Showing metabocard for (R)-mandelate (MMDBc0055046)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-17 19:40:43 UTC
Update Date2025-10-07 16:08:53 UTC
Metabolite IDMMDBc0055046
Metabolite Identification
Common Name(R)-mandelate
Description(R)-mandelate is a chiral compound belonging to the class of organic acids, specifically a mandelate derivative. Its chemical structure features a mandelic acid backbone, characterized by a phenyl group attached to a carbon atom adjacent to a carboxylic acid, with the (R) configuration denoting the specific spatial arrangement of its substituents. In biochemical pathways, (R)-mandelate is involved in various enzymatic reactions, including its role as a substrate and inhibitor in enzymatic assays, where it can influence the activity of certain enzymes, as indicated by studies that demonstrate its competitive inhibition properties (PMID:30745990 ). Additionally, (R)-mandelate is a product of engineered enzymatic reactions, showcasing its importance in synthetic biology for the stereodivergent synthesis of mandelate derivatives (PMID:36929048 ). The compound's kinetic parameters have been characterized, revealing a Km value of 1.2 mM, suggesting its affinity in enzymatic contexts (PMID:24472022 ). Furthermore, (R)-mandelate's interactions with proteins have been studied, revealing significant conformational changes in enzyme loops upon binding (PMID:24472022 ), highlighting its relevance in metabolic pathways and potential applications in pharmaceuticals.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fadd49c92b0>


  Mrv1652306172221402D          

 12 12  0  0  1  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  7  9  1  6  0  0  0
 10  8  2  0  0  0  0
 11  8  1  0  0  0  0
  7 12  1  6  0  0  0
M  CHG  1  11  -1
M  END
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3D MOL for #<Metabolite:0x00007fadd49c92b0>

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3D SDF for #<Metabolite:0x00007fadd49c92b0>

  Mrv1652306172221402D          

 12 12  0  0  1  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  7  9  1  6  0  0  0
 10  8  2  0  0  0  0
 11  8  1  0  0  0  0
  7 12  1  6  0  0  0
M  CHG  1  11  -1
M  END
> <DATABASE_ID>
MMDBc0055046

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(C([O-])=O)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C8H8O3/c9-7(8(10)11)6-4-2-1-3-5-6/h1-5,7,9H,(H,10,11)/p-1/t7-/m1/s1

> <INCHI_KEY>
IWYDHOAUDWTVEP-SSDOTTSWSA-M

> <FORMULA>
C8H7O3

> <MOLECULAR_WEIGHT>
151.142

> <EXACT_MASS>
151.040067665

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.225879732988497

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxy-2-phenylacetate

> <JCHEM_LOGP>
0.8958356446666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.568490699995834

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.751233575646761

> <JCHEM_PKA_STRONGEST_BASIC>
-4.110158859648652

> <JCHEM_POLAR_SURFACE_AREA>
60.36

> <JCHEM_REFRACTIVITY>
49.5409

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(R)-hydroxy(phenyl)acetate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007fadd49c92b0>
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PDB for #<Metabolite:0x00007fadd49c92b0>
HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O-1
HETATM   12  H   UNK     0       2.667   3.080   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5    7                                                  
CONECT    7    6    8    9   12                                             
CONECT    8    7   10   11                                                  
CONECT    9    7                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12    7                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for #<Metabolite:0x00007fadd49c92b0>
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SMILES for #<Metabolite:0x00007fadd49c92b0>
[H][C@](O)(C([O-])=O)C1=CC=CC=C1
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INCHI for #<Metabolite:0x00007fadd49c92b0>
InChI=1S/C8H8O3/c9-7(8(10)11)6-4-2-1-3-5-6/h1-5,7,9H,(H,10,11)/p-1/t7-/m1/s1
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Synonyms
ValueSource
(R)-2-Hydroxy-2-phenylacetateChEBI
(R)-2-Hydroxy-2-phenylacetic acidGenerator
(R)-Mandelic acidGenerator
Molecular FormulaC8H7O3
Average Mass151.142
Monoisotopic Mass151.040067665
IUPAC Name(2R)-2-hydroxy-2-phenylacetate
Traditional Name(R)-hydroxy(phenyl)acetate
CAS Registry NumberNot Available
SMILES
[H][C@](O)(C([O-])=O)C1=CC=CC=C1
InChI Identifier
InChI=1S/C8H8O3/c9-7(8(10)11)6-4-2-1-3-5-6/h1-5,7,9H,(H,10,11)/p-1/t7-/m1/s1
InChI KeyIWYDHOAUDWTVEP-SSDOTTSWSA-M