MiMeDB: Showing metabocard for 3-deoxy-D-arabino-heptulosonate-7-phosphate (MMDBc0032107)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:02:39 UTC

Update Date

2022-08-31 18:30:36 UTC

Metabolite ID

MMDBc0032107

Metabolite Identification

Common Name

3-deoxy-D-arabino-heptulosonate-7-phosphate

Description

3-Deoxy-D-arabino-heptulosonate-7-phosphate is a member of the chemical class known as Medium-chain Keto Acids and Derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain. DAHPS is involved in the biosynthesis of aromatic amino acids. Maritima DAHP synthase is a metalloenzyme. This report is the first description of a thermophilic eubacterial DAHP synthase. (PMID 12743122 ) DAHPS(Phe) is a metal-catalyzed oxidation system wherein bound substrate protects active-site residues from oxidative attack catalyzed by bound redox metal cofactor. (PMID 10049398 ) The first regulatory step in the synthesis of aromatic amino acids is catalyzed by 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS). (PMID 15378531 ) While several similarities exist between the two enzymatic reactions, classic studies on the Escherichia coli enzymes have established that DAHPS is a metalloenzyme, whereas KDO8PS has no metal requirement. aeolicus KDO8PS is a metalloenzyme in vivo and point to a previously unrecognized relationship between the KDO8PS and DAHPS families. (PMID 10811802 )

Structure

MOL SDF PDB SMILES InChI

      
  Mrv1533005211518442D          

 21 20  0  0  0  0            999 V2000
    1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.2062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.2062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8578   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723    0.2062    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.8578   -1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5723   -0.6187    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -3.2703    0.5082    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.4453   -0.9207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8578   -0.2062    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144   -0.6187    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144   -0.6187    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6187    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  1  0  0  0  0
  3  8  1  1  0  0  0
  9  4  2  0  0  0  0
  5 10  1  6  0  0  0
  6 11  1  1  0  0  0
 12  7  1  0  0  0  0
 13  7  2  0  0  0  0
 17  2  1  0  0  0  0
 18 14  1  0  0  0  0
 18 15  1  0  0  0  0
 18 16  2  0  0  0  0
 18 17  1  0  0  0  0
  3 19  1  1  0  0  0
  5 20  1  6  0  0  0
  6 21  1  1  0  0  0
M  CHG  3  12  -1  14  -1  15  -1
M  END
> <DATABASE_ID>
MMDBc0032107

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H13O10P/c8-3(1-4(9)7(12)13)6(11)5(10)2-17-18(14,15)16/h3,5-6,8,10-11H,1-2H2,(H,12,13)(H2,14,15,16)/p-3/t3-,5-,6+/m1/s1

> <INCHI_KEY>
PJWIPEXIFFQAQZ-PUFIMZNGSA-K

> <FORMULA>
C7H10O10P

> <MOLECULAR_WEIGHT>
285.122

> <EXACT_MASS>
285.00280426

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
21.763715688743606

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5S,6R)-4,5,6-trihydroxy-2-oxo-7-(phosphonatooxy)heptanoate

> <ALOGPS_LOGP>
-1.59

> <JCHEM_LOGP>
-2.5289322136666668

> <ALOGPS_LOGS>
-0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.9174480444633493

