Np mrd loader

Showing NP-Card for UDP-β-L-arabinofuranose (NP0339960)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2024-09-12 00:27:57 UTC
Updated at2024-09-12 00:27:57 UTC
NP-MRD IDNP0339960
Secondary Accession NumbersNone
Natural Product Identification
Common NameUDP-β-L-arabinofuranose
DescriptionUDP-β-L-arabinofuranose belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. Based on a literature review very few articles have been published on UDP-β-L-arabinofuranose.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0339960 (UDP-β-L-arabinofuranose)


  Mrv2104 05272303002D          

 34 36  0  0  0  0            999 V2000
   -1.0435   -6.4788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3291   -6.0663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0435   -7.3038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3761   -7.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4085   -7.5338    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6310   -8.5733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1461   -9.2408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4560   -8.5733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7110   -7.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9410   -9.2408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6054   -9.9945    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3591  -10.3300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8517   -9.6589    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.2699  -10.7481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7548  -11.4156    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4222  -10.9306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0873  -11.9005    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.2397  -12.0830    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9041  -12.8367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3891  -13.5041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1341  -14.2887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016  -14.7737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4690  -14.2887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2536  -14.5437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2141  -13.5041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6990  -12.8367    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016  -15.5987    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0871  -16.0112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0871  -16.8362    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016  -17.2487    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016  -18.0737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5160  -16.8362    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5160  -16.0112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2305  -15.5987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  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
  3  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 20 25  1  0  0  0  0
 22 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 27 33  1  0  0  0  0
M  CHG  2  13  -1  17  -1
M  END
Download

3D MOL for NP0339960 (UDP-β-L-arabinofuranose)

Download
3D SDF for NP0339960 (UDP-β-L-arabinofuranose)

  Mrv2104 05272303002D          

 34 36  0  0  0  0            999 V2000
   -1.0435   -6.4788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3291   -6.0663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0435   -7.3038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3761   -7.7887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4085   -7.5338    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6310   -8.5733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1461   -9.2408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4560   -8.5733    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7110   -7.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9410   -9.2408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6054   -9.9945    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3591  -10.3300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8517   -9.6589    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.2699  -10.7481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7548  -11.4156    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4222  -10.9306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0873  -11.9005    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.2397  -12.0830    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9041  -12.8367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3891  -13.5041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1341  -14.2887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016  -14.7737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4690  -14.2887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2536  -14.5437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2141  -13.5041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6990  -12.8367    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016  -15.5987    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0871  -16.0112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0871  -16.8362    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016  -17.2487    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016  -18.0737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5160  -16.8362    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5160  -16.0112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2305  -15.5987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  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
  3  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 20 25  1  0  0  0  0
 22 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 27 33  1  0  0  0  0
M  CHG  2  13  -1  17  -1
M  END
> <DATABASE_ID>
NP0339960

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OP([O-])(=O)OP([O-])(=O)OCC2OC(C(O)C2O)N2C=CC(=O)NC2=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1/C14H22N2O16P2/c17-3-5-8(19)11(22)13(30-5)31-34(26,27)32-33(24,25)28-4-6-9(20)10(21)12(29-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/p-2

> <INCHI_KEY>
QGNZSCRNMXQWNR-UHFFFAOYNA-L

> <FORMULA>
C14H20N2O16P2

> <MOLECULAR_WEIGHT>
534.261

> <EXACT_MASS>
534.029903728

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
43.11694665202627

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl ({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphonate

