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Showing NP-Card for d-arabinofuranose (NP0304244)

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Record Information
Version2.0
Created at2022-09-10 19:11:59 UTC
Updated at2022-09-10 19:11:59 UTC
NP-MRD IDNP0304244
Secondary Accession NumbersNone
Natural Product Identification
Common Named-arabinofuranose
DescriptionD-arabinofuranose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. d-arabinofuranose is found in Mycoplasma bovis. d-arabinofuranose was first documented in 2019 (PMID: 31529780). Based on a literature review a small amount of articles have been published on D-arabinofuranose (PMID: 34606245) (PMID: 34048882) (PMID: 30864132) (PMID: 30553321).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0304244 (d-arabinofuranose)


  Mrv1652309102221122D          

 10 10  0  0  1  0            999 V2000
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  6  0  0  0
M  END
Download

3D MOL for NP0304244 (d-arabinofuranose)

     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
    2.8543    0.0554   -0.9658 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0067    0.1101    0.1250 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6229    0.6195   -0.2908 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0776   -0.2208   -1.2282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2903   -0.3254   -0.9621 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7953   -1.4333   -1.6036 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2564   -0.4988    0.5563 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6166   -1.6957    0.8110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2989    0.6498    0.9020 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0158    1.8487    0.9733 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4570   -0.7235   -0.8345 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8865   -0.9105    0.5434 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3695    0.8189    0.9184 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7398    1.6415   -0.6959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7591    0.6264   -1.2480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7841   -1.2805   -1.7031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2296   -0.3827    1.0209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1616   -1.6659    1.6916 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2347    0.4371    1.8607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0411    2.3299    0.1295 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  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  6
  5 15  1  1
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
Download

3D SDF for NP0304244 (d-arabinofuranose)


  Mrv1652309102221122D          

 10 10  0  0  1  0            999 V2000
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0304244

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
HMFHBZSHGGEWLO-ZRMNMSDTSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.13

> <EXACT_MASS>
150.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.66966567049113

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol

> <JCHEM_LOGP>
-2.302204276

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.899514700313038

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.30569577774193

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811390578102284

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
29.960899999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0304244 (d-arabinofuranose)

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PDB for NP0304244 (d-arabinofuranose)
HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.306   1.175   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    3   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0304244 (d-arabinofuranose)
Download
SMILES for NP0304244 (d-arabinofuranose)
OC[C@H]1OC(O)[C@@H](O)[C@@H]1O
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INCHI for NP0304244 (d-arabinofuranose)
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4+,5?/m1/s1
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View in JSmol
Synonyms
ValueSource
WURCS=2.0/1,1,0/[a122h-1x_1-4]/1/ChEBI
Chemical FormulaC5H10O5
Average Mass150.1300 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(3S,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Name(3S,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
CAS Registry NumberNot Available
SMILES
OC[C@H]1OC(O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4+,5?/m1/s1
InChI KeyHMFHBZSHGGEWLO-ZRMNMSDTSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Mycoplasmopsis bovisLOTUS Database
Chemical Taxonomy
Description 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
    • 

  • Tetrahydrofuran
    • 

  • Secondary alcohol
    • 

  • Hemiacetal
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • 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-2.3ChemAxon
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.96 m³·mol⁻¹ChemAxon
Polarizability13.67 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 ID9052560  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10877291  
PDB IDNot Available
ChEBI ID79054  
Good Scents IDNot Available
References
General References
  1. Marando VM, Kim DE, Calabretta PJ, Kraft MB, Bryson BD, Kiessling LL: Biosynthetic Glycan Labeling. J Am Chem Soc. 2021 Oct 13;143(40):16337-16342. doi: 10.1021/jacs.1c07430. Epub  2021 Oct 4. [PubMed:34606245  ] 
  2. Oliva P, Scortichini M, Dobelmann C, Jain S, Gopinatth V, Toti KS, Phung NB, Junker A, Jacobson KA: Structure-activity relationships of pyrimidine nucleotides containing a 5'-alpha,beta-methylene diphosphonate at the P2Y(6) receptor. Bioorg Med Chem Lett. 2021 Aug 1;45:128137. doi: 10.1016/j.bmcl.2021.128137. Epub  2021 May 26. [PubMed:34048882  ] 
  3. Mikhailov SN, Drenichev MS, Oslovsky VE, Kulikova IV, Herdewijn P: Synthesis of Poly(ADP-ribose) Monomer Containing 2'-O-alpha-D-Ribofuranosyl Adenosine. Curr Protoc Nucleic Acid Chem. 2019 Sep;78(1):e92. doi: 10.1002/cpnc.92. [PubMed:31529780  ] 
  4. Angala SK, Jackson M: Characterization of Arabinosyl Transfer Reactions in the Biosynthesis of Mycobacterial Cell Envelope (Lipo)Polysaccharides. Methods Mol Biol. 2019;1954:175-186. doi: 10.1007/978-1-4939-9154-9_14. [PubMed:30864132  ] 
  5. Leelayuwapan H, Ruchirawat S, Boonyarattanakalin S: Rapid synthesis and immunogenicity of mycobacterial (1-->5)-alpha-d-arabinofuranan. Carbohydr Polym. 2019 Feb 15;206:262-272. doi: 10.1016/j.carbpol.2018.10.048.  Epub 2018 Oct 24. [PubMed:30553321  ] 
  6. LOTUS database [Link]