MiMeDB: Showing metabocard for 2,3-Dihydroxybenzoylserine (MMDBc0031555)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:39:00 UTC

Update Date

2022-08-31 18:21:44 UTC

Metabolite ID

MMDBc0031555

Metabolite Identification

Common Name

2,3-Dihydroxybenzoylserine

Description

2,3-dihydroxybenzoylserine is a member of the chemical class known as Catechols. These are compounds containing a 1,2-benzenediol moeity. 2,3-dihydroxybenzoylserine is invovled in Enterobactin degradation. It is a product of the enzyme 2,3-dihydroxybenzoate-serine ligase (EC 6.3.2.14) is an enzyme that catalyzes the chemical reaction ATP + 2,3-dihydroxybenzoate + L-serine ‚Üµightleftharpoons products of ATP breakdown + N-(2,3-dihydroxybenzoyl)-L-serine. (PMID 4966114 ).

Structure

MOL SDF PDB SMILES InChI

DBS
  Mrv0541 02231216242D          

 18 18  0  0  0  0            999 V2000
   -2.5868    0.4279    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8723    0.8404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8723    1.6654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1578    0.4279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1578   -0.3971    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4434    0.8404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4434    1.6654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1578    2.0779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2711    0.4279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9856    0.8404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2711   -0.3971    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9856   -0.8096    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9856   -1.6346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7000   -2.0471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7000   -0.3971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7000    0.4279    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4145   -0.8096    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4799   -1.1016    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  7  8  2  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 12 11  1  6  0  0  0
 12 13  1  0  0  0  0
 12 15  1  0  0  0  0
 12 18  1  1  0  0  0
 13 14  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031555

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H11NO6/c12-4-6(10(16)17)11-9(15)5-2-1-3-7(13)8(5)14/h1-3,6,12-14H,4H2,(H,11,15)(H,16,17)/t6-/m0/s1

> <INCHI_KEY>
VDTYHTVHFIIEIL-LURJTMIESA-N

> <FORMULA>
C10H11NO6

> <MOLECULAR_WEIGHT>
241.1974

> <EXACT_MASS>
241.058637089

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
22.059942803245626

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-2-[(2,3-dihydroxyphenyl)formamido]-3-hydroxypropanoic acid

> <ALOGPS_LOGP>
0.33

> <JCHEM_LOGP>
0.09026911666666641

> <ALOGPS_LOGS>
-1.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.307034640441366

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9795039022968606

> <JCHEM_PKA_STRONGEST_BASIC>
-2.0257261660426527

> <JCHEM_POLAR_SURFACE_AREA>
127.09000000000002

> <JCHEM_REFRACTIVITY>
56.11710000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.76e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,-dihydroxybenzoylserine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: DBS                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      -4.829   0.799   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -3.495   1.569   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.495   3.109   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.161   0.799   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.161  -0.741   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.828   1.569   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.828   3.109   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.161   3.879   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.506   0.799   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.840   1.569   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       0.506  -0.741   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       1.840  -1.511   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.840  -3.051   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.173  -3.821   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.173  -0.741   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.173   0.799   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.507  -1.511   0.000  0.00  0.00           O+0
HETATM   18  H   UNK     0       0.896  -2.056   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2    8                                                       
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    3    7                                                       
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   15   18                                             
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   12                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Value	Source
2,3-Dihydroxy-N-benzoyl-L-serine	ChEBI
N-(2,3-Dihydroxybenzoyl)-L-serine	MeSH

Molecular Formula

C₁₀H₁₁NO₆

Average Mass

241.1974

Monoisotopic Mass

241.058637089

IUPAC Name

(2S)-2-[(2,3-dihydroxyphenyl)formamido]-3-hydroxypropanoic acid

Traditional Name

2,3,-dihydroxybenzoylserine

CAS Registry Number

127658-43-9

SMILES

[H][C@@](CO)(NC(=O)C1=C(O)C(O)=CC=C1)C(O)=O

InChI Identifier

InChI=1S/C10H11NO6/c12-4-6(10(16)17)11-9(15)5-2-1-3-7(13)8(5)14/h1-3,6,12-14H,4H2,(H,11,15)(H,16,17)/t6-/m0/s1

InChI Key

VDTYHTVHFIIEIL-LURJTMIESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hippuric acids. Hippuric acids are compounds containing hippuric acid, which consists of a of a benzoyl group linked to the N-terminal of a glycine.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Hippuric acids

