Showing NP-Card for Levoglucosan (NP0000318)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Show more...
Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 23:58:01 UTC
NP-MRD IDNP0000318
Secondary Accession NumbersNone
Natural Product Identification
Common NameLevoglucosan
DescriptionLevoglucosan is an anhydrohexose that is the 1,6-anhydro-derivative of beta-D-glucopyranose. It is formed from the pyrolysis of carbohydrates, such as starch and cellulose. As a result, levoglucosan is often used as a chemical tracer for biomass burning in atmospheric chemistry studies, particularly with respect to airborne particulate matter. Levoglucosan in urine has been shown to be highly correlated with regional fires and as a biomarker for wood smoke exposure (PMID: 19165390 ). This is because the gas emitted by the pyrolysis of wood (biomass) contains significant amounts of levoglucosan. The hydrolysis of levoglucosan generates the fermentable sugar glucose, and therefore lignocellulosic material exhibits great potential as a renewable feedstock for the production of bioethanol. Levoglucosan can also be utilized in the synthesis of chiral polymers such as unhydrolysable glucose polymers. Levoglucosan is also produced via caramelization of sugar. Consumption of caramel or caramel-containing sweets can lead to a short-term 5X increase in urinary levels of levoglucosan (from 20 uM/mM creatinine to 100 uM/mM creatinine) (PMID: 19707249 ). Urinary levoglucosan levels increase within 2 h of caramel consumption and return to pre-exposure levels within 24 h. These data suggest that diet is a major factor in determining urinary levoglucosan levels and that recent dietary history needs to be taken into account to use levoglucosan as a marker for wood smoke exposure. Excretory levels of levoglucosan vary widely from zero up to 5.3 Mmol/L (PMID: 3757263 , 16448658 , 16317539 ).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000318 (Levoglucosan)

  Mrv1652304202019212D          

 12 13  0  0  1  0            999 V2000
   17.7488  -13.9652    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.3312  -14.6766    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.3415  -13.2477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5062  -14.6707    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.5165  -13.2418    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.0988  -13.9532    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.5738  -13.9711    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.7385  -15.3941    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0885  -15.3821    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2739  -13.9473    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5067  -12.5244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7587  -12.5239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  1  6  0  0  0
  2  8  1  6  0  0  0
  4  9  1  1  0  0  0
  6 10  1  6  0  0  0
  5 11  1  1  0  0  0
 12 11  1  0  0  0  0
  1 12  1  0  0  0  0
M  END
Download

3D MOL for NP0000318 (Levoglucosan)

HMDB0000640
     RDKit          3D
Levoglucosan
 21 22  0  0  0  0  0  0  0  0999 V2000
   -0.1943   -2.4874    0.5039 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2762   -1.1180    0.4033 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1043   -0.4779    0.3216 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9278   -0.8365    1.3512 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8664    1.0146    0.2187 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0223    1.7529    0.1937 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0262    1.2447   -0.9790 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3120    1.6064   -0.6368 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0471    0.4476   -0.4452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0486   -0.6461   -0.8059 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2261    0.0529   -1.7101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5375   -2.7412    1.4156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7529   -0.6558    1.3173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5097   -0.7866   -0.6864 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8211   -1.0751    0.9434 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2976    1.2928    1.1507 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2449    2.1616    1.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4870    1.9675   -1.6385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4674    0.3339    0.5523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8140    0.4261   -1.2646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5788   -1.4766   -1.2933 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
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10  2  1  0
 11  7  1  0
  1 12  1  0
  2 13  1  1
  3 14  1  6
  4 15  1  0
  5 16  1  1
  6 17  1  0
  7 18  1  6
  9 19  1  0
  9 20  1  0
 10 21  1  6
M  END
Download

3D SDF for NP0000318 (Levoglucosan)

  Mrv1652304202019212D          

 12 13  0  0  1  0            999 V2000
   17.7488  -13.9652    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.3312  -14.6766    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.3415  -13.2477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5062  -14.6707    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.5165  -13.2418    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.0988  -13.9532    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.5738  -13.9711    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.7385  -15.3941    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0885  -15.3821    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2739  -13.9473    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.5067  -12.5244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7587  -12.5239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  1  0  0  0  0
  1  7  1  6  0  0  0
  2  8  1  6  0  0  0
  4  9  1  1  0  0  0
  6 10  1  6  0  0  0
  5 11  1  1  0  0  0
 12 11  1  0  0  0  0
  1 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000318

