NP-MRD: Showing NP-Card for (2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid (NP0253360)

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Record Information

Version

2.0

Created at

2022-09-07 17:12:50 UTC

Updated at

2022-09-07 17:12:50 UTC

NP-MRD ID

NP0253360

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid

Description

CHEBI:34020 Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. (2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid is found in Apis cerana. Based on a literature review very few articles have been published on CHEBI:34020.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072219122D          

 15 15  0  0  1  0            999 V2000
   -0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  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
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  0  0  0  0
  2 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0253360

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H](CN1C=C(F)C(O)=NC1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10FN3O4/c8-3-1-11(2-4(9)6(13)14)7(15)10-5(3)12/h1,4,7,15H,2,9H2,(H,10,12)(H,13,14)/t4-,7?/m0/s1

> <INCHI_KEY>
YIBVSVWKLVBIKS-LRYVRFSDSA-N

> <FORMULA>
C7H10FN3O4

> <MOLECULAR_WEIGHT>
219.172

> <EXACT_MASS>
219.065533977

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
18.417807869814247

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-3-(5-fluoro-2,4-dihydroxy-1,2-dihydropyrimidin-1-yl)propanoic acid

> <JCHEM_LOGP>
-3.28589703237485

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
4.096480642870771

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8190215948429103

> <JCHEM_PKA_STRONGEST_BASIC>
8.394423838790866

> <JCHEM_POLAR_SURFACE_AREA>
119.38000000000001

> <JCHEM_REFRACTIVITY>
46.7813

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(S)-F-willardiine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  N   UNK     0      -1.334   3.850   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    7  F   UNK     0       4.001  -0.770   0.000  0.00  0.00           F+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.334   6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10    4   12                                                  
CONECT   12   11                                                            
CONECT   13    2   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Value	Source
5-Fluorowillardiine	Kegg

Chemical Formula

C₇H₁₀FN₃O₄

Average Mass

219.1720 Da

Monoisotopic Mass

219.06553 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

N[C@@H](CN1C=C(F)C(O)=NC1O)C(O)=O

InChI Identifier

InChI=1S/C7H10FN3O4/c8-3-1-11(2-4(9)6(13)14)7(15)10-5(3)12/h1,4,7,15H,2,9H2,(H,10,12)(H,13,14)/t4-,7?/m0/s1

InChI Key

YIBVSVWKLVBIKS-LRYVRFSDSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Hydropyrimidine
1,2,3,4-tetrahydropyrimidine
Vinylogous amide
Carboxamide group
Lactam
Amino acid
Orthocarboxylic acid derivative
Secondary carboxylic acid amide
Alkanolamine
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Vinyl fluoride
Vinyl halide
Fluoroalkene
Organoheterocyclic compound
Haloalkene
Organonitrogen compound
Organofluoride
Organohalogen compound
Amine
Primary aliphatic amine
Organooxygen compound
Hydrocarbon derivative
Primary amine
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

non-proteinogenic alpha-amino acid (CHEBI:34020 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

571044

KEGG Compound ID

C13671

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

656706

PDB ID

Not Available

ChEBI ID

34020

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid (NP0253360)

MOL for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)

3D MOL for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)

3D SDF for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)

3D-SDF for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)

PDB for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)

3D PDB for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)

SMILES for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)

INCHI for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)

Structure for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)

3D Structure for NP0253360 ((2s)-2-amino-3-(5-fluoro-2,4-dihydroxy-2h-pyrimidin-1-yl)propanoic acid)