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Showing NP-Card for L-Rhamnulose (NP0062929)

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Record Information
Version2.0
Created at2022-04-28 07:27:14 UTC
Updated at2022-04-28 07:27:14 UTC
NP-MRD IDNP0062929
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-Rhamnulose
DescriptionL-rhamnulose belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms. L-Rhamnulose is found in Escherichia coli. L-Rhamnulose was first documented in 2020 (PMID: 31874684). L-rhamnulose is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 32912675) (PMID: 32533303) (PMID: 32249029) (PMID: 31874042).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0062929 (L-Rhamnulose)


  Mrv1652309152021512D          

 11 10  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    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  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  9  1  6  0  0  0
  3 10  1  6  0  0  0
  2 11  1  1  0  0  0
M  END
Download

3D MOL for NP0062929 (L-Rhamnulose)

     RDKit          3D

 23 22  0  0  0  0  0  0  0  0999 V2000
   -1.8120    1.0510    0.6669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5904   -0.1775   -0.1705 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2910   -1.2807    0.6256 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6140    0.0158   -1.2847 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6365   -1.1262   -2.0853 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7844    0.3149   -0.8342 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9104    1.4153   -0.0443 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4544   -0.8470   -0.2120 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4555   -1.9505   -0.7728 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1280   -0.6819    1.0936 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9975    0.6238    1.5235 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9880    1.3213    1.3159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7200    0.8383    1.3031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0599    1.9215    0.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5770   -0.4101   -0.6505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1452   -1.5178    1.1042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9891    0.8476   -1.9166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0236   -1.9138   -1.6183 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3703    0.4921   -1.7906 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7541    2.2604   -0.5683 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5583   -1.2973    1.8570 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1918   -1.0123    1.0616 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8420    1.1130    1.3671 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  6
  3 16  1  0
  4 17  1  6
  5 18  1  0
  6 19  1  6
  7 20  1  0
 10 21  1  0
 10 22  1  0
 11 23  1  0
M  END
Download

3D SDF for NP0062929 (L-Rhamnulose)


  Mrv1652309152021512D          

 11 10  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    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  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  9  1  6  0  0  0
  3 10  1  6  0  0  0
  2 11  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0062929

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h3,5-8,10-11H,2H2,1H3/t3-,5-,6-/m0/s1

> <INCHI_KEY>
QZNPNKJXABGCRC-FUTKDDECSA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.157

> <EXACT_MASS>
164.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.480513944227456

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5S)-1,3,4,5-tetrahydroxyhexan-2-one

> <ALOGPS_LOGP>
-1.79

> <JCHEM_LOGP>
-2.2201219253333333

> <ALOGPS_LOGS>
0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.868998423237066

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.471629095473586

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0542936306726167

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
36.0181

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.88e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4S,5S)-1,3,4,5-tetrahydroxyhexan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0062929 (L-Rhamnulose)

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PDB for NP0062929 (L-Rhamnulose)
HEADER    PROTEIN                                 15-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-SEP-20         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7                                                            
CONECT    9    4                                                            
CONECT   10    3                                                            
CONECT   11    2                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0062929 (L-Rhamnulose)
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SMILES for NP0062929 (L-Rhamnulose)
C[C@H](O)[C@H](O)[C@@H](O)C(=O)CO
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INCHI for NP0062929 (L-Rhamnulose)
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h3,5-8,10-11H,2H2,1H3/t3-,5-,6-/m0/s1
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View in JSmol
Synonyms
ValueSource
6-Deoxy-L-arabino-hex-2-uloseChEBI
6-Deoxy-L-fructoseKegg
Chemical FormulaC6H12O5
Average Mass164.1570 Da
Monoisotopic Mass164.06847 Da
IUPAC Name(3R,4S,5S)-1,3,4,5-tetrahydroxyhexan-2-one
Traditional Name(3R,4S,5S)-1,3,4,5-tetrahydroxyhexan-2-one
CAS Registry NumberNot Available
SMILES
C[C@H](O)[C@H](O)[C@@H](O)C(=O)CO
InChI Identifier
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h3,5-8,10-11H,2H2,1H3/t3-,5-,6-/m0/s1
InChI KeyQZNPNKJXABGCRC-FUTKDDECSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Escherichia coliBacteria
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty alcohols  
Direct ParentFatty alcohols  
Alternative Parents
Substituents
  • Fatty alcohol
    • 

  • Acyloin
    • 

  • Beta-hydroxy ketone
    • 

  • Monosaccharide
    • 

  • Alpha-hydroxy ketone
    • 

  • Ketone
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-1.8ALOGPS
logP-2.2ChemAxon
logS0.37ALOGPS
pKa (Strongest Acidic)10.47ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity36.02 m³·mol⁻¹ChemAxon
Polarizability15.48 ųChemAxon
Number of Rings0ChemAxon
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 IDC00019652  
Chemspider ID28532985  
KEGG Compound IDC00861  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14461866  
PDB IDNot Available
ChEBI ID17897  
Good Scents IDNot Available
References
General References
  1. Chen Z, Li Z, Li F, Wang M, Wang N, Gao XD: Cascade synthesis of rare ketoses by whole cells based on L-rhamnulose-1-phosphate aldolase. Enzyme Microb Technol. 2020 Feb;133:109456. doi: 10.1016/j.enzmictec.2019.109456. Epub 2019 Oct 24. [PubMed:31874684  ] 
  2. Ju X, Xu X, Shen M, Mo X, Fan H, Li L: Biochemical and structural insights into an Ochrobactrum sp. CSL1 ribose-5-phosphate isomerase A and its roles in isomerization of rare sugars. Enzyme Microb Technol. 2020 Oct;140:109604. doi: 10.1016/j.enzmictec.2020.109604. Epub 2020 May 26. [PubMed:32912675  ] 
  3. Chen J, Wu H, Zhang W, Mu W: Ribose-5-phosphate isomerases: characteristics, structural features, and applications. Appl Microbiol Biotechnol. 2020 Aug;104(15):6429-6441. doi: 10.1007/s00253-020-10735-4. Epub 2020 Jun 12. [PubMed:32533303  ] 
  4. Chen Z, Li Z, Li F, Wang N, Gao XD: Characterization of alditol oxidase from Streptomyces coelicolor and its application in the production of rare sugars. Bioorg Med Chem. 2020 May 15;28(10):115464. doi: 10.1016/j.bmc.2020.115464. Epub  2020 Mar 29. [PubMed:32249029  ] 
  5. Du M, Zhou K, Wang X, Zhang J, Zhang Y, Dong J, Wu L, Qiao Z, Chen G, Wang Q: Precise Fabrication of De Novo Nanoparticle Lattices on Dynamic 2D Protein Crystalline Lattices. Nano Lett. 2020 Feb 12;20(2):1154-1160. doi: 10.1021/acs.nanolett.9b04574. Epub 2019 Dec 30. [PubMed:31874042  ]