MiMeDB: Showing metabocard for 4,5-dihydroxyphthalate (MMDBc0055544)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:58:31 UTC

Update Date

2025-10-07 16:09:11 UTC

Metabolite ID

MMDBc0055544

Metabolite Identification

Common Name

4,5-dihydroxyphthalate

Description

4,5-dihydroxyphthalate is a dihydroxy derivative of phthalate, belonging to the class of aromatic compounds. Its chemical structure features a phthalate backbone with hydroxyl groups at the 4 and 5 positions, making it a crucial intermediate in the biodegradation of phthalates. This compound is primarily involved in microbial metabolic pathways where it serves as a substrate for enzymes such as phthalate dioxygenase (PDO) and 4,5-dihydroxyphthalate decarboxylase, facilitating the conversion of phthalate to protocatechuate (PMID:22805854 ). The aerobic breakdown of phthalate is initiated by PDO, which generates cis-4,5-dihydro-4,5-dihydroxyphthalate, leading to further degradation (PMID:16922496 ; PMID:16866348 ). In soil environments, the 2,3-epoxy-2,3-dihydrobenzoyl-CoA and 4,5-dihydroxyphthalate pathways are particularly active, highlighting its role in bioremediation processes (PMID:40997471 ). Additionally, the presence of genes encoding for enzymes involved in its metabolism underscores its significance in microbial catabolic pathways (PMID:9851995 ; PMID:12844210 ). Overall, 4,5-dihydroxyphthalate is a key metabolite in the microbial degradation of phthalates, contributing to the ecological cycling of aromatic compounds.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221582D          

 14 14  0  0  0  0            999 V2000
    1.4289    0.8250    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
    0.7145    1.2375    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
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    2.1434   -0.4125    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  5  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    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  6  5  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  2  0  0  0  0
 12  7  1  0  0  0  0
 13  8  2  0  0  0  0
 14  8  1  0  0  0  0
M  CHG  2   9  -1  10  -1
M  END
> <DATABASE_ID>
MMDBc0055544

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)C1=CC([O-])=C([O-])C=C1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H6O6/c9-5-1-3(7(11)12)4(8(13)14)2-6(5)10/h1-2,9-10H,(H,11,12)(H,13,14)/p-2

> <INCHI_KEY>
YZBCICVNBHNLTK-UHFFFAOYSA-L

> <FORMULA>
C8H4O6

> <MOLECULAR_WEIGHT>
196.115

> <EXACT_MASS>
196.001885009

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
16.128369268731298

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5-dicarboxybenzene-1,2-bis(olate)

> <JCHEM_LOGP>
0.6812809886666665

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.554200111157202

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.998260759692661

> <JCHEM_PKA_STRONGEST_BASIC>
-6.44249504607856

> <JCHEM_POLAR_SURFACE_AREA>
120.72000000000001

> <JCHEM_REFRACTIVITY>
65.6328

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4,5-dicarboxybenzene-1,2-bis(olate)

> <JCHEM_VEBER_RULE>
0

$$$$

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       2.667   1.540   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       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   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      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    4    7                                                  
CONECT    4    2    3    8                                                  
CONECT    5    1    6    9                                                  
CONECT    6    2    5   10                                                  
CONECT    7    3   11   12                                                  
CONECT    8    4   13   14                                                  
CONECT    9    5                                                            
CONECT   10    6                                                            
CONECT   11    7                                                            
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14    8                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

Synonyms

Value	Source
4,5-Dihydroxybenzene-1,2-dicarboxylate	ChEBI
4,5-Dihydroxyphthalate	ChEBI
4,5-Dihydroxyphthalate dianion	ChEBI
4,5-Dihydroxybenzene-1,2-dicarboxylic acid	Generator
4,5-Dihydroxyphthalic acid	Generator
4,5-Dihydroxyphthalic acid dianion	Generator
4,5-Dihydroxyphthalic acid(2-)	Generator

Molecular Formula

C₈H₄O₆

Average Mass

196.115

Monoisotopic Mass

196.001885009

IUPAC Name

4,5-dicarboxybenzene-1,2-bis(olate)

Traditional Name

4,5-dicarboxybenzene-1,2-bis(olate)

