Np mrd loader

Showing NP-Card for D-Xylonate (NP0002637)

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Record Information
Version2.0
Created at2020-11-23 18:25:47 UTC
Updated at2021-08-12 19:51:43 UTC
NP-MRD IDNP0002637
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Xylonate
Provided ByBMRBBMRB logo
DescriptionD-lyxonic acid is also known as lyxonate. D-lyxonic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. D-Xylonate is found in Bergera koenegii, Carica papaya , Citrus sinensis and Murraya paniculata . D-Xylonate was first documented in 2002 (PMID: 11841815). Based on a literature review very few articles have been published on D-lyxonic acid (PMID: 22541300).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002637 (D-Xylonate)


     RDKit          2D

 21 20  0  0  0  0  0  0  0  0999 V2000
    2.2989    1.7578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4648    0.2670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9019   -0.1627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740   -0.7627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2833   -1.7924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3443    0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6854    1.4188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7464   -0.7016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8372   -1.7313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7761    0.3891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8058    1.4799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9926    0.8670    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4037   -1.8534    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6297   -3.2518    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3014    1.4831    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2556    2.8559    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3557   -1.3965    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3159   -1.4799    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669    1.6521    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9842   -0.4999    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2653    1.1335    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  1
  7 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  6
 10 20  1  0
 11 21  1  0
M  END
Download

3D MOL for NP0002637 (D-Xylonate)

NP0002637
     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.4174   -0.9810    1.4875 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0784   -0.4233    0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6243   -0.8997   -0.7606 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1087    0.7303    0.4130 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6871    1.0469    1.6770 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0043    0.4594   -0.5653 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8119    1.5817   -0.6925 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8717   -0.6974   -0.1893 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2082   -1.8829   -0.0261 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7299   -0.3949    1.0205 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3949    0.8232    0.8222 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1447   -0.3046   -1.3958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6899    1.5913    0.0211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4081    0.8191    2.3352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4677    0.2676   -1.5537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3562    2.3824   -0.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5910   -0.8372   -1.0423 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6554   -2.3880    0.7013 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5204   -1.1712    1.0767 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1801   -0.4100    1.9653 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3109    0.6883    0.4768 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  6
  7 16  1  0
  8 17  1  6
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
Download

3D SDF for NP0002637 (D-Xylonate)


     RDKit          2D

 21 20  0  0  0  0  0  0  0  0999 V2000
    2.2989    1.7578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4648    0.2670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9019   -0.1627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740   -0.7627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2833   -1.7924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3443    0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6854    1.4188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7464   -0.7016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8372   -1.7313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7761    0.3891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8058    1.4799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9926    0.8670    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4037   -1.8534    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6297   -3.2518    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3014    1.4831    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2556    2.8559    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3557   -1.3965    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3159   -1.4799    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669    1.6521    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9842   -0.4999    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2653    1.1335    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  1
  7 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  6
 10 20  1  0
 11 21  1  0
M  END
> <DATABASE_ID>
NP0002637

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@](O)(CO)[C@]([H])(O)[C@]([H])(O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4+/m1/s1

> <INCHI_KEY>
QXKAIJAYHKCRRA-UZBSEBFBSA-N

> <FORMULA>
C5H10O6

> <MOLECULAR_WEIGHT>
166.1293

> <EXACT_MASS>
166.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
14.360723963996495

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid

> <ALOGPS_LOGP>
-2.48

> <JCHEM_LOGP>
-2.7794093686666668

> <ALOGPS_LOGS>
0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.768659694136133

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.393139811550542

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974562302797298

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
32.308499999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002637 (D-Xylonate)

NP0002637
     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.4174   -0.9810    1.4875 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0784   -0.4233    0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6243   -0.8997   -0.7606 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1087    0.7303    0.4130 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6871    1.0469    1.6770 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0043    0.4594   -0.5653 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8119    1.5817   -0.6925 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8717   -0.6974   -0.1893 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2082   -1.8829   -0.0261 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7299   -0.3949    1.0205 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3949    0.8232    0.8222 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1447   -0.3046   -1.3958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6899    1.5913    0.0211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4081    0.8191    2.3352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4677    0.2676   -1.5537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3562    2.3824   -0.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5910   -0.8372   -1.0423 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6554   -2.3880    0.7013 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5204   -1.1712    1.0767 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1801   -0.4100    1.9653 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3109    0.6883    0.4768 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  6
  7 16  1  0
  8 17  1  6
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
Download

PDB for NP0002637 (D-Xylonate)

HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    6                                                       
CONECT    2    1    3    7   12                                             
CONECT    3    2    4    8   13                                             
CONECT    4    3    5    9   14                                             
CONECT    5    4   10   11                                                  
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    2                                                            
CONECT   13    3                                                            
CONECT   14    4                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for NP0002637 (D-Xylonate)

