MiMeDB: Showing metabocard for Sedoheptulose (MMDBc0000421)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:37:23 UTC

Update Date

2024-04-30 19:32:21 UTC

Metabolite ID

MMDBc0000421

Metabolite Identification

Common Name

Sedoheptulose

Description

Sedoheptulose (CAS: 3019-74-7) is a ketoheptose, a monosaccharide with seven carbon atoms and a ketone functional group. It is one of the few heptoses found in nature. Sedoheptulose is a seven-carbon ketose sugar originally found in Sedum spectabile, a common perennial garden plant. Later it was shown to be widely distributed in the plants of the Crassulaceae family. The Crassulaceae, or orpine family, is a family of dicotyledons. They store water in their succulent leaves. They are found worldwide, but mostly occur in the northern hemisphere and southern Africa, typically in dry and/or cold areas where water may be scarce. The family includes about 1,400 species in 33 genera. As a result, this sugar is often found to be part of the human diet. This sugar, D-sedoheptulose, is a significant intermediary compound in the cyclic regeneration of D-ribulose. It also plays an important role as a transitory compound in the cyclic regeneration of D-ribulose for carbon dioxide fixation in plant photosynthesis.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652309201916212D          

 14 14  0  0  0  0            999 V2000
   -0.3099    0.3287    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3099   -0.4963    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0245   -0.9089    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7391   -0.4963    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7390    0.3289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0245    0.7403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4510    0.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4022   -0.9075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0245   -1.7312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4511   -0.9075    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1629    0.3290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4043    0.7416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1191    0.3294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3106    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  1  0  0  0
  2  8  1  1  0  0  0
  3  9  1  6  0  0  0
  4 10  1  6  0  0  0
  7 11  1  0  0  0  0
  1 12  1  0  0  0  0
 12 13  1  0  0  0  0
  1 14  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000421

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@](O)(CO)[C@@H](O)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C7H14O7/c8-1-3-4(10)5(11)6(12)7(13,2-9)14-3/h3-6,8-13H,1-2H2/t3-,4-,5-,6+,7-/m1/s1

> <INCHI_KEY>
HAIWUXASLYEWLM-BNWJMWRWSA-N

> <FORMULA>
C7H14O7

> <MOLECULAR_WEIGHT>
210.1819

> <EXACT_MASS>
210.073952802

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
18.789543872812335

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5S,6R)-2,6-bis(hydroxymethyl)oxane-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-2.60

> <JCHEM_LOGP>
-3.38833426

> <ALOGPS_LOGS>
0.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.56502527822953

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.28360347326985

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9813603412699186

> <JCHEM_POLAR_SURFACE_AREA>
130.61

> <JCHEM_REFRACTIVITY>
42.32329999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.16e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-D-sedoheptulopyranose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-SEP-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-SEP-19         0                                  
HETATM    1  C   UNK     0      -0.578   0.614   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.578  -0.926   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.912  -1.697   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.246  -0.926   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.246   0.614   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.912   1.382   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -4.575   1.382   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.751  -1.694   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.912  -3.232   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -4.575  -1.694   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -5.904   0.614   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.755   1.384   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.089   0.615   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -0.580   2.154   0.000  0.00  0.00           O+0
CONECT    1    2    6   12   14                                             
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                                                            
CONECT   12    1   13                                                       
CONECT   13   12                                                            
CONECT   14    1                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

COMPND    HMDB0003219
HETATM    1  O1  UNL     1       3.240  -1.470   0.088  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.443  -0.575   0.801  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.519   0.178  -0.169  1.00  0.00           C  
HETATM    4  O2  UNL     1       0.754  -0.775  -0.788  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.533  -0.888  -0.303  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.496  -1.023   1.084  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.159  -2.106  -0.935  1.00  0.00           C  
HETATM    8  O4  UNL     1      -2.478  -2.233  -0.446  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.237   0.385  -0.637  1.00  0.00           C  
HETATM   10  O5  UNL     1      -2.596   0.356  -0.397  1.00  0.00           O  
HETATM   11  C6  UNL     1      -0.615   1.466   0.214  1.00  0.00           C  
HETATM   12  O6  UNL     1      -0.839   2.708  -0.421  1.00  0.00           O  
HETATM   13  C7  UNL     1       0.813   1.260   0.525  1.00  0.00           C  
HETATM   14  O7  UNL     1       1.494   2.475   0.271  1.00  0.00           O  
HETATM   15  H1  UNL     1       2.719  -1.707  -0.732  1.00  0.00           H  
HETATM   16  H2  UNL     1       1.822  -1.204   1.500  1.00  0.00           H  
HETATM   17  H3  UNL     1       3.062   0.105   1.385  1.00  0.00           H  
HETATM   18  H4  UNL     1       2.224   0.587  -0.952  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.406  -0.734   1.407  1.00  0.00           H  
HETATM   20  H6  UNL     1      -0.629  -3.010  -0.571  1.00  0.00           H  
HETATM   21  H7  UNL     1      -1.116  -2.112  -2.019  1.00  0.00           H  
HETATM   22  H8  UNL     1      -2.392  -2.573   0.477  1.00  0.00           H  
HETATM   23  H9  UNL     1      -1.051   0.684  -1.705  1.00  0.00           H  
HETATM   24  H10 UNL     1      -3.044   0.934  -1.086  1.00  0.00           H  
HETATM   25  H11 UNL     1      -1.235   1.517   1.150  1.00  0.00           H  
HETATM   26  H12 UNL     1      -1.117   3.394   0.218  1.00  0.00           H  
HETATM   27  H13 UNL     1       0.928   1.116   1.640  1.00  0.00           H  
HETATM   28  H14 UNL     1       0.922   3.246   0.401  1.00  0.00           H  
CONECT    1    2   15
CONECT    2    3   16   17
CONECT    3    4   13   18
CONECT    4    5
CONECT    5    6    7    9
CONECT    6   19
CONECT    7    8   20   21
CONECT    8   22
CONECT    9   10   11   23
CONECT   10   24
CONECT   11   12   13   25
CONECT   12   26
CONECT   13   14   27
CONECT   14   28
END

