data_UP1
# 
_chem_comp.id                                    UP1 
_chem_comp.name                                  "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H23 F N2 O16 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2006-12-22 
_chem_comp.pdbx_modified_date                    2011-06-04 
_chem_comp.pdbx_ambiguous_flag                   ? 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        568.293 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UP1 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        "OpenEye/OEToolkits V1.4.2" 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
UP1 N1     N1   N 0 1 N N N -4.474 9.098  -10.661 1.969  -1.518 1.997  N1     UP1 1  
UP1 C2     C2   C 0 1 N N N -4.375 8.899  -12.150 1.579  -1.865 3.312  C2     UP1 2  
UP1 N3     N3   N 0 1 N N N -4.476 10.039 -12.973 0.214  -1.713 3.588  N3     UP1 3  
UP1 C4     C4   C 0 1 N N N -4.659 11.307 -12.408 -0.765 -1.266 2.715  C4     UP1 4  
UP1 C5     C5   C 0 1 N N N -4.733 11.390 -11.074 -0.276 -0.925 1.364  C5     UP1 5  
UP1 C6     C6   C 0 1 N N N -4.639 10.354 -10.403 1.022  -1.065 1.085  C6     UP1 6  
UP1 O2     O2   O 0 1 N N N -4.220 7.812  -12.673 2.362  -2.274 4.172  O2     UP1 7  
UP1 O4     O4   O 0 1 N N N -4.737 12.246 -13.091 -1.952 -1.149 3.003  O4     UP1 8  
UP1 "C1'"  C1*  C 0 1 N N R -4.364 7.882  -9.678  3.334  -1.624 1.571  "C1'"  UP1 9  
UP1 "C2'"  C2*  C 0 1 N N R -2.935 7.225  -9.652  3.626  -2.952 0.890  "C2'"  UP1 10 
UP1 "O2'"  O2*  O 0 1 N N N -2.865 5.872  -9.916  4.153  -3.886 1.815  "O2'"  UP1 11 
UP1 "C3'"  C3*  C 0 1 N N R -2.354 7.431  -8.396  4.651  -2.555 -0.149 "C3'"  UP1 12 
UP1 "C4'"  C4*  C 0 1 N N R -3.403 8.169  -7.653  4.128  -1.196 -0.577 "C4'"  UP1 13 
UP1 "O4'"  O4*  O 0 1 N N N -4.563 8.314  -8.375  3.606  -0.588 0.614  "O4'"  UP1 14 
UP1 "O3'"  O3*  O 0 1 N N N -1.188 8.061  -8.657  4.680  -3.456 -1.239 "O3'"  UP1 15 
UP1 "C5'"  C5*  C 0 1 N N N -3.273 8.852  -6.364  5.196  -0.303 -1.183 "C5'"  UP1 16 
UP1 "O5'"  O5*  O 0 1 N N N -2.982 10.138 -6.859  4.609  0.930  -1.558 "O5'"  UP1 17 
UP1 PA     PA   P 0 1 N N S -1.808 11.024 -6.577  5.525  2.263  -1.526 PA     UP1 18 
UP1 O1A    O1A  O 0 1 N N N -2.267 11.981 -7.417  4.850  3.540  -1.933 O1A    UP1 19 
UP1 O2A    O2A  O 0 1 N N N -0.626 10.269 -6.944  6.830  1.872  -2.398 O2A    UP1 20 
UP1 O3A    O3A  O 0 1 N N N -2.064 11.767 -5.328  6.069  2.231  -0.004 O3A    UP1 21 
UP1 PB     PB   P 0 1 N N R -1.097 11.979 -3.968  7.146  3.166  0.758  PB     UP1 22 
UP1 O1B    O1B  O 0 1 N N N 0.318  11.865 -4.215  8.536  2.845  -0.005 O1B    UP1 23 
UP1 O2B    O2B  O 0 1 N N N -1.490 13.196 -3.478  6.788  4.623  0.806  O2B    UP1 24 
UP1 O3B    O3B  O 0 1 N N N -1.373 10.795 -3.548  7.292  2.455  2.201  O3B    UP1 25 
UP1 C1     C1   C 0 1 N N R -1.821 10.349 -2.231  7.630  1.070  2.278  C1     UP1 26 
UP1 C23    C23  C 0 1 N N S -2.005 8.783  -2.303  6.982  0.514  3.540  C23    UP1 27 
UP1 C3     C3   C 0 1 N N R -3.449 8.249  -2.128  7.433  -0.909 3.842  C3     UP1 28 
UP1 C45    C45  C 0 1 N N R -4.649 9.155  -2.370  8.953  -1.018 3.777  C45    UP1 29 
