MiMeDB: Showing metabocard for (S)-mandelate (MMDBc0055072)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:41:19 UTC

Update Date

2025-10-07 16:08:54 UTC

Metabolite ID

MMDBc0055072

Metabolite Identification

Common Name

(S)-mandelate

Description

(S)-mandelate is a chiral metabolite belonging to the class of organic acids. Its chemical structure features a mandelic acid backbone, characterized by a phenyl group attached to a carbon bearing both a hydroxyl and a carboxyl functional group. In biochemical pathways, (S)-mandelate is involved in the enzymatic interconversion with its (R)-enantiomer, a process catalyzed by mandelate racemase (MR), which operates in a magnesium-dependent manner and stabilizes the transition state by approximately 26 kcal/mol (PMID:37285384 ). MR recognizes the chiral nature of its substrates through specific interactions between the phenyl ring of (R)- or (S)-mandelate and distinct hydrophobic pockets within the enzyme's active site (PMID:37245900 ). Additionally, (S)-mandelate plays a role in multi-enzyme cascades aimed at synthesizing benzaldehyde from l-phenylalanine, involving various enzymes such as l-amino acid deaminase, 4-hydroxymandelate synthase, and (S)-mandelate dehydrogenase, all expressed in Escherichia coli (PMID:36214415 ). This cascade incorporates enzymes from multiple organisms, highlighting the metabolic versatility and importance of (S)-mandelate in synthetic biology applications (PMID:35415641 ).

Structure

MOL SDF PDB SMILES InChI

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

Synonyms

Value	Source
(S)-Mandelic acid	Generator

Molecular Formula

C₈H₇O₃

Average Mass

151.142

Monoisotopic Mass

151.040067665

IUPAC Name

(2S)-2-hydroxy-2-phenylacetate

Traditional Name

(S)-hydroxy(phenyl)acetate

CAS Registry Number

Not 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-/m0/s1

InChI Key

IWYDHOAUDWTVEP-ZETCQYMHSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Not Available

Direct Parent

Benzene and substituted derivatives

Alternative Parents

Substituents

Monocyclic benzene moiety
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Aromatic alcohol
Organooxygen compound
Carbonyl group
Alcohol
Organic anion
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

mandelate (CHEBI:17756 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	0.9	ChemAxon
pKa (Strongest Acidic)	3.75	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	60.36 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	49.54 m³·mol⁻¹	ChemAxon
Polarizability	14.23 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

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
MMDBr0024513	(S)-mandelate	phenylglyoxylate	(S)-mandelate dehydrogenase	Dehydrogenation	RHEA	34755880

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

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

C00037426

Chemspider ID

4573909

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5460348

PDB ID

Not Available

ChEBI ID

17756

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (S)-mandelate (MMDBc0055072)

MOL for #<Metabolite:0x0000561535da2d98>

3D MOL for #<Metabolite:0x0000561535da2d98>

3D SDF for #<Metabolite:0x0000561535da2d98>

3D-SDF for #<Metabolite:0x0000561535da2d98>

PDB for #<Metabolite:0x0000561535da2d98>

3D PDB for #<Metabolite:0x0000561535da2d98>

SMILES for #<Metabolite:0x0000561535da2d98>

INCHI for #<Metabolite:0x0000561535da2d98>

Structure for #<Metabolite:0x0000561535da2d98>

3D Structure for #<Metabolite:0x0000561535da2d98>