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Showing NP-Card for L-Xylulose (NP0341782)

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Record Information
Version2.0
Created at2024-09-12 10:50:38 UTC
Updated at2024-09-25 12:06:52 UTC
NP-MRD IDNP0341782
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-Xylulose
Description It was first documented in 2022 (PMID: 36275448). Based on a literature review a significant number of articles have been published on L-Xylulose (PMID: 38775624) (PMID: 38473992) (PMID: 36562355) (PMID: 36172018).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0341782 (L-Xylulose)


  Mrv2104 05272313222D          

 10 10  0  0  0  0            999 V2000
10000.779010000.8748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.494010000.4635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.6963 9999.9316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.2705 9999.0121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.4758 9999.0204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.389710000.9566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.722310000.4716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9772 9999.6870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.8022 9999.6870    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.057110000.4716    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10  3  1  6  0  0  0
  9  4  1  6  0  0  0
  8  5  1  1  0  0  0
M  END
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3D MOL for NP0341782 (L-Xylulose)

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3D SDF for NP0341782 (L-Xylulose)

  Mrv2104 05272313222D          

 10 10  0  0  0  0            999 V2000
10000.779010000.8748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.494010000.4635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.6963 9999.9316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.2705 9999.0121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.4758 9999.0204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.389710000.9566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.722310000.4716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9772 9999.6870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.8022 9999.6870    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.057110000.4716    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10  3  1  6  0  0  0
  9  4  1  6  0  0  0
  8  5  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0341782

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4+,5-/s2

> <INCHI_KEY>
LQXVFWRQNMEDEE-HWYZPOORNA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.13

> <EXACT_MASS>
150.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.605708079715683

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol

> <JCHEM_LOGP>
-2.1276643760000002

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.844123223152558

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.292639879315793

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4506959694674992

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
30.3983

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0341782 (L-Xylulose)
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PDB for NP0341782 (L-Xylulose)
HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0    8668.1218668.300   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8669.4558667.532   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8667.9668666.539   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8667.1728664.823   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8663.8218664.838   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8665.5278668.452   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8664.2828667.547   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8664.7578666.082   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8666.2978666.082   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8666.7738667.547   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1                                                            
CONECT    3   10                                                            
CONECT    4    9                                                            
CONECT    5    8                                                            
CONECT    6    7   10                                                       
CONECT    7    8    6                                                       
CONECT    8    7    9    5                                                  
CONECT    9    8   10    4                                                  
CONECT   10    9    6    1    3                                             
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0341782 (L-Xylulose)
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SMILES for NP0341782 (L-Xylulose)
OC[C@]1(O)OC[C@H](O)[C@H]1O
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INCHI for NP0341782 (L-Xylulose)
InChI=1/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4+,5-/s2
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View in JSmol
SynonymsNot Available
Chemical FormulaC5H10O5
Average Mass150.1300 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(2S,3R,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Name(2S,3R,4S)-2-(hydroxymethyl)oxolane-2,3,4-triol
CAS Registry NumberNot Available
SMILES
OC[C@]1(O)OC[C@H](O)[C@H]1O
InChI Identifier
InChI=1/C5H10O5/c6-2-5(9)4(8)3(7)1-10-5/h3-4,6-9H,1-2H2/t3-,4+,5-/s2
InChI KeyLQXVFWRQNMEDEE-HWYZPOORNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentPentoses  
Alternative Parents
Substituents
  • Pentose monosaccharide
    • 

  • Oxolane
    • 

  • Secondary alcohol
    • 

  • Hemiacetal
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.1ChemAxon
pKa (Strongest Acidic)10.29ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity30.4 m³·mol⁻¹ChemAxon
Polarizability13.61 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkXylulose  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Merignac-Lacombe J, Kornbausch N, Sivarajan R, Boichot V, Berg K, Oberwinkler H, Saliba AE, Loos HM, Ehret Kasemo T, Scherzad A, Bodem J, Buettner A, Neiers F, Erhard F, Hackenberg S, Heydel JM, Steinke M: Characterization of a Human Respiratory Mucosa Model to Study Odorant Metabolism. J Agric Food Chem. 2024 Jun 5;72(22):12696-12706. doi: 10.1021/acs.jafc.4c00752.  Epub 2024 May 22. [PubMed:38775624  ] 
  2. Patel SKS, Gupta RK, Karuppanan KK, Kim IW, Lee JK: Sequential Co-Immobilization of Enzymes on Magnetic Nanoparticles for Efficient l-Xylulose Production. Int J Mol Sci. 2024 Feb 27;25(5):2746. doi: 10.3390/ijms25052746. [PubMed:38473992  ] 
  3. Jin Y, Zhang M, Tong Y, Qiu L, Ye Y, Zhao B: DCXR promotes cell proliferation by promoting the activity of aerobic glycolysis in breast cancer. Mol Med Rep. 2023 Feb;27(2):31. doi: 10.3892/mmr.2022.12918. Epub 2022 Dec 23. [PubMed:36562355  ] 
  4. Kim YN, Kim SH, Son LT, Ahnn J, Lee SK: Dicarbonyl/L-xylulose reductase (DCXR) producing xylitol regulates egg retention through osmolality control in Caenorhabditis elegans. Anim Cells Syst (Seoul). 2022 Oct 6;26(5):223-231. doi:  10.1080/19768354.2022.2126886. eCollection 2022. [PubMed:36275448  ] 
  5. Kumar A, Li J, Kondaveeti S, Singh B, Shanmugam R, Kalia VC, Kim IW, Lee JK: Characterization of a xylitol dehydrogenase from Aspergillus flavus and its application in l-xylulose production. Front Bioeng Biotechnol. 2022 Sep 12;10:1001726. doi: 10.3389/fbioe.2022.1001726.  eCollection 2022. [PubMed:36172018  ]