MiMeDB: Showing metabocard for D-Sedoheptulose 7-phosphate (MMDBc0029543)

Plant

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:31:40 UTC

Update Date

2022-12-15 22:51:46 UTC

Metabolite ID

MMDBc0029543

Metabolite Identification

Common Name

D-Sedoheptulose 7-phosphate

Description

D-sedoheptulose 7-phosphate is a member of the chemical class known as Heptoses. These are monosaccharides in which the sugar unit is an heptose. D-sedoheptulose 7-phosphate is invovled in lipopolysaccharide biosynthesis, the pentose phosphate pathway (non-oxidative), the biosynthesis of secondary metabolites, the pentose phosphate pathway, and microbial metabolism in diverse environments. Sedoheptulose 7-phosphate is an intermediate in the pentose phosphate pathway. It is formed by transketolase and acted upon by transaldolase.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305221918582D          

 18 18  0  0  0  0            999 V2000
   -1.7338    0.3287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7338   -0.4963    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0192   -0.9089    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3046   -0.4963    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3047    0.3289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0192    0.7403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4073    0.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4460   -0.9075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0192   -1.7312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4074   -0.9075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1192    0.3290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8315    0.7403    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.4204    1.4525    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5437    1.1514    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2427    0.0281    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4481    0.7416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629    0.3294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7331    1.1538    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  1  1  0  0  0  0
  5  7  1  6  0  0  0
  2  8  1  6  0  0  0
  3  9  1  1  0  0  0
  4 10  1  1  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  0  0  0  0
  1 16  1  0  0  0  0
 16 17  1  0  0  0  0
  1 18  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029543

> <DATABASE_NAME>
MIME

> <SMILES>
OCC1(O)O[C@H](COP(O)(O)=O)[C@@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C7H15O10P/c8-2-7(12)6(11)5(10)4(9)3(17-7)1-16-18(13,14)15/h3-6,8-12H,1-2H2,(H2,13,14,15)/t3-,4-,5-,6+,7?/m1/s1

> <INCHI_KEY>
CBIDVWSRUUODHL-QTSLKERKSA-N

> <FORMULA>
C7H15O10P

> <MOLECULAR_WEIGHT>
290.1618

> <EXACT_MASS>
290.040283212

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.215651978200704

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5S)-3,4,5,6-tetrahydroxy-6-(hydroxymethyl)oxan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.26

> <JCHEM_LOGP>
-3.5119002913333333

> <ALOGPS_LOGS>
-0.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.247741993726048

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2219618298166233

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4509675882027384

> <JCHEM_POLAR_SURFACE_AREA>
177.14

> <JCHEM_REFRACTIVITY>
53.19619999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.07e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5S)-3,4,5,6-tetrahydroxy-6-(hydroxymethyl)oxan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0      -3.236   0.614   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.236  -0.926   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.903  -1.697   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.569  -0.926   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.569   0.614   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.903   1.382   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.760   1.381   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -4.566  -1.694   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.903  -3.232   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.761  -1.694   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       2.089   0.614   0.000  0.00  0.00           O+0
HETATM   12  P   UNK     0       3.419   1.382   0.000  0.00  0.00           P+0
HETATM   13  O   UNK     0       2.651   2.711   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.748   2.149   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.186   0.052   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -4.570   1.384   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -5.904   0.615   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -3.235   2.154   0.000  0.00  0.00           O+0
CONECT    1    2    6   16   18                                             
CONECT    2    1    3    8                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5   11                                                       
CONECT    8    2                                                            
CONECT    9    3                                                            
CONECT   10    4                                                            
CONECT   11    7   12                                                       
CONECT   12   11   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12                                                            
CONECT   16    1   17                                                       
CONECT   17   16                                                            
CONECT   18    1                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Value	Source
D-Sedoheptulose 7-phosphoric acid	Generator
7-(Dihydrogen phosphate) sedoheptulose	HMDB
D-Sedoheptulose-7-p	HMDB
D-Sedoheptulose-7-phosphate	HMDB
Heptulose-7-phosphate	HMDB
Sedoheptulose 7-phosphate	HMDB
Sedoheptulose-7-p	HMDB
Sedoheptulose-7-phosphate	HMDB

Molecular Formula

C₇H₁₅O₁₀P

Average Mass

290.1618

Monoisotopic Mass

290.040283212

IUPAC Name

{[(2R,3S,4R,5S)-3,4,5,6-tetrahydroxy-6-(hydroxymethyl)oxan-2-yl]methoxy}phosphonic acid

Traditional Name

[(2R,3S,4R,5S)-3,4,5,6-tetrahydroxy-6-(hydroxymethyl)oxan-2-yl]methoxyphosphonic acid

CAS Registry Number

2646-35-7

SMILES

OCC1(O)O[C@H](COP(O)(O)=O)[C@@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C7H15O10P/c8-2-7(12)6(11)5(10)4(9)3(17-7)1-16-18(13,14)15/h3-6,8-12H,1-2H2,(H2,13,14,15)/t3-,4-,5-,6+,7?/m1/s1

InChI Key

CBIDVWSRUUODHL-QTSLKERKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hexose phosphates. These are carbohydrate derivatives containing a hexose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Hexose phosphates

Alternative Parents

Substituents

Hexose phosphate
C-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Monoalkyl phosphate
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Alkyl phosphate
Hemiacetal
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Polyol
Organic oxide
Alcohol
Primary alcohol
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	30.7 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-3.5	ChemAxon
logS	-0.98	ALOGPS
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	177.14 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	53.2 m³·mol⁻¹	ChemAxon
Polarizability	23.22 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Cellular Cytoplasm
Feces
Fibroblasts
Placenta
Saliva
Urine