CAS Registry Number

Not Available

SMILES

OC(=O)C1=CC([O-])=C([O-])C=C1C(O)=O

InChI Identifier

InChI=1S/C8H6O6/c9-5-1-3(7(11)12)4(8(13)14)2-6(5)10/h1-2,9-10H,(H,11,12)(H,13,14)/p-2

InChI Key

YZBCICVNBHNLTK-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzoic acids. These are organic Compounds containing a benzene ring which bears at least one carboxyl group.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Benzoic acids

Alternative Parents

Substituents

Benzoic acid
Benzoyl
Phenoxide
Dicarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organic anion
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

dicarboxylic acid dianion (CHEBI:58051 )
a small molecule (CPD-636 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	0.68	ChemAxon
pKa (Strongest Acidic)	3	ChemAxon
pKa (Strongest Basic)	-6.4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	120.72 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	65.63 m³·mol⁻¹	ChemAxon
Polarizability	16.13 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

Name	SMPDB/PathBank	Species
Phthalate degradation		Pseudomonas aeruginosa Escherichia coli SMS-3-5 Escherichia coli 55989 Escherichia coli SE11 Mycobacterium marinum M Pseudomonas aeruginosa PA7 Myxococcus xanthus DK 1622 Klebsiella pneumoniae Pseudomonas fluorescens Pf-5 Streptomyces griseus subsp. griseus NBRC 13350 Saccharopolyspora erythraea NRRL 2338 Methylobacterium nodulans Comamonas testosteroni Burkholderia cepacia Pseudomonas fluorescens Pseudomonas mendocina Pseudomonas putida Pseudomonas syringae Xanthomonas campestris Bradyrhizobium japonicum Mesorhizobium loti Sinorhizobium meliloti Methylococcus capsulatus Chromobacterium violaceum Shigella sonnei Rhodopseudomonas palustris Priestia megaterium Corynebacterium glutamicum Mycobacterium avium Thermotoga neapolitana Roseobacter denitrificans Brachyspira pilosicoli Burkholderia vietnamiensis Enterobacter cancerogenus Burkholderia multivorans Burkholderia cenocepacia Citrobacter youngae Burkholderia ambifaria Methylocella silvestris Agrobacterium tumefaciens Klebsiella variicola Bacillus megaterium QM B1551 Bacillus cereus B4264 Priestia megaterium DSM 319 Bradyrhizobium japonicum USDA 110 Delftia acidovorans SPH-1 Enterobacter cloacae subsp. cloacae ATCC 13047 Escherichia coli E24377A Escherichia coli UMN026 Escherichia coli ED1a Escherichia coli IAI39 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 Methylobacterium radiotolerans JCM 2831 Methylobacterium populi BJ001 Mycobacterium avium subsp. paratuberculosis K-10 Mycobacterium avium 104 Escherichia coli 042 Pseudomonas putida KT2440 Pseudomonas fluorescens SBW25 Pseudomonas putida GB-1 Rhizobium leguminosarum bv. viciae 3841 Rhizobium leguminosarum bv. trifolii WSM2304 Rhodococcus erythropolis PR4 Shigella sonnei Ss046 Sulfolobus solfataricus P2 Bradyrhizobium elkanii Methylobacterium mesophilicum Methylobacterium mesophilicum SR1.6/6 Rhizobium etli Xanthobacter autotrophicus Alcaligenes faecalis Burkholderia cepacia GG4 Neisseria macacae Neisseria macacae ATCC 33926 Cedecea davisae Cedecea davisae DSM 4568 Citrobacter freundii Citrobacter youngae ATCC 29220 Klebsiella aerogenes Providencia stuartii ATCC 25827 Serratia marcescens subsp. marcescens Db11 Yersinia pseudotuberculosis Acinetobacter pittii Acinetobacter junii SH205 Vibrio fluvialis Vibrio fluvialis PG41 Brachyspira pilosicoli B2904 Rhodococcus erythropolis