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Showing NP-Card for 2-Deoxyuridine (NP0044219)

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Record Information
Version1.0
Created at2022-01-08 18:24:16 UTC
Updated at2022-01-08 18:38:42 UTC
NP-MRD IDNP0044219
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Deoxyuridine
Description2'-Desoxyuridine belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. It was first documented in 2021 (PMID: 33099678). 2'-Desoxyuridine is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0044219 (2-Deoxyuridine)


  Mrv1533004171500212D          

 16 17  0  0  0  0            999 V2000
    0.0000   -0.0000    0.0000 O   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
    0.0470   -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  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
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  2  0  0  0  0
M  END
Download

3D MOL for NP0044219 (2-Deoxyuridine)

     RDKit          3D

 28 29  0  0  0  0  0  0  0  0999 V2000
    5.2333    0.4620    0.8247 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0407    0.2741    0.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4708   -0.9738    0.6011 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1613   -1.2154    0.2283 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4524   -0.1975   -0.2611 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0965   -0.3467   -0.6725 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6705   -1.4464   -0.0593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0090   -0.8078    0.3022 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0176   -1.1860   -0.5668 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7065    0.6399    0.2195 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8179    1.4281   -0.4701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0217    1.2445    0.2049 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5548    0.8476   -0.4702 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0297    1.0159   -0.3740 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3777    2.0127   -0.8393 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2943    1.2662   -0.0183 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0308   -1.8222    0.9988 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6744   -2.1596    0.3036 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1104   -0.5153   -1.7900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8784   -2.2704   -0.7774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2746   -1.8891    0.8441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3126   -1.0657    1.3461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4097   -2.0531   -0.2533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5660    1.0689    1.2548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8729    1.1454   -1.5268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5569    2.5050   -0.4190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0378    1.8368    0.9998 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7345    2.2018   -0.1069 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11 10  1  0
 10 13  1  0
 13  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  6  5  1  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  2 16  1  0
 16 14  1  0
 14 15  2  0
  8 10  1  0
 14  5  1  0
 12 27  1  0
 11 25  1  0
 11 26  1  0
 10 24  1  1
  6 19  1  6
  7 20  1  0
  7 21  1  0
  8 22  1  1
  9 23  1  0
  4 18  1  0
  3 17  1  0
 16 28  1  0
M  END
Download

3D SDF for NP0044219 (2-Deoxyuridine)


  Mrv1533004171500212D          

 16 17  0  0  0  0            999 V2000
    0.0000   -0.0000    0.0000 O   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
    0.0470   -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  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
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0044219

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(CC1O)N1C=CC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)

> <INCHI_KEY>
MXHRCPNRJAMMIM-UHFFFAOYSA-N

> <FORMULA>
C9H12N2O5

> <MOLECULAR_WEIGHT>
228.204

> <EXACT_MASS>
228.074621494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
20.9591143541604

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-1.49

> <JCHEM_LOGP>
-1.514604078666666

> <ALOGPS_LOGS>
-0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.907903439872065

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.705729612726527

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9780835884997945

> <JCHEM_POLAR_SURFACE_AREA>
99.1

> <JCHEM_REFRACTIVITY>
51.05489999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
deoxyuridine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0044219 (2-Deoxyuridine)

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PDB for NP0044219 (2-Deoxyuridine)
HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+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  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.377  -2.739   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       3.009  -5.926   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       4.540  -5.765   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.446  -7.011   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.819  -8.417   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.724  -9.663   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0       3.288  -8.578   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.382  -7.333   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.851  -7.494   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7                                                            
CONECT    9    5   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    9   16                                                  
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

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3D PDB for NP0044219 (2-Deoxyuridine)
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SMILES for NP0044219 (2-Deoxyuridine)
OCC1OC(CC1O)N1C=CC(=O)NC1=O
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INCHI for NP0044219 (2-Deoxyuridine)
InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)
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View in JSmol
SynonymsNot Available
Chemical FormulaC9H12N2O5
Average Mass228.2040 Da
Monoisotopic Mass228.07462 Da
IUPAC Name1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namedeoxyuridine
CAS Registry NumberNot Available
SMILES
OCC1OC(CC1O)N1C=CC(=O)NC1=O
InChI Identifier
InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)
InChI KeyMXHRCPNRJAMMIM-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2022-01-08View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, experimental)Ahselim2022-01-08View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 100.72 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
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 OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomOrganic compounds  
Super ClassNucleosides, nucleotides, and analogues  
ClassPyrimidine nucleosides  
Sub ClassPyrimidine 2'-deoxyribonucleosides  
Direct ParentPyrimidine 2'-deoxyribonucleosides  
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
    • 

  • Pyrimidone
    • 

  • Hydropyrimidine
    • 

  • Pyrimidine
    • 

  • Heteroaromatic compound
    • 

  • Tetrahydrofuran
    • 

  • Vinylogous amide
    • 

  • Lactam
    • 

  • Secondary alcohol
    • 

  • Urea
    • 

  • Oxacycle
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Organic nitrogen compound
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic 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-1.5ALOGPS
logP-1.5ChemAxon
logS-0.4ALOGPS
pKa (Strongest Acidic)9.71ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area99.1 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity51.05 m³·mol⁻¹ChemAxon
Polarizability20.96 ųChemAxon
Number of Rings2ChemAxon
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 Compound640  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Taflin H, Odin E, Carlsson G, Tell R, Gustavsson B, Wettergren Y: Plasma deoxyuridine as a surrogate marker for toxicity and early clinical response in patients with metastatic colorectal cancer after 5-FU-based therapy in combination with arfolitixorin. Cancer Chemother Pharmacol. 2021 Jan;87(1):31-41. doi: 10.1007/s00280-020-04173-2. Epub 2020 Oct 24. [PubMed:33099678  ]