamnose	Generator
dTDP-6-Deoxy-L-mannose	HMDB
dTDP-L-Rhamnose	HMDB

Molecular Formula

C₁₆H₂₆N₂O₁₅P₂

Average Mass

548.3296

Monoisotopic Mass

548.080841196

IUPAC Name

{[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy}({[(3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphinic acid

Traditional Name

dtdp-L-rhamnose

CAS Registry Number

2147-59-3

SMILES

C[C@@H]1OC(OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N2C=C(C)C(=O)NC2=O)[C@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,11-,12+,13+,15?/m0/s1

InChI Key

ZOSQFDVXNQFKBY-CZRCVJRHSA-N

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 2'-deoxyribonucleoside diphosphate
Pentose phosphate
Monosaccharide phosphate
Organic pyrophosphate
Monoalkyl phosphate
Pyrimidone
Hydropyrimidine
Phosphoric acid ester
Monosaccharide
Organic phosphoric acid derivative
Oxane
Alkyl phosphate
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Urea
Lactam
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organic nitrogen compound
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

dTDP-rhamnose (CHEBI:35452 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	11.6 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-2.7	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	251.08 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	107.76 m³·mol⁻¹	ChemAxon
Polarizability	46.26 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 GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0036-6922340000-5b7bbefa46231e0401e7	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00bc-8441509000-f72396e274d70b76dce1	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-a235a91a2d2afe7e5b0e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-3921000000-f27277a5a22d8b1a6e62	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-4900000000-385a0d128de7afa0ef56	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f6t-3303290000-8fb8bdb50a4d4dd37d52	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ufu-5915010000-0710c988c191bfa8f10b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a6u-4901000000-ac82c124189fc9d5bf1d	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0002206	dTDP-4-Dehydro-6-deoxy-L-mannose	Deoxythymidine diphosphate-L-rhamnose	Not Available	DTDP-4-Dehydrorhamnose Reductase	VMH	9893952
MMDBr0007971	dTDP-4-Dehydro-6-deoxy-L-mannose	Deoxythymidine diphosphate-L-rhamnose	Not Available	DTDP-4-dehydrorhamnose reductase, reversible	VMH	30371894
MMDBr0019262	Hydrogen Ion	NADP	dTDP-4-dehydrorhamnose reductase	Reduction	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	Proteobacteria	167	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	253	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	118	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	126	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	17	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

HMDB0006354

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023902

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439975

PDB ID

Not Available

ChEBI ID

35452

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Giraud MF, Leonard GA, Field RA, Berlind C, Naismith JH: RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase. Nat Struct Biol. 2000 May;7(5):398-402. doi: 10.1038/75178. [PubMed:10802738 ]
Dong C, Beis K, Giraud MF, Blankenfeldt W, Allard S, Major LL, Kerr ID, Whitfield C, Naismith JH: A structural perspective on the enzymes that convert dTDP-d-glucose into dTDP-l-rhamnose. Biochem Soc Trans. 2003 Jun;31(Pt 3):532-6. doi: 10.1042/bst0310532. [PubMed:12773151 ]

Showing metabocard for Deoxythymidine diphosphate-L-rhamnose (MMDBc0029827)

MOL for #<Metabolite:0x00007f5ab0113228>

3D MOL for #<Metabolite:0x00007f5ab0113228>

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3D-SDF for #<Metabolite:0x00007f5ab0113228>

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3D PDB for #<Metabolite:0x00007f5ab0113228>

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Structure for #<Metabolite:0x00007f5ab0113228>

3D Structure for #<Metabolite:0x00007f5ab0113228>