Synonyms

Value	Source
beta-D-Sedoheptulose	ChEBI
D-Altro-heptulose	ChEBI
D-Sedoheptulose	ChEBI
Volemulose	ChEBI
b-D-Sedoheptulose	Generator
Β-D-sedoheptulose	Generator
b-D-Sedoheptulopyranose	HMDB
Β-D-sedoheptulopyranose	HMDB
D-Altroheptulose	HMDB
beta-D-Sedoheptulopyranose	HMDB
beta-D-Altro-2-heptulopyranose	HMDB
Β-D-altro-2-heptulopyranose	HMDB
Sedoheptulose	HMDB

Molecular Formula

C₇H₁₄O₇

Average Mass

210.1819

Monoisotopic Mass

210.073952802

IUPAC Name

(2R,3S,4R,5S,6R)-2,6-bis(hydroxymethyl)oxane-2,3,4,5-tetrol

Traditional Name

β-D-sedoheptulopyranose

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@](O)(CO)[C@@H](O)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C7H14O7/c8-1-3-4(10)5(11)6(12)7(13,2-9)14-3/h3-6,8-13H,1-2H2/t3-,4-,5-,6+,7-/m1/s1

InChI Key

HAIWUXASLYEWLM-BNWJMWRWSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

C-glycosyl compounds

Alternative Parents

Substituents

Hexose monosaccharide
C-glycosyl compound
Oxane
Monosaccharide
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

sedoheptulose (CHEBI:27520 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	916 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-3.4	ChemAxon
logS	0.64	ALOGPS
pKa (Strongest Acidic)	10.28	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	130.61 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	42.32 m³·mol⁻¹	ChemAxon
Polarizability	18.79 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

Not Available

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces
Placenta

Tissue Locations

Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192420	Transketolase-like protein 1	Unknown	P51854	Homo sapiens
MMDBp0192422	Transaldolase	Enzyme	P37837	Homo sapiens
MMDBp0192425	Transketolase	Unknown	P29401	Homo sapiens
MMDBp0192803	Ketohexokinase	Enzyme	P50053	Homo sapiens
MMDBp0194056	Transketolase-like protein 2	Unknown	Q9H0I9	Homo sapiens
MMDBp0194072	Sedoheptulokinase	Enzyme	Q9UHJ6	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

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	Firmicutes	10	Human stool; Human feces; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Proteobacteria	2	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Human mucosa; Human supragingival plaque; Human saliva; Human subgingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Placenta	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0003219

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00001132

Chemspider ID

390207

KEGG Compound ID

C08355

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Sedoheptulose

METLIN ID

Not Available

PubChem Compound

441483

PDB ID

Not Available

ChEBI ID

27520

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Pitkanen E, Sahlstrom K: The occurrence of sedoheptulose in human urine. Ann Med Exp Biol Fenn. 1968;46(3):295-300. [PubMed:5731228 ]
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 Sedoheptulose (MMDBc0000421)

MOL for #<Metabolite:0x00007f922cd5f5c8>

3D MOL for #<Metabolite:0x00007f922cd5f5c8>

3D SDF for #<Metabolite:0x00007f922cd5f5c8>

3D-SDF for #<Metabolite:0x00007f922cd5f5c8>

PDB for #<Metabolite:0x00007f922cd5f5c8>

3D PDB for #<Metabolite:0x00007f922cd5f5c8>

SMILES for #<Metabolite:0x00007f922cd5f5c8>

INCHI for #<Metabolite:0x00007f922cd5f5c8>

Structure for #<Metabolite:0x00007f922cd5f5c8>

3D Structure for #<Metabolite:0x00007f922cd5f5c8>