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12OC[C@@H](O1)[C@@H](O)[C@H](O)[C@H]2O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O5/c7-3-2-1-10-6(11-2)5(9)4(3)8/h2-9H,1H2/t2-,3-,4+,5-,6-/m1/s1

> <INCHI_KEY>
TWNIBLMWSKIRAT-VFUOTHLCSA-N

> <FORMULA>
C6H10O5

> <MOLECULAR_WEIGHT>
162.1406

> <EXACT_MASS>
162.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.130250612602248

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,3S,4R,5R)-6,8-dioxabicyclo[3.2.1]octane-2,3,4-triol

> <ALOGPS_LOGP>
-2.18

> <JCHEM_LOGP>
-1.7708356456666667

> <ALOGPS_LOGS>
0.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.215582381313808

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.212605412524747

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6486679661074968

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
32.41329999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.60e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
levoglucosan

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000318 (Levoglucosan)

HMDB0000640
     RDKit          3D
Levoglucosan
 21 22  0  0  0  0  0  0  0  0999 V2000
   -0.1943   -2.4874    0.5039 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2762   -1.1180    0.4033 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1043   -0.4779    0.3216 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9278   -0.8365    1.3512 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8664    1.0146    0.2187 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0223    1.7529    0.1937 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0262    1.2447   -0.9790 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3120    1.6064   -0.6368 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0471    0.4476   -0.4452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0486   -0.6461   -0.8059 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2261    0.0529   -1.7101 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5375   -2.7412    1.4156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7529   -0.6558    1.3173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5097   -0.7866   -0.6864 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8211   -1.0751    0.9434 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2976    1.2928    1.1507 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2449    2.1616    1.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4870    1.9675   -1.6385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4674    0.3339    0.5523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8140    0.4261   -1.2646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5788   -1.4766   -1.2933 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
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10  2  1  0
 11  7  1  0
  1 12  1  0
  2 13  1  1
  3 14  1  6
  4 15  1  0
  5 16  1  1
  6 17  1  0
  7 18  1  6
  9 19  1  0
  9 20  1  0
 10 21  1  6
M  END
Download

PDB for NP0000318 (Levoglucosan)

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0      33.131 -26.068   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      32.352 -27.396   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      32.371 -24.729   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      30.812 -27.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      30.831 -24.718   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      30.051 -26.046   0.000  0.00  0.00           C+0
HETATM    7  H   UNK     0      34.671 -26.079   0.000  0.00  0.00           H+0
HETATM    8  O   UNK     0      33.112 -28.736   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      30.032 -28.713   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      28.511 -26.035   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      30.813 -23.379   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      33.150 -23.378   0.000  0.00  0.00           O+0
CONECT    1    2    3    7   12                                             
CONECT    2    1    4    8                                                  
CONECT    3    1    5                                                       
CONECT    4    2    6    9                                                  
CONECT    5    3    6   11                                                  
CONECT    6    4    5   10                                                  
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    4                                                            
CONECT   10    6                                                            
CONECT   11    5   12                                                       
CONECT   12   11    1                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
Download

3D PDB for NP0000318 (Levoglucosan)

COMPND    HMDB0000640
HETATM    1  O1  UNL     1      -0.194  -2.487   0.504  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.276  -1.118   0.403  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.104  -0.478   0.322  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.928  -0.836   1.351  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.866   1.015   0.219  1.00  0.00           C  
HETATM    6  O3  UNL     1       2.022   1.753   0.194  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.026   1.245  -0.979  1.00  0.00           C  
HETATM    8  O4  UNL     1      -1.312   1.606  -0.637  1.00  0.00           O  
HETATM    9  C5  UNL     1      -2.047   0.448  -0.445  1.00  0.00           C  
HETATM   10  C6  UNL     1      -1.049  -0.646  -0.806  1.00  0.00           C  
HETATM   11  O5  UNL     1      -0.226   0.053  -1.710  1.00  0.00           O  
HETATM   12  H1  UNL     1      -0.538  -2.741   1.416  1.00  0.00           H  
HETATM   13  H2  UNL     1      -0.753  -0.656   1.317  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.510  -0.787  -0.686  1.00  0.00           H  
HETATM   15  H4  UNL     1       2.821  -1.075   0.943  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.298   1.293   1.151  1.00  0.00           H  
HETATM   17  H6  UNL     1       2.245   2.162   1.088  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.487   1.968  -1.639  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.467   0.334   0.552  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.814   0.426  -1.265  1.00  0.00           H  
HETATM   21  H10 UNL     1      -1.579  -1.477  -1.293  1.00  0.00           H  
CONECT    1    2   12
CONECT    2    3   10   13
CONECT    3    4    5   14
CONECT    4   15
CONECT    5    6    7   16
CONECT    6   17
CONECT    7    8   11   18
CONECT    8    9
CONECT    9   10   19   20
CONECT   10   11   21
END
Download