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

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Alzheimer's disease		Association	Human Saliva	HMDB	23857558
Frontotemporal dementia		Association	Human Saliva	HMDB	23857558
Transaldolase deficiency	Increased	Association	Human Blood	HMDB	12881455

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	471	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Chicken ; Cattle ; River trout ; Rat ; Turkey ; Sheep	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	455	Human feces; Human pleural fluid plaque; Pig ; Human ; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	155	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Cattle	Metabolic reconstruction
Bacteria	Verrucomicrobia	2	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	129	Human feces; Human appendix biopsy; Human	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	9	Human feces; Human ; Pig	Metabolic reconstruction
Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	4	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Candidatus Melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	6	Human feces; Human	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Aquificae	4
Bacteria	Cyanobacteria	31	Human
Eukaryota/Fungi	Ascomycota	9	Human feces	Unknown
Archaea/Archaea	Euryarchaeota	10	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Acidobacteria	1
Bacteria	Chlamydiae	8	Human ; Sheep ; Cat
Bacteria	Chlorobi	11
Bacteria	Chloroflexi	4
Bacteria	Deinococcus-Thermus	3
Bacteria/NULL	Proteobacteria	2	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Chicken ; Cattle ; River trout ; Rat ; Turkey ; Sheep	Unknown; Metabolic reconstruction
Bacteria	Dictyoglomi	1
Bacteria	Thermotogae	9
Archaea/Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	nah	1
Bacteria	Nitrospirae	1
Bacteria/NULL	Firmicutes	1	Human feces; Human pleural fluid plaque; Pig ; Human ; Cattle	Metabolic reconstruction
Bacteria/NULL	Actinobacteria	3	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Cattle	Metabolic reconstruction

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified						HMDB
Human	Detected and Quantified	0.91	0.26	Adult (>18 years old)	Male	Alzheimer's disease	HMDB	23857558
Human	Detected and Quantified	0.84	0.13	Adult (>18 years old)	Male	Frontotemporal lobe dementia	HMDB	23857558
Human	Detected and Quantified	1.60	1.55	Adult (>18 years old)	Both	Lewy body disease	HMDB	23857558
Human	Detected and Quantified	5.19	0.84	Adult (>18 years old)	Both	Transaldolase deficiency	HMDB	12881455
Human	Detected and Quantified	74.9		Adult (>18 years old)	Both	Normal	HMDB	15882454
Human	Detected and Quantified	0.89	0.41	Adult (>18 years old)	Both	Normal	HMDB	12881455
Human	Detected and Quantified	1.15	0.44	Adult (>18 years old)	Female	Normal	HMDB	23857558
Human	Detected and Quantified	1.15	0.66	Children (1-13 years old)	Both	Normal	HMDB	12881455
Human	Detected and Quantified	0.299	0.236	Adult (>18 years old)	Not Specified	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human	Detected and Quantified	0.360	1.20	Adult (>18 years old)	Not Specified	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Fibroblasts	Detected but not Quantified			Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified			Not Specified	Not Specified	Normal	HMDB	34986597
Human Urine	Detected but not Quantified			Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified			Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0001068

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022407

KNApSAcK ID

Not Available

Chemspider ID

17216052

KEGG Compound ID

C05382

BioCyc ID

Not Available

BiGG ID

34485

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

22833559

PDB ID

Not Available

ChEBI ID

15721

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Makarov SA, Kudriavtseva GV, Kolotilova AI: [Effect of prostaglandins F2 and F2 alpha on the pentosephosate pathway in human blood platelets]. Vopr Med Khim. 1983 Sep-Oct;29(5):27-32. [PubMed:6316661 ]
Thornalley PJ, Jahan I, Ng R: Suppression of the accumulation of triosephosphates and increased formation of methylglyoxal in human red blood cells during hyperglycaemia by thiamine in vitro. J Biochem. 2001 Apr;129(4):543-9. doi: 10.1093/oxfordjournals.jbchem.a002889. [PubMed:11275553 ]
Huck JH, Struys EA, Verhoeven NM, Jakobs C, van der Knaap MS: Profiling of pentose phosphate pathway intermediates in blood spots by tandem mass spectrometry: application to transaldolase deficiency. Clin Chem. 2003 Aug;49(8):1375-80. doi: 10.1373/49.8.1375. [PubMed:12881455 ]
Nakayama Y, Kinoshita A, Tomita M: Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model. 2005 May 9;2:18. doi: 10.1186/1742-4682-2-18. [PubMed:15882454 ]
Wamelink MM, Struys EA, Huck JH, Roos B, van der Knaap MS, Jakobs C, Verhoeven NM: Quantification of sugar phosphate intermediates of the pentose phosphate pathway by LC-MS/MS: application to two new inherited defects of metabolism. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Aug 25;823(1):18-25. doi: 10.1016/j.jchromb.2005.01.001. Epub 2005 Jan 23. [PubMed:16055050 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for D-Sedoheptulose 7-phosphate (MMDBc0029543)

MOL for #<Metabolite:0x0000560be2125e28>

3D MOL for #<Metabolite:0x0000560be2125e28>

3D SDF for #<Metabolite:0x0000560be2125e28>

3D-SDF for #<Metabolite:0x0000560be2125e28>

PDB for #<Metabolite:0x0000560be2125e28>

3D PDB for #<Metabolite:0x0000560be2125e28>

SMILES for #<Metabolite:0x0000560be2125e28>

INCHI for #<Metabolite:0x0000560be2125e28>

Structure for #<Metabolite:0x0000560be2125e28>

3D Structure for #<Metabolite:0x0000560be2125e28>