Np mrd loader

Showing NP-Card for D-(+)-Xylose (NP0002603)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2020-11-23 18:25:03 UTC
Updated at2021-08-12 19:51:38 UTC
NP-MRD IDNP0002603
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-(+)-Xylose
Provided ByBMRBBMRB logo
DescriptionAlpha-D-Xylopyranose is also known as α-D-xylopyranose. Alpha-D-Xylopyranose exists in all living organisms, ranging from bacteria to humans. Alpha-D-Xylopyranose is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. D-(+)-Xylose is found in Chlamydomonas reinhardtii, Citrobacter freundii, Primula veris and Prunus avium. D-(+)-Xylose was first documented in 2016 (PMID: 27474598). Based on a literature review a small amount of articles have been published on alpha-D-Xylopyranose (PMID: 33445012) (PMID: 29393398) (PMID: 26755723).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002603 (D-(+)-Xylose)


     RDKit          2D

 20 20  0  0  0  0  0  0  0  0999 V2000
    2.6428   -1.7581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6111   -0.6693    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7180   -1.8744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7722   -1.7035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3693   -0.3275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4011    0.7613    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4762    0.8776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0491    2.3155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0140    0.7067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4728    1.0558    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2157   -3.1961    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8626    0.1577    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6818   -3.2008    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2311   -2.0526    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6208   -1.1545    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8599    0.4122    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8181    1.5479    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0809    3.4044    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9235    2.2040    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8999    2.4937    0.0000 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  2 12  1  6
  4 13  1  6
  4 14  1  0
  5 15  1  6
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
M  END
Download

3D MOL for NP0002603 (D-(+)-Xylose)

NP0002603
     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
    2.5781   -0.0855    0.8368 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4317   -0.5127    0.1367 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6732   -1.2725    1.0009 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4552   -1.7044    0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3914   -0.4988    0.2601 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9950   -0.4228    1.5094 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7174    0.7527   -0.1694 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3579    1.2835   -1.3124 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7293    0.6339   -0.4809 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3532    1.8325   -0.0571 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9876    0.6092    0.2356 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7982   -1.2148   -0.6649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2019   -2.0493   -0.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9786   -2.5261    0.8026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1949   -0.7589   -0.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9689    0.4661    1.9150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8941    1.5244    0.6304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0245    0.7259   -2.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8972    0.6299   -1.5977 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7313    2.5877   -0.0595 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  2 12  1  6
  4 13  1  0
  4 14  1  0
  5 15  1  6
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
M  END
Download

3D SDF for NP0002603 (D-(+)-Xylose)


     RDKit          2D

 20 20  0  0  0  0  0  0  0  0999 V2000
    2.6428   -1.7581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6111   -0.6693    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7180   -1.8744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7722   -1.7035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3693   -0.3275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4011    0.7613    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4762    0.8776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0491    2.3155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0140    0.7067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4728    1.0558    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2157   -3.1961    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8626    0.1577    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6818   -3.2008    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2311   -2.0526    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6208   -1.1545    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8599    0.4122    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8181    1.5479    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0809    3.4044    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9235    2.2040    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8999    2.4937    0.0000 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  2 12  1  6
  4 13  1  6
  4 14  1  0
  5 15  1  6
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
M  END
> <DATABASE_ID>
NP0002603

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5+/m1/s1

> <INCHI_KEY>
SRBFZHDQGSBBOR-LECHCGJUSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
13.184993960607123

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.57

> <JCHEM_LOGP>
-2.302204276

> <ALOGPS_LOGS>
0.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.786263151759016

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.310624247742409

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265718350182684

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
29.9609

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.22e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-D-xylose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002603 (D-(+)-Xylose)

NP0002603
     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
    2.5781   -0.0855    0.8368 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4317   -0.5127    0.1367 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6732   -1.2725    1.0009 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4552   -1.7044    0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3914   -0.4988    0.2601 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9950   -0.4228    1.5094 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7174    0.7527   -0.1694 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3579    1.2835   -1.3124 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7293    0.6339   -0.4809 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3532    1.8325   -0.0571 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9876    0.6092    0.2356 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7982   -1.2148   -0.6649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2019   -2.0493   -0.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9786   -2.5261    0.8026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1949   -0.7589   -0.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9689    0.4661    1.9150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8941    1.5244    0.6304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0245    0.7259   -2.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8972    0.6299   -1.5977 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7313    2.5877   -0.0595 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  2 12  1  6
  4 13  1  0
  4 14  1  0
  5 15  1  6
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
M  END
Download

