NP-MRD: Showing NP-Card for amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid (NP0158980)

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Record Information

Version

2.0

Created at

2022-09-02 16:39:30 UTC

Updated at

2022-09-02 16:39:30 UTC

NP-MRD ID

NP0158980

Secondary Accession Numbers

None

Natural Product Identification

Common Name

amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid

Description

2-Amino-2-[3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]acetic acid belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid is found in Streptomyces tendae. 2-Amino-2-[3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]acetic acid is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 34  0  0  0  0  0  0  0  0999 V2000
   -3.0861    0.0357    1.8481 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3535    0.9109    0.9230 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1843    1.2956   -0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7141    2.0370   -1.1079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4782    0.8458   -0.3437 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1010    0.1833    0.5369 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3110    0.8889   -0.3328 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5266    0.0341   -0.9911 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8906    0.1846   -0.5526 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1940    1.2325    0.2273 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4681    1.4697    0.7018 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4491    0.5590    0.3316 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6289    0.7373    0.7432 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0957   -0.4727   -0.4497 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8485   -0.6819   -0.8988 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6021   -1.6932   -1.6400 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0151   -1.3805   -0.7658 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7283   -2.0211    0.2444 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3700   -1.0957   -0.2181 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1946   -0.8473   -1.3097 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8540   -0.4506    1.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5764    0.6278    2.5698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0718    1.7979    1.5272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0777    0.9545    0.4884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5144   -0.0735    1.4294 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5180    0.2908   -2.0834 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4218    1.9517    0.5203 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6549    2.3212    1.3208 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8754   -1.1393   -0.7055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0111   -1.9597   -1.7089 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8316   -2.9952    0.0847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7406   -1.9057    0.4355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1101   -1.6422   -1.9156 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  6  1  0
  6  7  1  0
  7  8  1  0
  8 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
  2  3  1  0
  3  5  1  0
  3  4  2  0
 19  6  1  0
 15  9  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  1
  6 25  1  1
  8 26  1  6
 17 30  1  6
 18 31  1  0
 19 32  1  1
 20 33  1  0
 10 27  1  0
 11 28  1  0
 14 29  1  0
  5 24  1  0
M  END


  Mrv1533004241501152D          

 20 21  0  0  0  0            999 V2000
    0.0000   -0.0000    0.0000 N   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559   -4.0144    0.0000 O   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
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    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  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 10 16  1  0  0  0  0
 16 17  2  0  0  0  0
  2 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0158980

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(C1OC(C(O)C1O)N1C=CC(=O)NC1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N3O7/c11-4(9(17)18)7-5(15)6(16)8(20-7)13-2-1-3(14)12-10(13)19/h1-2,4-8,15-16H,11H2,(H,17,18)(H,12,14,19)

> <INCHI_KEY>
OTBZTPBBZITZBP-UHFFFAOYSA-N

> <FORMULA>
C10H13N3O7

> <MOLECULAR_WEIGHT>
287.228

> <EXACT_MASS>
287.075349771

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.09674317445864

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-2-[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

> <ALOGPS_LOGP>
-2.17

> <JCHEM_LOGP>
-5.093393399558362

> <ALOGPS_LOGS>
-0.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.714264019387182

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6034800350441407

> <JCHEM_PKA_STRONGEST_BASIC>
8.187050313723361

> <JCHEM_POLAR_SURFACE_AREA>
162.42

> <JCHEM_REFRACTIVITY>
60.053

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.13e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
amino[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  N   UNK     0       0.000  -0.000   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.580  -3.215   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.342  -5.926   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.377  -2.739   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       3.009  -5.926   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       4.540  -5.765   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.446  -7.011   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.819  -8.417   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.724  -9.663   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       3.288  -8.578   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       2.382  -7.333   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.851  -7.494   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   18                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    3    9                                                  
CONECT    9    8                                                            
CONECT   10    5   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   10   17                                                  
CONECT   17   16                                                            
CONECT   18    2   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol

Synonyms

Value	Source
2-Amino-2-[3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]acetate	Generator

Chemical Formula

C₁₀H₁₃N₃O₇

Average Mass

287.2280 Da

Monoisotopic Mass

287.07535 Da

IUPAC Name

2-amino-2-[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

Traditional Name

amino[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid

CAS Registry Number

Not Available

SMILES

NC(C1OC(C(O)C1O)N1C=CC(=O)NC1=O)C(O)=O

InChI Identifier

InChI=1S/C10H13N3O7/c11-4(9(17)18)7-5(15)6(16)8(20-7)13-2-1-3(14)12-10(13)19/h1-2,4-8,15-16H,11H2,(H,17,18)(H,12,14,19)

InChI Key

OTBZTPBBZITZBP-UHFFFAOYSA-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
Streptomyces tendae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

Not Available

Direct Parent

5'-deoxyribonucleosides

Alternative Parents

Substituents

5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
Alpha-amino acid
Alpha-amino acid or derivatives
Pyrimidone
Pyrimidine
Hydropyrimidine
Oxolane
Heteroaromatic compound
Vinylogous amide
Urea
Secondary alcohol
Amino acid or derivatives
Amino acid
Lactam
1,2-diol
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organic oxide
Organic oxygen compound
Alcohol
Organic nitrogen compound
Carbonyl group
Amine
Primary amine
Primary aliphatic amine
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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
logP	-2.2	ALOGPS
logP	-5.1	ChemAxon
logS	-0.96	ALOGPS
pKa (Strongest Acidic)	1.6	ChemAxon
pKa (Strongest Basic)	8.19	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	162.42 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	60.05 m³·mol⁻¹	ChemAxon
Polarizability	25.1 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13996426

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid (NP0158980)

MOL for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D MOL for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D SDF for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D-SDF for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

PDB for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D PDB for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

SMILES for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

INCHI for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

Structure for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)

3D Structure for NP0158980 (amino[3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]acetic acid)