SMILES for NP0000318 (Levoglucosan)

[H][C@@]12OC[C@@H](O1)[C@@H](O)[C@H](O)[C@H]2O
Download

INCHI for NP0000318 (Levoglucosan)

InChI=1S/C6H10O5/c7-3-2-1-10-6(11-2)5(9)4(3)8/h2-9H,1H2/t2-,3-,4+,5-,6-/m1/s1
Download
View in JSmol
Synonyms
Chemical FormulaC6H10O5
Average Mass162.1406 Da
Monoisotopic Mass162.05282 Da
IUPAC Name(1R,2S,3S,4R,5R)-6,8-dioxabicyclo[3.2.1]octane-2,3,4-triol
Traditional Namelevoglucosan
CAS Registry Number498-07-7
SMILES
[H][C@@]12OC[C@@H](O1)[C@@H](O)[C@H](O)[C@H]2O
InChI Identifier
InChI=1S/C6H10O5/c7-3-2-1-10-6(11-2)5(9)4(3)8/h2-9H,1H2/t2-,3-,4+,5-,6-/m1/s1
InChI KeyTWNIBLMWSKIRAT-VFUOTHLCSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Agave americanaLOTUS Database
Arabidopsis thalianaKNApSAcK Database
Averrhoa carambolaKNApSAcK Database
Lotus burttiiLOTUS Database
Lotus corniculatusLOTUS Database
Salmonella entericaLOTUS Database
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oxepanes. Oxepanes are compounds containing an oxepane ring, which is a seven-member saturated aliphatic heterocycle with one oxygen and six carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassOxepanes
Sub ClassNot Available
Direct ParentOxepanes
Alternative Parents
Substituents
  • Oxepane
  • Oxane
  • Monosaccharide
  • Meta-dioxolane
  • Secondary alcohol
  • Oxacycle
  • Polyol
  • Acetal
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point183 °CNot Available
Boiling Point383.00 to 384.00 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility62.3 mg/mLNot Available
LogP-1.694 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility1600 g/LALOGPS
logP-2.2ALOGPS
logP-1.8ChemAxon
logS0.99ALOGPS
pKa (Strongest Acidic)12.21ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area79.15 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity32.41 m³·mol⁻¹ChemAxon
Polarizability14.13 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000640
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB112163
KNApSAcK IDC00007411
Chemspider ID9587432
KEGG Compound IDNot Available
BioCyc IDCPD-12923
BiGG IDNot Available
Wikipedia LinkLevoglucosan
METLIN ID5613
PubChem Compound2724705
PDB IDNot Available
ChEBI ID30997
Good Scents IDrw1149771
References
General References
  1. Migliaccio CT, Bergauff MA, Palmer CP, Jessop F, Noonan CW, Ward TJ: Urinary levoglucosan as a biomarker of wood smoke exposure: observations in a mouse model and in children. Environ Health Perspect. 2009 Jan;117(1):74-9. doi: 10.1289/ehp.11378. Epub 2008 Aug 15. [PubMed:19165390 ]
  2. Bergauff MA, Ward TJ, Noonan CW, Migliaccio CT, Simpson CD, Evanoski AR, Palmer CP: Urinary levoglucosan as a biomarker of wood smoke: results of human exposure studies. J Expo Sci Environ Epidemiol. 2010 Jun;20(4):385-92. doi: 10.1038/jes.2009.46. Epub 2009 Aug 26. [PubMed:19707249 ]
  3. Dorland L, Wadman SK, Fabery de Jonge H, Ketting D: 1,6-Anhydro-beta-D-glucopyranose (beta-glucosan), a constituent of human urine. Clin Chim Acta. 1986 Aug 30;159(1):11-6. [PubMed:3757263 ]
  4. Dixon RW, Baltzell G: Determination of levoglucosan in atmospheric aerosols using high performance liquid chromatography with aerosol charge detection. J Chromatogr A. 2006 Mar 24;1109(2):214-21. Epub 2006 Jan 31. [PubMed:16448658 ]
  5. Schkolnik G, Rudich Y: Detection and quantification of levoglucosan in atmospheric aerosols: a review. Anal Bioanal Chem. 2006 May;385(1):26-33. Epub 2005 Nov 30. [PubMed:16317539 ]