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Showing metabocard for D-Psicose (HMDB0250793)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:54:04 UTC
Update Date2021-09-26 23:02:27 UTC
HMDB IDHMDB0250793
Secondary Accession NumbersNone
Metabolite Identification
Common NameD-Psicose
DescriptionD-Psicose belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn. Based on a literature review a significant number of articles have been published on D-Psicose. This compound has been identified in human blood as reported by (PMID: 31557052 ). D-psicose is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically D-Psicose is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0250793 (D-Psicose)

  Mrv1652309112109542D          

 12 12  0  0  0  0            999 V2000
    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
   -0.0000    0.0000    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
    0.7145    1.2375    0.0000 C   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
    0.3272    1.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4973    1.9947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1018    1.9659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    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
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  9  1  0  0  0  0
  4 10  1  0  0  0  0
  3 11  1  0  0  0  0
  2 12  1  0  0  0  0
M  END
Download

3D MOL for HMDB0250793 (D-Psicose)

HMDB0250793
     RDKit          3D
D-Psicose
 24 24  0  0  0  0  0  0  0  0999 V2000
    2.9567    0.9991    0.2916 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0071    0.3439   -0.4933 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8806   -0.1872    0.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5285   -1.0731    1.3004 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4260    0.8657    1.1364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9229    0.9343    1.3329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7436    0.8678    0.0767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0765    0.6408    0.4773 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2765   -0.1711   -0.8873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0135    0.3884   -2.1184 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271   -0.9719   -0.3349 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4903   -1.7163   -1.3216 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6496    0.3680    0.5931 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5888    1.1390   -1.1754 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4365   -0.4805   -1.0669 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0596   -0.5402    1.9248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3175    0.2013    2.0778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1382    1.9422    1.7956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6977    1.8831   -0.4098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0646   -0.2864    0.8665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1190   -0.9034   -1.0550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1510    0.1321   -2.4932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5835   -1.7121    0.3856 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2080   -2.6635   -1.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11  3  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  4 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  8 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  0
 12 24  1  0
M  END
Download

3D SDF for HMDB0250793 (D-Psicose)

  Mrv1652309112109542D          

 12 12  0  0  0  0            999 V2000
    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
   -0.0000    0.0000    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
    0.7145    1.2375    0.0000 C   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
    0.3272    1.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4973    1.9947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1018    1.9659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    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
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  9  1  0  0  0  0
  4 10  1  0  0  0  0
  3 11  1  0  0  0  0
  2 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250793

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1(O)OCC(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2

> <INCHI_KEY>
LKDRXBCSQODPBY-UHFFFAOYSA-N

> <FORMULA>
C6H12O6

> <MOLECULAR_WEIGHT>
180.156

> <EXACT_MASS>
180.063388106

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.019080753629673

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)oxane-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-2.51

> <JCHEM_LOGP>
-2.7579993179999995

> <ALOGPS_LOGS>
0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.643871080491373

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.291030669254257

> <JCHEM_PKA_STRONGEST_BASIC>
-3.450704169945884

> <JCHEM_POLAR_SURFACE_AREA>
110.38000000000001

> <JCHEM_REFRACTIVITY>
36.3608

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.19e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
laevosan

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0250793 (D-Psicose)

HMDB0250793
     RDKit          3D
D-Psicose
 24 24  0  0  0  0  0  0  0  0999 V2000
    2.9567    0.9991    0.2916 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0071    0.3439   -0.4933 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8806   -0.1872    0.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5285   -1.0731    1.3004 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4260    0.8657    1.1364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9229    0.9343    1.3329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7436    0.8678    0.0767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0765    0.6408    0.4773 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2765   -0.1711   -0.8873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0135    0.3884   -2.1184 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271   -0.9719   -0.3349 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4903   -1.7163   -1.3216 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6496    0.3680    0.5931 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5888    1.1390   -1.1754 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4365   -0.4805   -1.0669 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0596   -0.5402    1.9248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3175    0.2013    2.0778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1382    1.9422    1.7956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6977    1.8831   -0.4098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0646   -0.2864    0.8665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1190   -0.9034   -1.0550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1510    0.1321   -2.4932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5835   -1.7121    0.3856 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2080   -2.6635   -1.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11  3  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  4 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  8 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  0
 12 24  1  0
M  END
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PDB for HMDB0250793 (D-Psicose)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000   0.000   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       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.611   3.670   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.928   3.723   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       2.057   3.670   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   12                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7    9                                             
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7                                                            
CONECT    9    5                                                            
CONECT   10    4                                                            
CONECT   11    3                                                            
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for HMDB0250793 (D-Psicose)

COMPND    HMDB0250793
HETATM    1  O1  UNL     1       2.957   0.999   0.292  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.007   0.344  -0.493  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.881  -0.187   0.405  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.529  -1.073   1.300  1.00  0.00           O  
HETATM    5  O3  UNL     1       0.426   0.866   1.136  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.923   0.934   1.333  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.744   0.868   0.077  1.00  0.00           C  
HETATM    8  O4  UNL     1      -3.077   0.641   0.477  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.276  -0.171  -0.887  1.00  0.00           C  
HETATM   10  O5  UNL     1      -1.013   0.388  -2.118  1.00  0.00           O  
HETATM   11  C6  UNL     1      -0.127  -0.972  -0.335  1.00  0.00           C  
HETATM   12  O6  UNL     1       0.490  -1.716  -1.322  1.00  0.00           O  
HETATM   13  H1  UNL     1       3.650   0.368   0.593  1.00  0.00           H  
HETATM   14  H2  UNL     1       1.589   1.139  -1.175  1.00  0.00           H  
HETATM   15  H3  UNL     1       2.436  -0.481  -1.067  1.00  0.00           H  
HETATM   16  H4  UNL     1       2.060  -0.540   1.925  1.00  0.00           H  
HETATM   17  H5  UNL     1      -1.317   0.201   2.078  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.138   1.942   1.796  1.00  0.00           H  
HETATM   19  H7  UNL     1      -1.698   1.883  -0.410  1.00  0.00           H  
HETATM   20  H8  UNL     1      -3.065  -0.286   0.866  1.00  0.00           H  
HETATM   21  H9  UNL     1      -2.119  -0.903  -1.055  1.00  0.00           H  
HETATM   22  H10 UNL     1      -0.151   0.132  -2.493  1.00  0.00           H  
HETATM   23  H11 UNL     1      -0.584  -1.712   0.386  1.00  0.00           H  
HETATM   24  H12 UNL     1       0.208  -2.663  -1.308  1.00  0.00           H  
CONECT    1    2   13
CONECT    2    3   14   15
CONECT    3    4    5   11
CONECT    4   16
CONECT    5    6
CONECT    6    7   17   18
CONECT    7    8    9   19
CONECT    8   20
CONECT    9   10   11   21
CONECT   10   22
CONECT   11   12   23
CONECT   12   24
END
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SMILES for HMDB0250793 (D-Psicose)

OCC1(O)OCC(O)C(O)C1O
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INCHI for HMDB0250793 (D-Psicose)

InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H12O6
Average Molecular Weight180.156
Monoisotopic Molecular Weight180.063388106
IUPAC Name2-(hydroxymethyl)oxane-2,3,4,5-tetrol
Traditional Namelaevosan
CAS Registry NumberNot Available
SMILES
OCC1(O)OCC(O)C(O)C1O
InChI Identifier
InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2
InChI KeyLKDRXBCSQODPBY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentMonosaccharides
Alternative Parents
Substituents
  • Oxane
  • Monosaccharide
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID3308
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPsicose
METLIN IDNot Available
PubChem Compound3426
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]