> <JCHEM_LOGP>
-4.366273136666667

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1763251289034224

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.732600308044126

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811597109999717

> <JCHEM_POLAR_SURFACE_AREA>
276.9699999999999

> <JCHEM_REFRACTIVITY>
98.2499

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl {[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0339960 (UDP-β-L-arabinofuranose)
Download
PDB for NP0339960 (UDP-β-L-arabinofuranose)
HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0      -1.948 -12.094   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.614 -11.324   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.948 -13.634   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.702 -14.539   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.763 -14.063   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.178 -16.004   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.273 -17.249   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.718 -16.004   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -3.194 -14.539   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -3.623 -17.249   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      -2.997 -18.656   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      -4.404 -19.283   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -1.590 -18.030   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0      -2.370 -20.063   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0      -3.276 -21.309   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0      -4.521 -20.404   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -2.030 -22.214   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0      -4.181 -22.555   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -3.554 -23.962   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.460 -25.208   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -3.984 -26.672   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -5.230 -27.578   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -6.475 -26.672   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -7.940 -27.148   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -6.000 -25.208   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -6.905 -23.962   0.000  0.00  0.00           O+0
HETATM   27  N   UNK     0      -5.230 -29.118   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      -3.896 -29.888   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.896 -31.428   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -5.230 -32.198   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -5.230 -33.738   0.000  0.00  0.00           O+0
HETATM   32  N   UNK     0      -6.563 -31.428   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      -6.563 -29.888   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -7.897 -29.118   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1                                                            
CONECT    3    1    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8    3                                                       
CONECT   10    8   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   27                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   20                                                  
CONECT   26   25                                                            
CONECT   27   22   28   33                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   34   27                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

Download
3D PDB for NP0339960 (UDP-β-L-arabinofuranose)
Download
SMILES for NP0339960 (UDP-β-L-arabinofuranose)
OCC1OC(OP([O-])(=O)OP([O-])(=O)OCC2OC(C(O)C2O)N2C=CC(=O)NC2=O)C(O)C1O
Download
INCHI for NP0339960 (UDP-β-L-arabinofuranose)
InChI=1/C14H22N2O16P2/c17-3-5-8(19)11(22)13(30-5)31-34(26,27)32-33(24,25)28-4-6-9(20)10(21)12(29-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/p-2
Download
View in JSmol
SynonymsNot Available
Chemical FormulaC14H20N2O16P2
Average Mass534.2610 Da
Monoisotopic Mass534.02990 Da
IUPAC Name3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl ({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphonate
Traditional Name3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl {[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphonate
CAS Registry NumberNot Available
SMILES
OCC1OC(OP([O-])(=O)OP([O-])(=O)OCC2OC(C(O)C2O)N2C=CC(=O)NC2=O)C(O)C1O
InChI Identifier
InChI=1/C14H22N2O16P2/c17-3-5-8(19)11(22)13(30-5)31-34(26,27)32-33(24,25)28-4-6-9(20)10(21)12(29-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/p-2
InChI KeyQGNZSCRNMXQWNR-UHFFFAOYNA-L
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.
KingdomOrganic compounds  
Super ClassNucleosides, nucleotides, and analogues  
ClassPyrimidine nucleotides  
Sub ClassPyrimidine nucleotide sugars  
Direct ParentPyrimidine nucleotide sugars  
Alternative Parents
Substituents
  • Pyrimidine nucleotide sugar
    • 

  • Pyrimidine ribonucleoside diphosphate
    • 

  • Pentose phosphate
    • 

  • Pentose-5-phosphate
    • 

  • Glycosyl compound
    • 

  • N-glycosyl compound
    • 

  • Monosaccharide phosphate
    • 

  • Organic pyrophosphate
    • 

  • Pyrimidone
    • 

  • Hydropyrimidine
    • 

  • Monosaccharide
    • 

  • Organic phosphoric acid derivative
    • 

  • Phosphoric acid ester
    • 

  • Pyrimidine
    • 

  • Alkyl phosphate
    • 

  • Vinylogous amide
    • 

  • Heteroaromatic compound
    • 

  • Tetrahydrofuran
    • 

  • Lactam
    • 

  • Urea
    • 

  • Secondary alcohol
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • Oxacycle
    • 

  • Alcohol
    • 

  • Primary alcohol
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Organooxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Organic anion
    • 

  • 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-4.4ChemAxon
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area276.97 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity98.25 m³·mol⁻¹ChemAxon
Polarizability43.12 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
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 CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References