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4688872906407804

> <JCHEM_PKA_STRONGEST_BASIC>
-3.271766798649698

> <JCHEM_POLAR_SURFACE_AREA>
190.31

> <JCHEM_REFRACTIVITY>
61.745400000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.11e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5S,6R)-4,5,6-trihydroxy-2-oxo-7-(phosphonatooxy)heptanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-MAY-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-MAY-15         0                                  
HETATM    1  C   UNK     0       2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334   0.385   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -0.385   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335  -0.385   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334   1.925   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.001   1.925   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.334   1.925   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000  -1.925   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       6.668   0.385   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       5.335  -1.925   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -6.668  -1.155   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0      -6.105   0.949   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0      -4.565  -1.719   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -4.001   0.385   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0      -5.335  -0.385   0.000  0.00  0.00           P+0
HETATM   19  H   UNK     0       1.334  -1.155   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      -1.334  -1.155   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   1.155   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    5   17                                                       
CONECT    3    1    6    8   19                                             
CONECT    4    1    7    9                                                  
CONECT    5    2    6   10   20                                             
CONECT    6    3    5   11   21                                             
CONECT    7    4   12   13                                                  
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    7                                                            
CONECT   13    7                                                            
CONECT   14   18                                                            
CONECT   15   18                                                            
CONECT   16   18                                                            
CONECT   17    2   18                                                       
CONECT   18   14   15   16   17                                             
CONECT   19    3                                                            
CONECT   20    5                                                            
CONECT   21    6                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   40    0
END

Synonyms

Value	Source
3-Deoxy-D-arabino-2-heptulosonate 7-phosphate	ChEBI
3-Deoxy-D-erythro-hept-2-ulosonate 7-phosphate	ChEBI
7-Phospho-2-dehydro-3-deoxy-D-arabino-heptonate anion	ChEBI
7-Phospho-2-dehydro-3-deoxy-D-arabino-heptonate(1-)	ChEBI
3-Deoxy-D-arabino-2-heptulosonic acid 7-phosphoric acid	Generator
3-Deoxy-D-erythro-hept-2-ulosonic acid 7-phosphoric acid	Generator
7-Phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid anion	Generator
7-Phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid(1-)	Generator
3-Deoxy-D-arabino-heptulosonic acid-7-phosphoric acid	Generator
7-phospho-2-dehydro-3-Deoxy-D-arabino-heptonic acid	Generator
DAHP	MeSH
2-dehydro-3-Deoxy-D-arabino-heptulosonic acid-7-phosphate	MeSH
2-DAHP	MeSH
3-Deoxyarabinoheptulosonate-7-phosphate	MeSH
5-DAHP	MeSH
3-Deoxy-D-arabino-2-heptulosonic acid	MeSH
7-phospho-2-keto-3-Deoxy-D-arabinoheptonate	MeSH
3-Deoxy-D-arabino-heptulosonate-7-phosphate	MeSH
5-dehydro-3-Deoxy-D-arabino-heptulosonic acid-7-phosphate	MeSH

Molecular Formula

C₇H₁₀O₁₀P

Average Mass

285.122

Monoisotopic Mass

285.00280426

IUPAC Name

(4R,5S,6R)-4,5,6-trihydroxy-2-oxo-7-(phosphonatooxy)heptanoate

Traditional Name

(4R,5S,6R)-4,5,6-trihydroxy-2-oxo-7-(phosphonatooxy)heptanoate

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(COP([O-])([O-])=O)[C@@]([H])(O)[C@]([H])(O)CC(=O)C([O-])=O

InChI Identifier

InChI=1S/C7H13O10P/c8-3(1-4(9)7(12)13)6(11)5(10)2-17-18(14,15)16/h3,5-6,8,10-11H,1-2H2,(H,12,13)(H2,14,15,16)/p-3/t3-,5-,6+/m1/s1

InChI Key

PJWIPEXIFFQAQZ-PUFIMZNGSA-K

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Heptose monosaccharide
Monosaccharide phosphate
Medium-chain keto acid
Sugar acid
Alpha-keto acid
Beta-hydroxy ketone
Alkyl phosphate
Keto acid
Phosphoric acid ester
Organic phosphoric acid derivative
Secondary alcohol
Ketone
Carboxylic acid derivative
Carboxylic acid
Polyol
Monocarboxylic acid or derivatives
Alcohol
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