PDB for NP0002603 (D-(+)-Xylose)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    2   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
Download

3D PDB for NP0002603 (D-(+)-Xylose)

COMPND    NP0002603
HETATM    1  O1  UNL     1       2.578  -0.085   0.837  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.432  -0.513   0.137  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.673  -1.272   1.001  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.455  -1.704   0.287  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.391  -0.499   0.260  1.00  0.00           C  
HETATM    6  O3  UNL     1      -1.995  -0.423   1.509  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.717   0.753  -0.169  1.00  0.00           C  
HETATM    8  O4  UNL     1      -1.358   1.284  -1.312  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.729   0.634  -0.481  1.00  0.00           C  
HETATM   10  O5  UNL     1       1.353   1.832  -0.057  1.00  0.00           O  
HETATM   11  H1  UNL     1       2.988   0.609   0.236  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.798  -1.215  -0.665  1.00  0.00           H  
HETATM   13  H3  UNL     1      -0.202  -2.049  -0.730  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.979  -2.526   0.803  1.00  0.00           H  
HETATM   15  H5  UNL     1      -2.195  -0.759  -0.463  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.969   0.466   1.915  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.894   1.524   0.630  1.00  0.00           H  
HETATM   18  H8  UNL     1      -1.024   0.726  -2.079  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.897   0.630  -1.598  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.731   2.588  -0.060  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3    9   12
CONECT    3    4
CONECT    4    5   13   14
CONECT    5    6    7   15
CONECT    6   16
CONECT    7    8    9   17
CONECT    8   18
CONECT    9   10   19
CONECT   10   20
END
Download

SMILES for NP0002603 (D-(+)-Xylose)

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

INCHI for NP0002603 (D-(+)-Xylose)

InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5+/m1/s1
Download
View in JSmol
Synonyms
ValueSource
WURCS=2.0/1,1,0/[a212h-1a_1-5]/1/ChEBI
a-D-XylopyranoseGenerator
Α-D-xylopyranoseGenerator
a-D-XyloseGenerator
Α-D-xyloseGenerator
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(2S,3R,4S,5R)-oxane-2,3,4,5-tetrol
Traditional Nameα-D-xylose
CAS Registry NumberNot Available
SMILES
O[C@@H]1CO[C@H](O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5+/m1/s1
InChI KeySRBFZHDQGSBBOR-LECHCGJUSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Chlamydomonas reinhardtiiLOTUS Database
Citrobacter freundiiLOTUS Database
Primula verisLOTUS Database
Prunus aviumLOTUS Database
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
  • Oxane
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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-2.6ALOGPS
logP-2.3ChemAxon
logS0.91ALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.96 m³·mol⁻¹ChemAxon
Polarizability13.18 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0062082
DrugBank IDDB03389
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID5805
KEGG Compound IDC02205
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID28518
Good Scents IDNot Available
References
General References
  1. Kant Bhatia S, Gurav R, Choi YK, Choi TR, Kim HJ, Song HS, Mi Lee S, Lee Park S, Soo Lee H, Kim YG, Ahn J, Yang YH: Bioprospecting of exopolysaccharide from marine Sphingobium yanoikuyae BBL01: Production, characterization, and metal chelation activity. Bioresour Technol. 2021 Mar;324:124674. doi: 10.1016/j.biortech.2021.124674. Epub 2021 Jan 7. [PubMed:33445012 ]
  2. Zhao D, Ding X, Hou Y, Hou W, Liu L, Xu T, Yang D: Structural characterization, immune regulation and antioxidant activity of a new heteropolysaccharide from Cantharellus cibarius Fr. Int J Mol Med. 2018 May;41(5):2744-2754. doi: 10.3892/ijmm.2018.3450. Epub 2018 Feb 1. [PubMed:29393398 ]
  3. Ding HH, Cui SW, Goff HD, Chen J, Guo Q, Wang Q: Xyloglucans from flaxseed kernel cell wall: Structural and conformational characterisation. Carbohydr Polym. 2016 Oct 20;151:538-545. doi: 10.1016/j.carbpol.2016.05.094. Epub 2016 May 27. [PubMed:27474598 ]
  4. Matsuzawa T, Mitsuishi Y, Kameyama A, Yaoi K: Identification of the Gene Encoding Isoprimeverose-producing Oligoxyloglucan Hydrolase in Aspergillus oryzae. J Biol Chem. 2016 Mar 4;291(10):5080-7. doi: 10.1074/jbc.M115.701474. Epub 2016 Jan 11. [PubMed:26755723 ]