Alternative Parents

Substituents

N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
Hippuric acid
Serine or derivatives
Alpha-amino acid or derivatives
Salicylamide
Salicylic acid or derivatives
Benzoyl
Catechol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Beta-hydroxy acid
Hydroxy acid
Vinylogous acid
Carboxamide group
Secondary carboxylic acid amide
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Primary alcohol
Hydrocarbon derivative
Organic nitrogen compound
Alcohol
Organic oxide
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

L-serine derivative (CHEBI:17455 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	5.76 g/L	ALOGPS
logP	0.33	ALOGPS
logP	0.09	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	2.98	ChemAxon
pKa (Strongest Basic)	-2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	127.09 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	56.12 m³·mol⁻¹	ChemAxon
Polarizability	22.06 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00dl-0390000000-1c8bd41059bced330983	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-2920000000-bc9d7862d6e634ce299e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00n0-9500000000-dca0ea7939deb8a40bf0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-0490000000-5529ba05e060a66aa481	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0nvm-2940000000-7ab5cdf84a6c5cab4263	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0pbl-9500000000-4a04c984745c207267b5	2015-09-15	View Spectrum

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

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014964	Fe(III)-enterobactin	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]	Iron(III) enterobactin esterase	Ester hydrolysis	RHEA	34755880
MMDBr0014965	Fe(III)-enterobactin	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]	Iron(III) enterobactin esterase	Ester hydrolysis	RHEA	34755880
MMDBr0016988	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]3	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]2	Iron(III) enterobactin esterase	Ester hydrolysis	RHEA	34755880
MMDBr0016989	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]3	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]2	Iron(III) enterobactin esterase	Ester hydrolysis	RHEA	34755880
MMDBr0016990	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]2	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]	Iron(III) enterobactin esterase	Ester hydrolysis	RHEA	34755880
MMDBr0016991	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]2	Fe(III)-[N-(2,3-dihydroxybenzoyl)-L-serine]	Iron(III) enterobactin esterase	Ester hydrolysis	RHEA	34755880
MMDBr0017063	Fe(III)-{N-(2,3-dihydroxybenzoyl)-L-seryl-[N-(C-5-[deoxy-beta-D-glucosyl]-2,3-dihydroxybenzoyl)-L-serine]2}	Fe(III)-[N-(C-5-[deoxy-beta-D-glucosyl]-2,3-dihydroxybenzoyl)-L-serine]2	Iron(III) salmochelin esterase	Ester hydrolysis	RHEA	34755880
MMDBr0017065	Fe(III)-{di[N-(2,3-dihydroxybenzoyl)-L-seryl]-N-(C-5-[deoxy-beta-D-glucosyl]-2,3-dihydroxybenzoyl)-L-serine}	Fe(III)-{N-(2,3-dihydroxybenzoyl)-L-seryl-N-(C-5-[deoxy-beta-D-glucosyl]-2,3-dihydroxybenzoyl)-L-serine}	Iron(III) salmochelin esterase	Ester hydrolysis	RHEA	34755880
MMDBr0019029	Water	Iron(3+)	Iron(III) enterobactin esterase	Hydrolysis of an ester group	PathBank	31602464
MMDBr0036105	2,3-Dihydroxybenzoylserine	L-Serine	Acylamidase	Hydrolysis	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	Proteobacteria	5	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

External Links

HMDB ID

Not Available

DrugBank ID

DB02710

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C04204

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

151483

PDB ID

Not Available

ChEBI ID

17455

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 ]
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 2,3-Dihydroxybenzoylserine (MMDBc0031555)

MOL for #<Metabolite:0x00007fa4eca96c10>

3D MOL for #<Metabolite:0x00007fa4eca96c10>

3D SDF for #<Metabolite:0x00007fa4eca96c10>

3D-SDF for #<Metabolite:0x00007fa4eca96c10>

PDB for #<Metabolite:0x00007fa4eca96c10>

3D PDB for #<Metabolite:0x00007fa4eca96c10>

SMILES for #<Metabolite:0x00007fa4eca96c10>

INCHI for #<Metabolite:0x00007fa4eca96c10>

Structure for #<Metabolite:0x00007fa4eca96c10>

3D Structure for #<Metabolite:0x00007fa4eca96c10>