Brevibacterium casei Brevibacterium casei S18 Aneurinibacillus aneurinilyticus Aneurinibacillus aneurinilyticus ATCC 12856 [Eubacterium] cellulosolvens 6 Streptomyces coelicolor A3(2) Bordetella pertussis Tohama I Bordetella parapertussis 12822 Xanthomonas campestris pv. campestris str. ATCC 33913 Xanthomonas campestris pv. campestris str. B100 Xanthomonas campestris pv. campestris str. 8004 Corynebacterium glutamicum ATCC 13032 Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 Amycolatopsis mediterranei U32 Arthrobacter sp. FB24 Arthrobacter aurescens TC1 Catenulispora acidiphila DSM 44928 Clostridium thermocellum ATCC 27405 Conexibacter woesei DSM 14684 Corynebacterium glutamicum R Frankia alni ACN14a Frankia sp. EuI1c Gordonia bronchialis DSM 43247 Mycobacterium ulcerans Agy99 Mycobacterium vanbaalenii PYR-1 Mycobacterium abscessus ATCC 19977 Mycobacterium sp. Spyr1 Mycobacterium sp. JDM601 Nakamurella multipartita DSM 44233 Nocardia farcinica IFM 10152 Nocardioides sp. JS614 Bacillus tusciae DSM 2912 Pseudonocardia dioxanivorans CB1190 Rhodococcus opacus B4 Rhodococcus jostii RHA1 Rhodococcus equi 103S Rubrobacter xylanophilus DSM 9941 Saccharomonospora viridis DSM 43017 Salinispora tropica CNB-440 Stackebrandtia nassauensis DSM 44728 Streptomyces scabiei 87.22 Streptomyces violaceusniger Tu 4113 Streptosporangium roseum DSM 43021 Tsukamurella paurometabola DSM 20162 Fusarium acutatum Fusarium fujikuroi IMI 58289 Fusarium mangiferae Fusarium nygamai Fusarium proliferatum ET1 Fusarium subglutinans Fusarium verticillioides 7600 Fusarium oxysporum Fo5176 Fusarium oxysporum f. sp. lycopersici 4287 Paraburkholderia graminis C4D1M Mycolicibacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 Rhodococcus hoagii ATCC 33707 Cutibacterium granulosum DSM 20700 Klebsiella aerogenes KCTC 2190 Acaryochloris marina MBIC11017 Acidobacterium capsulatum ATCC 51196 Agrobacterium vitis S4 Agrobacterium radiobacter K84 Rhodoferax ferrireducens T118 Alkalilimnicola ehrlichii MLHE-1 Anabaena variabilis ATCC 29413 Azotobacter vinelandii DJ Bordetella petrii DSM 12804 Bordetella avium 197N Brachyspira hyodysenteriae WA1 Brachyspira murdochii DSM 12563 Brachyspira pilosicoli 95/1000 Bradyrhizobium sp. ORS278 Bradyrhizobium sp. BTAi1 Burkholderia mallei ATCC 23344 Burkholderia pseudomallei 1710b Burkholderia sp. 383 Burkholderia xenovorans LB400 Burkholderia ambifaria AMMD Burkholderia mallei NCTC 10229 Burkholderia pseudomallei 1106a Burkholderia vietnamiensis G4 Burkholderia cenocepacia MC0-3 Burkholderia ambifaria MC40-6 Burkholderia phymatum STM815 Burkholderia phytofirmans PsJN Burkholderia cenocepacia J2315 Caulobacter crescentus CB15 Caulobacter crescentus NA1000 Caulobacter segnis ATCC 21756 Chromohalobacter salexigens DSM 3043 Citrobacter rodentium ICC168 Cupriavidus metallidurans CH34 Cupriavidus necator N-1 Cyanothece sp. ATCC 51142 Cyanothece sp. PCC 8801 Cyanothece sp. PCC 7424 Dickeya zeae Ech1591 Dinoroseobacter shibae DFL 12 Erwinia tasmaniensis Et1/99 Erwinia amylovora CFBP1430 Erwinia billingiae Eb661 Fervidobacterium nodosum Rt17-B1 Gloeobacter violaceus PCC 7421 Gluconacetobacter diazotrophicus PAl 5 Gluconobacter oxydans 621H Granulibacter bethesdensis CGDNIH1 Hahella chejuensis KCTC 2396 Haliangium ochraceum DSM 14365 Hyphomonas neptunium ATCC 15444 Jannaschia sp. CCS1 Janthinobacterium sp. Marseille Klebsiella pneumoniae 342 Legionella longbeachae NSW150 Leptothrix