carbohydrate acid derivative anion (CHEBI:58394 )
monocarboxylic acid anion (CHEBI:58394 )
organophosphate oxoanion (CHEBI:58394 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	51.1 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-2.5	ChemAxon
logS	-0.82	ALOGPS
pKa (Strongest Acidic)	1.47	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	190.31 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	61.75 m³·mol⁻¹	ChemAxon
Polarizability	21.76 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0090000000-d66aa66ec73357727eaa	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-056r-1190000000-7e7cc8d6f1ccf3f95354	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-056s-8910000000-81bf72773f8d70e9afa1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-1190000000-9a6594a4f74076f0556c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-6390000000-d23ab2618c147f679d11	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001j-9100000000-19ff6079df0f5e0b8b80	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
MMDBr0013345	D-Erythrose 4-phosphate	3-deoxy-D-arabino-heptulosonate-7-phosphate	Phospho-2-dehydro-3-deoxyheptonate aldolase AMT16	Aldol addition (or reverse)	RHEA	34755880
MMDBr0013346	D-Erythrose 4-phosphate	3-deoxy-D-arabino-heptulosonate-7-phosphate	Phospho-2-dehydro-3-deoxyheptonate aldolase AroG	Aldol addition (or reverse)	RHEA	34755880
MMDBr0014160	3-deoxy-D-arabino-heptulosonate-7-phosphate	3-Dehydroquinate	Pentafunctional AROM polypeptide	Phosphorylation; Synthesis	RHEA	34755880
MMDBr0018290	Phosphoenolpyruvic acid	Phosphate	Phospho-2-dehydro-3-deoxyheptonate aldolase, Trp-sensitive	Aldol addition (or reverse)	PathBank	31602464
MMDBr0018291	3-deoxy-D-arabino-heptulosonate-7-phosphate	Phosphate	3-dehydroquinate synthase	Synthesis	PathBank	31602464

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	308	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Human subgingival plaque; Pig ; Cattle ; River trout ; Rat ; Sheep ; Chicken	Unknown
Eukaryota/Fungi	Ascomycota	54	Human feces; Human supragingival plaque; Human saliva
Bacteria	Actinobacteria	32	Human ; Human feces; Cattle
Bacteria	Thermotogae	1
Bacteria	Firmicutes	115	Human feces; Human ; Catfish ; Cattle
Eukaryota/Fungi	Basidiomycota	7
Bacteria	Cyanobacteria	27	Human
Bacteria	Acidobacteria	3
Archaea/Archaea	Crenarchaeota	7
Bacteria	Chlamydiae	10	Human ; Sheep ; Cat
Bacteria	Chlorobi	4
Bacteria	Chloroflexi	3
Bacteria	Deinococcus-thermus	1
Bacteria	Dictyoglomi	2
Bacteria	Elusimicrobia	1
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Spirochaetes	2
Bacteria	Verrucomicrobia	2
Bacteria	Bacteroidetes	2	Human ; Human feces
Archaea/Archaea	Euryarchaeota	6
Bacteria	Planctomycetes	1
Archaea	Crenarchaeota	1
Bacteria	nah	1
Bacteria	Nitrospirae	1
Bacteria/NULL	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Human subgingival plaque; Pig ; Cattle ; River trout ; Rat ; Sheep ; Chicken	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

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

3-Deoxy-D-arabino-heptulosonic acid 7-phosphate

METLIN ID

Not Available

PubChem Compound

5460215

PDB ID

Not Available

ChEBI ID

58394

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 3-deoxy-D-arabino-heptulosonate-7-phosphate (MMDBc0032107)

MOL for #<Metabolite:0x00007fe2b4979b60>

3D MOL for #<Metabolite:0x00007fe2b4979b60>

3D SDF for #<Metabolite:0x00007fe2b4979b60>

3D-SDF for #<Metabolite:0x00007fe2b4979b60>

PDB for #<Metabolite:0x00007fe2b4979b60>

3D PDB for #<Metabolite:0x00007fe2b4979b60>

SMILES for #<Metabolite:0x00007fe2b4979b60>

INCHI for #<Metabolite:0x00007fe2b4979b60>

Structure for #<Metabolite:0x00007fe2b4979b60>

3D Structure for #<Metabolite:0x00007fe2b4979b60>