NP-MRD: Showing NP-Card for 5-Arabinofuranosyl-hydroxy-dC (NP0351009)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2025-05-10 09:45:22 UTC

Updated at

2025-07-30 22:43:59 UTC

NP-MRD ID

NP0351009

Natural Product DOI

https://doi.org/10.57994/3996

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-Arabinofuranosyl-hydroxy-dC

Description

Based on a literature review very few articles have been published on 5-Arabinofuranosyl-hydroxy-dC.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02202312112D          

 28 30  0  0  1  0            999 V2000
    0.7145   -1.2375    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
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4496   -0.8630    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1830   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1526   -3.9282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -2.5070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6119   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819   -1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9653   -2.3058    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1665   -1.4675    0.0000 O   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 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0470    2.5474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    3.3320    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830    3.9995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    3.3320    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6119    3.9995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763    4.7532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.5474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    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
    2.1434    1.2375    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
  5  4  1  1  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  8  7  1  0  0  0  0
  8  9  1  6  0  0  0
  9 10  1  0  0  0  0
 11  8  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13  5  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  6  0  0  0
  3 16  2  0  0  0  0
 16 17  1  0  0  0  0
 18 17  1  1  0  0  0
 18 19  1  0  0  0  0
 20 19  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 22 25  1  0  0  0  0
 18 25  1  0  0  0  0
  2 26  2  0  0  0  0
 26 27  1  0  0  0  0
 17 27  1  0  0  0  0
 27 28  2  0  0  0  0
M  END


  Mrv2104 02202312112D          

 28 30  0  0  1  0            999 V2000
    0.7145   -1.2375    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
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4496   -0.8630    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0470   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1830   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1526   -3.9282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -2.5070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6119   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819   -1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9653   -2.3058    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1665   -1.4675    0.0000 O   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 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0470    2.5474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    3.3320    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830    3.9995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    3.3320    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6119    3.9995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763    4.7532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.5474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    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
    2.1434    1.2375    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
  5  4  1  1  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  8  7  1  0  0  0  0
  8  9  1  6  0  0  0
  9 10  1  0  0  0  0
 11  8  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13  5  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  6  0  0  0
  3 16  2  0  0  0  0
 16 17  1  0  0  0  0
 18 17  1  1  0  0  0
 18 19  1  0  0  0  0
 20 19  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 22 25  1  0  0  0  0
 18 25  1  0  0  0  0
  2 26  2  0  0  0  0
 26 27  1  0  0  0  0
 17 27  1  0  0  0  0
 27 28  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0351009

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(O)[C@H](O)[C@@H](CO)O[C@]1([H])OC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N=C1N

> <INCHI_IDENTIFIER>
InChI=1S/C14H21N3O9/c15-12-6(25-13-11(22)10(21)8(4-19)26-13)2-17(14(23)16-12)9-1-5(20)7(3-18)24-9/h2,5,7-11,13,18-22H,1,3-4H2,(H2,15,16,23)/t5-,7+,8+,9+,10+,11-,13-/m0/s1

> <INCHI_KEY>
BXPFMEDJPMIQSX-GCEXDXCZSA-N

> <FORMULA>
C14H21N3O9

> <MOLECULAR_WEIGHT>
375.334

> <EXACT_MASS>
375.127779268

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
34.81702600155103

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-5-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

> <JCHEM_LOGP>
-3.8145033873333336

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.567423059443481

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.254501808547513

> <JCHEM_PKA_STRONGEST_BASIC>
2.8588473896099784

> <JCHEM_POLAR_SURFACE_AREA>
187.52999999999997

> <JCHEM_REFRACTIVITY>
81.4523

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-5-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-FEB-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-FEB-23         0                                  
HETATM    1  N   UNK     0       1.334  -2.310   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      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0      -2.706  -1.611   0.000  0.00  0.00           H+0
HETATM    7  O   UNK     0      -0.088  -3.215   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.342  -5.926   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.285  -7.333   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.104  -4.680   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -3.009  -5.926   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.580  -3.215   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0      -3.669  -4.304   0.000  0.00  0.00           H+0
HETATM   15  O   UNK     0      -4.044  -2.739   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.088   4.755   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.564   6.220   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.342   7.466   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.104   6.220   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.009   7.466   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.382   8.873   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       2.580   4.755   0.000  0.00  0.00           O+0
HETATM   26  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4   16                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7   13                                             
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    5   14   15                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16    3   17                                                       
CONECT   17   16   18   27                                                  
CONECT   18   17   19   25                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   22   18                                                       
CONECT   26    2   27                                                       
CONECT   27   26   17   28                                                  
CONECT   28   27                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   60    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₂₁N₃O₉

Average Mass

375.3340 Da

Monoisotopic Mass

375.12778 Da

IUPAC Name

4-amino-5-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

4-amino-5-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)[C@H](O)[C@@H](CO)O[C@]1([H])OC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N=C1N

InChI Identifier

InChI=1S/C14H21N3O9/c15-12-6(25-13-11(22)10(21)8(4-19)26-13)2-17(14(23)16-12)9-1-5(20)7(3-18)24-9/h2,5,7-11,13,18-22H,1,3-4H2,(H2,15,16,23)/t5-,7+,8+,9+,10+,11-,13-/m0/s1

InChI Key

BXPFMEDJPMIQSX-GCEXDXCZSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	seetharamsing.b@ntu.edu.sg	Nanyang Technological University	Balamkundu Seetharamsing	2025-05-10	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	seetharamsing.b@ntu.edu.sg	Nanyang Technological University	Balamkundu Seetharamsing	2025-05-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	seetharamsing.b@ntu.edu.sg	Nanyang Technological University	Balamkundu Seetharamsing	2025-05-10	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	seetharamsing.b@ntu.edu.sg	Nanyang Technological University	Balamkundu Seetharamsing	2025-05-10	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	seetharamsing.b@ntu.edu.sg	Nanyang Technological University	Balamkundu Seetharamsing	2025-05-10	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Winklervirus unclassified Winklervirus		Not Available

Chemical Taxonomy

Classification

Not classified

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	-3.8	ChemAxon
pKa (Strongest Acidic)	12.25	ChemAxon
pKa (Strongest Basic)	2.86	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	187.53 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	81.45 m³·mol⁻¹	ChemAxon
Polarizability	34.82 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 5-Arabinofuranosyl-hydroxy-dC (NP0351009)

MOL for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)

3D MOL for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)

3D SDF for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)

3D-SDF for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)

PDB for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)

3D PDB for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)

SMILES for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)

INCHI for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)

Structure for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)

3D Structure for NP0351009 (5-Arabinofuranosyl-hydroxy-dC)