cholodnii SP-6 Magnetospirillum magneticum AMB-1 Maricaulis maris MCS10 Marinomonas mediterranea MMB-1 Marinomonas posidonica IVIA-Po-181 Methylobacterium chloromethanicum CM4 Methylobacterium nodulans ORS 2060 Methylobacterium extorquens AM1 Methylobacterium extorquens DM4 Methylovorus glucosetrophus SIP3-4 Microbacterium testaceum StLB037 Microcystis aeruginosa NIES-843 Nostoc sp. PCC 7120 Nostoc punctiforme PCC 73102 Novosphingobium aromaticivorans DSM 12444 Bordetella bronchiseptica RB50 Xanthomonas axonopodis pv. citri str. 306 Chromobacterium violaceum ATCC 12472 Bdellovibrio bacteriovorus HD100 Synechococcus sp. JA-2-3B'a(2-13) Sorangium cellulosum 'So ce 56' Phenylobacterium zucineum HLK1 Photorhabdus luminescens subsp. laumondii TTO1 Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949 Polaromonas sp. JS666 Polaromonas naphthalenivorans CJ2 Prochlorococcus marinus subsp. marinus str. CCMP1375 Prochlorococcus marinus str. MIT 9313 Prochlorococcus marinus subsp. pastoris str. CCMP1986 Prochlorococcus marinus str. NATL2A Prochlorococcus marinus str. MIT 9312 Prochlorococcus marinus str. AS9601 Prochlorococcus marinus str. MIT 9515 Prochlorococcus marinus str. NATL1A Prochlorococcus marinus str. MIT 9303 Prochlorococcus marinus str. MIT 9301 Prochlorococcus marinus str. MIT 9215 Prochlorococcus marinus str. MIT 9211 Pseudomonas syringae pv. tomato str. DC3000 Pseudomonas syringae pv. phaseolicola 1448A Pseudomonas syringae pv. syringae B728a Pseudomonas fulva 12-X Ralstonia solanacearum GMI1000 Rhizobium etli CFN 42 Rhizobium etli CIAT 652 Rhizobium leguminosarum bv. trifolii WSM1325 Rhodopirellula baltica SH 1 Rhodopseudomonas palustris CGA009 Rhodopseudomonas palustris HaA2 Rhodopseudomonas palustris BisB5 Roseobacter denitrificans OCh 114 Roseobacter litoralis Och 149 Ruegeria pomeroyi DSS-3 Sinorhizobium meliloti 1021 Sinorhizobium medicae WSM419 Sphingobium japonicum UT26S Sphingomonas wittichii RW1 Synechococcus sp. WH 8102 Synechococcus sp. CC9902 Synechococcus sp. CC9311 Synechococcus sp. WH 7803 Synechococcus sp. PCC 7002 Teredinibacter turnerae T7901 Thermosipho africanus TCF52B Thermotoga petrophila RKU-1 Thermotoga sp. RQ2 Thermotoga neapolitana DSM 4359 Thiobacillus denitrificans ATCC 25259 Variovorax paradoxus EPS Verminephrobacter eiseniae EF01-2 Xanthobacter autotrophicus Py2 Xanthomonas oryzae pv. oryzae KACC10331 Xanthomonas campestris pv. vesicatoria str. 85-10 Xanthomonas oryzae pv. oryzae PXO99A Klebsiella michiganensis KCTC 1686 Chania multitudinisentens RB-25

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

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	2	Human ; Human supragingival plaque

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

Not Available

Chemspider ID

7822056

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9543083

PDB ID

Not Available

ChEBI ID

58051

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 4,5-dihydroxyphthalate (MMDBc0055544)

MOL for #<Metabolite:0x00007fadd8022230>

3D MOL for #<Metabolite:0x00007fadd8022230>

3D SDF for #<Metabolite:0x00007fadd8022230>

3D-SDF for #<Metabolite:0x00007fadd8022230>

PDB for #<Metabolite:0x00007fadd8022230>

3D PDB for #<Metabolite:0x00007fadd8022230>

SMILES for #<Metabolite:0x00007fadd8022230>

INCHI for #<Metabolite:0x00007fadd8022230>

Structure for #<Metabolite:0x00007fadd8022230>

3D Structure for #<Metabolite:0x00007fadd8022230>