3D structure for 2',3'-dideoxy-3'-fluoro-urididine-5'-diphosphate (DB04068)

444503
  -OEChem-12051918323D

37 38  0     1  0  0  0  0  0999 V2000
   -3.1079    0.7933    0.8641 P   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8292   -1.5665   -0.7375 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9618    4.0708   -0.5738 F   0  0  0  0  0  0  0  0  0  0  0  0
    1.1172    1.6473    0.9166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6794    1.5452    0.9783 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7921    0.0645   -0.0081 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8241   -0.4738   -0.0992 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0047    1.7700   -0.0627 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7380    0.4372    2.1793 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9221   -4.1430    0.2056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3732   -2.3652    0.5579 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8312   -2.6244   -1.4427 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8914   -0.9943   -1.6291 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4661   -0.1014    0.1404 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8589   -2.0299    0.0976 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3147    2.6114    0.2075 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1453    3.0580   -0.9818 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2636    1.3172    0.1193 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0023    1.8551   -1.2757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9863    1.9319   -0.1956 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7774   -0.6314    0.0704 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3745   -0.9594    0.2296 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4681   -2.2906    0.2545 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8013   -2.9219    0.1852 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1156    3.4381    0.8978 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5652    3.4189   -1.8346 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1263    1.8266    0.5654 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4439    1.1358   -1.8862 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9321    2.0996   -1.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8078    1.0458   -0.8109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6106    2.6285   -0.7645 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3904   -0.5134    0.2753 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7914   -2.4308    0.0484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5935   -2.9259    0.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4240    2.5573    0.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0769   -3.0384    0.4400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2124   -3.3543   -1.9758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  2  0  0  0  0
  2  7  1  0  0  0  0
  2 11  1  0  0  0  0
  2 12  1  0  0  0  0
  2 13  2  0  0  0  0
  3 17  1  0  0  0  0
  4 16  1  0  0  0  0
  4 18  1  0  0  0  0
  5 20  1  0  0  0  0
  6 21  2  0  0  0  0
  8 35  1  0  0  0  0
 10 24  2  0  0  0  0
 11 36  1  0  0  0  0
 12 37  1  0  0  0  0
 14 18  1  0  0  0  0
 14 21  1  0  0  0  0
 14 22  1  0  0  0  0
 15 21  1  0  0  0  0
 15 24  1  0  0  0  0
 15 33  1  0  0  0  0
 16 17  1  0  0  0  0
 16 20  1  0  0  0  0
 16 25  1  0  0  0  0
 17 19  1  0  0  0  0
 17 26  1  0  0  0  0
 18 19  1  0  0  0  0
 18 27  1  0  0  0  0
 19 28  1  0  0  0  0
 19 29  1  0  0  0  0
 20 30  1  0  0  0  0
 20 31  1  0  0  0  0
 22 23  2  0  0  0  0
 22 32  1  0  0  0  0
 23 24  1  0  0  0  0
 23 34  1  0  0  0  0
M  END
> <DATABASE_ID>
DB04068

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

> <ORIGINAL_SOURCE_URL>
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WLQBZMZTRNPUDL-SHYZEUOFSA-N/SDF?record_type=3d

> <SMILES>
[H]N1C(=O)C=CN([C@H]2C[C@]([H])(F)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13FN2O10P2/c10-5-3-8(12-2-1-7(13)11-9(12)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8H,3-4H2,(H,18,19)(H,11,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

> <INCHI_KEY>
WLQBZMZTRNPUDL-SHYZEUOFSA-N

> <FORMULA>
C9H13FN2O10P2

> <MOLECULAR_WEIGHT>
390.1528

> <EXACT_MASS>
390.002945875

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
29.42648032990335

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-fluorooxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-0.40

> <JCHEM_LOGP>
-1.1688768149999993

> <ALOGPS_LOGS>
-1.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2103679912252376

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7717215182435941

> <JCHEM_PKA_STRONGEST_BASIC>
-4.273216938772873

> <JCHEM_POLAR_SURFACE_AREA>
171.93

> <JCHEM_REFRACTIVITY>
71.1086

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.13e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-{3-[4-(3-aminopropyl)piperazin-1-yl]propyl}-3-nitro-5-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzamide

> <JCHEM_VEBER_RULE>
0

$$$$

Similar Structures

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

3D structure for 2',3'-dideoxy-3'-fluoro-urididine-5'-diphosphate (DB04068)

Structure for 2',3'-dideoxy-3'-fluoro-urididine-5'-diphosphate (DB04068)