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Showing NP-Card for (2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid (NP0266773)

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Record Information
Version2.0
Created at2022-09-08 11:20:18 UTC
Updated at2022-09-08 11:20:18 UTC
NP-MRD IDNP0266773
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid
Description(2R,3S,4S)-5-Fluoro-2,3,4-trihydroxypentanoic acid belongs to the class of organic compounds known as halogenated fatty acids. These are fatty acids with a chain that carries a halogen atom (Cl,F,I,Br). (2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid is found in Streptomyces asterosporus. Based on a literature review very few articles have been published on (2R,3S,4S)-5-Fluoro-2,3,4-trihydroxypentanoic acid.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0266773 ((2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid)


  Mrv1652309082213202D          

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

3D MOL for NP0266773 ((2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
    3.0307    1.2871   -0.1469 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2081    0.3599   -0.2683 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6355   -0.9425   -0.1737 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7909    0.6870   -0.5114 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5530    2.0414   -0.5752 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0130    0.0472    0.5940 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2605   -1.3167    0.6186 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4858    0.2229    0.4366 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1051   -0.3922    1.5278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9892   -0.4741   -0.8095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3607   -0.3655   -0.9282 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.4295   -1.3149   -0.6789 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5309    0.2633   -1.5107 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2064    2.5916   -0.0772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3160    0.4896    1.5480 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7412   -1.5627    1.4550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8157    1.2778    0.4109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6775   -1.2993    1.6060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7504   -1.5528   -0.7911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5052   -0.0471   -1.7260 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8 10  1  0
 10 11  1  0
  8  6  1  0
  6  7  1  0
  6  4  1  0
  4  5  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  9 18  1  0
  8 17  1  6
 10 19  1  0
 10 20  1  0
  6 15  1  1
  7 16  1  0
  4 13  1  6
  5 14  1  0
  3 12  1  0
M  END
Download

3D SDF for NP0266773 ((2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid)


  Mrv1652309082213202D          

 11 10  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   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
    3.1895    1.8414    0.0000 C   0  0  2  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
    3.9039    1.4289    0.0000 C   0  0  2  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
    4.6184    1.8414    0.0000 C   0  0  2  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 F   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  6  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0266773

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H9FO5/c6-1-2(7)3(8)4(9)5(10)11/h2-4,7-9H,1H2,(H,10,11)/t2-,3-,4-/m1/s1

> <INCHI_KEY>
KYSLBCRHXBZYKG-BXXZVTAOSA-N

> <FORMULA>
C5H9FO5

> <MOLECULAR_WEIGHT>
168.12

> <EXACT_MASS>
168.043401553

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.336424757587096

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid

> <JCHEM_LOGP>
-1.8883175946666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.67073313981594

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.51286310405463

> <JCHEM_PKA_STRONGEST_BASIC>
-3.658904151407219

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
30.6164

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0266773 ((2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid)

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PDB for NP0266773 ((2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid)
HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   11  F   UNK     0      11.288   3.437   0.000  0.00  0.00           F+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0266773 ((2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid)
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SMILES for NP0266773 ((2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid)
O[C@H](CF)[C@@H](O)[C@@H](O)C(O)=O
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INCHI for NP0266773 ((2r,3s,4s)-5-fluoro-2,3,4-trihydroxypentanoic acid)
InChI=1S/C5H9FO5/c6-1-2(7)3(8)4(9)5(10)11/h2-4,7-9H,1H2,(H,10,11)/t2-,3-,4-/m1/s1
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View in JSmol
Synonyms
ValueSource
(2R,3S,4S)-5-Fluoro-2,3,4-trihydroxypentanoateGenerator
Chemical FormulaC5H9FO5
Average Mass168.1200 Da
Monoisotopic Mass168.04340 Da
IUPAC Name(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid
Traditional Name(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid
CAS Registry NumberNot Available
SMILES
O[C@H](CF)[C@@H](O)[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C5H9FO5/c6-1-2(7)3(8)4(9)5(10)11/h2-4,7-9H,1H2,(H,10,11)/t2-,3-,4-/m1/s1
InChI KeyKYSLBCRHXBZYKG-BXXZVTAOSA-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
Streptomyces calvusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as halogenated fatty acids. These are fatty acids with a chain that carries a halogen atom (Cl,F,I,Br).
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty acids and conjugates  
Direct ParentHalogenated fatty acids  
Alternative Parents
Substituents
  • Short-chain hydroxy acid
    • 

  • Hydroxy fatty acid
    • 

  • Halogenated fatty acid
    • 

  • Beta-hydroxy acid
    • 

  • Monosaccharide
    • 

  • Hydroxy acid
    • 

  • Alpha-hydroxy acid
    • 

  • Secondary alcohol
    • 

  • Halohydrin
    • 

  • Fluorohydrin
    • 

  • Polyol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organofluoride
    • 

  • Organohalogen compound
    • 

  • Carbonyl group
    • 

  • Alkyl halide
    • 

  • Alkyl fluoride
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-1.9ChemAxon
pKa (Strongest Acidic)3.51ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.62 m³·mol⁻¹ChemAxon
Polarizability13.34 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 IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound122225563  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]