ECMDB: (2,3-Dihydroxybenzoyl)adenylic acid (ECMDB04053) (M2MDB000585)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)XML

Proteins (4)

Record Information

Version

2.0

Creation Date

2012-05-31 14:03:38 -0600

Update Date

2015-06-03 15:54:41 -0600

Secondary Accession Numbers

ECMDB04053

Identification

Name:

(2,3-Dihydroxybenzoyl)adenylic acid

Description

(2,3-dihydroxybenzoyl)adenylate is a member of the chemical class known as Purine Ribonucleoside Monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

(2,3-Dihydroxybenzoyl)adenylate
2,3-Dihydroxybenzoyl adenylate
2,3-Dihydroxybenzoyl adenylic acid

Chemical Formula:

C₁₇H₁₈N₅O₁₀P

Weight:

Average: 483.3261
Monoisotopic: 483.079128333

InChI Key:

ULPVJDOMCRTJSN-RVXWVPLUSA-N

InChI:

InChI=1S/C17H18N5O10P/c18-14-10-15(20-5-19-14)22(6-21-10)16-13(26)12(25)9(31-16)4-30-33(28,29)32-17(27)7-2-1-3-8(23)11(7)24/h1-3,5-6,9,12-13,16,23-26H,4H2,(H,28,29)(H2,18,19,20)/t9-,12-,13-,16-/m1/s1

CAS number:

Not Available

IUPAC Name:

{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(2,3-dihydroxybenzoyloxy)phosphinic acid

Traditional IUPAC Name:

[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(2,3-dihydroxybenzoyloxy)phosphinic acid

SMILES:

[H][C@]1(COP(O)(=O)OC(=O)C2=C(O)C(O)=CC=C2)O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as purine ribonucleoside monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside monophosphates

Alternative Parents

Substituents

Purine ribonucleoside monophosphate
Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Salicylic acid or derivatives
6-aminopurine
Pentose monosaccharide
Monosaccharide phosphate
Imidazopyrimidine
Purine
Benzoic acid or derivatives
Catechol
Benzoyl
Acyl phosphate
Phenol
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Monoalkyl phosphate
Aminopyrimidine
Monocyclic benzene moiety
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Imidolactam
Benzenoid
Alkyl phosphate
Phosphoric acid ester
Pyrimidine
Azole
Tetrahydrofuran
Heteroaromatic compound
Imidazole
Vinylogous acid
Secondary alcohol
Amino acid or derivatives
1,2-diol
Carboxylic acid salt
Azacycle
Oxacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Carboxylic acid derivative
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organonitrogen compound
Amine
Organic salt
Organooxygen compound
Organopnictogen compound
Organic oxygen compound
Primary amine
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

adenosine 5'-phosphate (CHEBI:15572 )

Physical Properties

State:

Not Available

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	1.78 g/L	ALOGPS
logP	-0.59	ALOGPS
logP	-2.6	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	0.78	ChemAxon
pKa (Strongest Basic)	4.99	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	232.6 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	107.85 m³·mol⁻¹	ChemAxon
Polarizability	42.45 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

SMPDB Pathways:

Biosynthesis of siderophore group nonribosomal peptides	PW000760
Enterobactin Biosynthesis	PW002048

KEGG Pathways:

Biosynthesis of siderophore group nonribosomal peptides ec01053

EcoCyc Pathways:

Not Available

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0910100000-6cc966e42959845ce140	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-cac72a96ea912fac0134	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-3900000000-33d698b4dd44287997c1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-003r-2897700000-96e367950f88d2ffbae6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-3910000000-2730f7b44e981db61411	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003r-9600000000-b9455f923a6c6d2e397b	View in MoNA
MS	Mass Spectrum (Electron Ionization)	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	5572
HMDB ID	Not Available
Pubchem Compound ID	440201
Kegg ID	C04030
ChemSpider ID	389188
Wikipedia ID	Not Available
BioCyc ID	CPD-62
EcoCyc ID	CPD-62

Enzymes

Protein Details

1. Isochorismatase

General function:: Involved in isochorismatase activity
Specific function:: Required for production of 2,3-DHB. Also serves as an aryl carrier protein and plays a role in enterobactin assembly
Gene Name:: entB
Uniprot ID:: P0ADI4
Molecular weight:: 32554

Reactions

Isochorismate + H(2)O = 2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate.

Protein Details

2. Enterobactin synthase component E

General function:: Involved in catalytic activity
Specific function:: Activates the carboxylate group of 2,3-dihydroxy- benzoate (2,3-DHB), via ATP-dependent PPi exchange reactions, to the acyladenylate. Then, catalyzes the acylation of holo-entB with 2,3-DHB adenylate, preparing that molecule for amide bond formation with L-serine
Gene Name:: entE
Uniprot ID:: P10378
Molecular weight:: 59112

Reactions

ATP + 2,3-dihydroxybenzoate = diphosphate + (2,3-dihydroxybenzoyl)adenylate.
(2,3-dihydroxybenzoyl)adenylate + holo-entB = adenosine 5'-monophosphate + acyl-holo-entB.

Protein Details

3. Enterobactin synthase component F

General function:: Involved in ligase activity
Specific function:: Activates the carboxylate group of L-serine via ATP- dependent PPi exchange reactions to the aminoacyladenylate, preparing that molecule for the final stages of enterobactin synthesis. Holo-entF acts as the catalyst for the formation of the three amide and three ester bonds present in the cyclic (2,3- dihydroxybenzoyl)serine trimer enterobactin, using seryladenylate and acyl-holo-entB (acylated with 2,3-dihydroxybenzoate by entE)
Gene Name:: entF
Uniprot ID:: P11454
Molecular weight:: 141990

Reactions

ATP + L-serine = diphosphate + L-serine-adenylate.

Protein Details

4. 4'-phosphopantetheinyl transferase entD

General function:: Involved in magnesium ion binding
Specific function:: Catalyzes the transfer of the 4'-phosphopantetheine moiety from coenzyme A to apo-domains of both entB (an ArCP domain) and entF (a PCP domain). Plays an essential role in the assembly of the enterobactin
Gene Name:: entD
Uniprot ID:: P19925
Molecular weight:: 23604

Reactions

CoA + apo-EntB/F = adenosine 3',5'-bisphosphate + holo-EntB/F.

(2,3-Dihydroxybenzoyl)adenylic acid (ECMDB04053) (M2MDB000585)

Structure for #<Compound:0x9df817fc>

Enzymes

Reactions

Reactions

Reactions

Reactions