COMPND    NP0002637
HETATM    1  O1  UNL     1      -2.417  -0.981   1.488  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.078  -0.423   0.423  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.624  -0.900  -0.761  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.109   0.730   0.413  1.00  0.00           C  
HETATM    5  O3  UNL     1      -0.687   1.047   1.677  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.004   0.459  -0.565  1.00  0.00           C  
HETATM    7  O4  UNL     1       0.812   1.582  -0.692  1.00  0.00           O  
HETATM    8  C4  UNL     1       0.872  -0.697  -0.189  1.00  0.00           C  
HETATM    9  O5  UNL     1       0.208  -1.883  -0.026  1.00  0.00           O  
HETATM   10  C5  UNL     1       1.730  -0.395   1.020  1.00  0.00           C  
HETATM   11  O6  UNL     1       2.395   0.823   0.822  1.00  0.00           O  
HETATM   12  H1  UNL     1      -3.145  -0.305  -1.396  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.690   1.591   0.021  1.00  0.00           H  
HETATM   14  H3  UNL     1      -1.408   0.819   2.335  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.468   0.268  -1.554  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.356   2.382  -0.365  1.00  0.00           H  
HETATM   17  H6  UNL     1       1.591  -0.837  -1.042  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.655  -2.388   0.701  1.00  0.00           H  
HETATM   19  H8  UNL     1       2.520  -1.171   1.077  1.00  0.00           H  
HETATM   20  H9  UNL     1       1.180  -0.410   1.965  1.00  0.00           H  
HETATM   21  H10 UNL     1       3.311   0.688   0.477  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5    6   13
CONECT    5   14
CONECT    6    7    8   15
CONECT    7   16
CONECT    8    9   10   17
CONECT    9   18
CONECT   10   11   19   20
CONECT   11   21
END
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SMILES for NP0002637 (D-Xylonate)

[H][C@@](O)(CO)[C@]([H])(O)[C@]([H])(O)C(O)=O
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INCHI for NP0002637 (D-Xylonate)

InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4+/m1/s1
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View in JSmol
Synonyms
ValueSource
(2S,3S,4R)-2,3,4,5-Tetrahydroxypentanoic acidChEBI
Lyxonic acidChEBI
(2S,3S,4R)-2,3,4,5-TetrahydroxypentanoateGenerator
LyxonateGenerator
D-LyxonateGenerator
Chemical FormulaC5H10O6
Average Mass166.1293 Da
Monoisotopic Mass166.04774 Da
IUPAC Name(2S,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid
Traditional Name(2S,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(CO)[C@]([H])(O)[C@]([H])(O)C(O)=O
InChI Identifier
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4+/m1/s1
InChI KeyQXKAIJAYHKCRRA-UZBSEBFBSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Bergera koenegii-
Carica papaya L.Plant
Citrus X sinensis (L.) Osbeck (pro. sp.)Plant
Murraya paniculataPlant
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as sugar acids and derivatives. These are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar acids and derivatives
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Beta-hydroxy acid
  • Sugar acid
  • Short-chain hydroxy acid
  • Alpha-hydroxy acid
  • Fatty acid
  • Hydroxy acid
  • Monosaccharide
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Polyol
  • Primary alcohol
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.5ALOGPS
logP-2.8ChemAxon
logS0.19ALOGPS
pKa (Strongest Acidic)3.39ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area118.22 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.31 m³·mol⁻¹ChemAxon
Polarizability14.36 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID134810
KEGG Compound IDNot Available
BioCyc IDCPD-8902
BiGG IDNot Available
Wikipedia LinkXylonic acid
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID134538
Good Scents IDNot Available
References
General References
  1. Singh AK, Singh V, Singh AK, Gupta N, Singh B: Kinetics and mechanism of Ru(III) and Hg(II) co-catalyzed oxidation of D-galactose and D-ribose by N-bromoacetamide in perchloric acid. Carbohydr Res. 2002 Feb 18;337(4):345-51. doi: 10.1016/s0008-6215(01)00319-6. [PubMed:11841815 ]
  2. Kumar Singh A, Singh M, Srivastava J, Rahmani S: Kinetics of the oxidation of lactose by copper(II) complexed with bipyridyl in alkaline medium using chloro-complex of rhodium(III) in its nano-concentration range as homogeneous catalyst: a spectrophotometric study. Carbohydr Res. 2012 Jun 1;354:94-101. doi: 10.1016/j.carres.2012.03.035. Epub 2012 Apr 10. [PubMed:22541300 ]