UP1 C56    C56  C 0 1 N N R -4.236 10.600 -2.837  9.509  -0.420 2.480  C56    UP1 30 
UP1 C67    C67  C 0 1 N N N -5.372 11.606 -3.037  9.244  -1.257 1.227  C67    UP1 31 
UP1 F2     F2   F 0 1 N N N -1.278 8.261  -1.340  5.630  0.494  3.352  F2     UP1 32 
UP1 O3     O3   O 0 1 N N N -3.742 7.189  -2.954  7.012  -1.257 5.161  O3     UP1 33 
UP1 O45    O45  O 0 1 N N N -5.259 9.040  -1.149  9.352  -2.379 3.893  O45    UP1 34 
UP1 O5     O5   O 0 1 N N N -3.129 11.053 -1.892  9.047  0.923  2.316  O5     UP1 35 
UP1 O6     O6   O 0 1 N N N -5.274 12.844 -2.311  9.798  -0.586 0.110  O6     UP1 36 
UP1 H6     H6   H 0 1 N N N -4.721 10.608 -9.333  1.402  -0.820 0.099  H6     UP1 37 
UP1 "H1'"  H1*  H 0 1 N N N -5.124 7.150  -10.038 3.962  -1.457 2.453  "H1'"  UP1 38 
UP1 H3     H3   H 0 1 N N N -4.416 9.945  -13.987 -0.090 -1.956 4.527  H3     UP1 39 
UP1 H5     H5   H 0 1 N N N -4.874 12.331 -10.516 -0.985 -0.569 0.627  H5     UP1 40 
UP1 "H2'"  H2*  H 0 1 N N N -2.398 7.729  -10.489 2.737  -3.396 0.426  "H2'"  UP1 41 
UP1 HA     HA   H 0 1 N N N -2.002 5.475  -9.900  4.632  -3.378 2.491  HA     UP1 42 
UP1 "H3'"  H3*  H 0 1 N N N -2.076 6.556  -7.764  5.655  -2.499 0.286  "H3'"  UP1 43 
UP1 "H4'"  H4*  H 0 1 N N N -3.091 7.687  -6.697  3.306  -1.294 -1.297 "H4'"  UP1 44 
UP1 HB     HB   H 0 1 N N N -0.794 8.201  -7.804  5.403  -4.085 -1.072 HB     UP1 45 
UP1 "H5'1" 1H5* H 0 0 N N N -2.547 8.418  -5.637  5.629  -0.772 -2.072 "H5'1" UP1 46 
UP1 "H5'2" 2H5* H 0 0 N N N -4.135 8.768  -5.662  5.991  -0.109 -0.457 "H5'2" UP1 47 
UP1 H2A    H2A  H 0 1 N N N 0.119  10.831 -6.765  7.517  2.554  -2.558 H2A    UP1 48 
UP1 H1B    H1B  H 0 1 N N N 0.864  11.985 -3.447  8.713  3.273  -0.869 H1B    UP1 49 
UP1 H1     H1   H 0 1 N N N -1.084 10.597 -1.432  7.226  0.591  1.380  H1     UP1 50 
UP1 H2     H2   H 0 1 N N N -1.701 8.493  -3.336  7.169  1.169  4.399  H2     UP1 51 
UP1 H33    H33  H 0 1 N N N -3.363 8.038  -1.037  6.953  -1.623 3.163  H33    UP1 52 
UP1 H4     H4   H 0 1 N N N -5.327 8.887  -3.214  9.383  -0.485 4.634  H4     UP1 53 
UP1 HC     HC   H 0 1 N N N -4.627 6.862  -2.847  6.954  -0.428 5.661  HC     UP1 54 
UP1 H56    H56  H 0 1 N N N -3.864 10.552 -3.887  10.600 -0.365 2.576  H56    UP1 55 
UP1 HD     HD   H 0 1 N N N -6.008 9.605  -1.300  10.117 -2.392 4.489  HD     UP1 56 
UP1 H61    1H6  H 0 1 N N N -6.349 11.117 -2.812  8.170  -1.376 1.079  H61    UP1 57 
UP1 H62    2H6  H 0 1 N N N -5.496 11.819 -4.125  9.712  -2.237 1.327  H62    UP1 58 
UP1 H66    H66  H 0 1 N N N -5.979 13.468 -2.435  9.306  -0.884 -0.674 H66    UP1 59 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
UP1 N1    C2     SING N N 1  
UP1 N1    C6     SING N N 2  
UP1 N1    "C1'"  SING N N 3  
UP1 C2    N3     SING N N 4  
UP1 C2    O2     DOUB N N 5  
UP1 N3    C4     SING N N 6  
UP1 N3    H3     SING N N 7  
UP1 C4    C5     SING N N 8  
UP1 C4    O4     DOUB N N 9  
UP1 C5    C6     DOUB N N 10 
UP1 C5    H5     SING N N 11 
UP1 C6    H6     SING N N 12 
UP1 "C1'" "C2'"  SING N N 13 
UP1 "C1'" "O4'"  SING N N 14 
UP1 "C1'" "H1'"  SING N N 15 
UP1 "C2'" "O2'"  SING N N 16 
UP1 "C2'" "C3'"  SING N N 17 
UP1 "C2'" "H2'"  SING N N 18 
UP1 "O2'" HA     SING N N 19 
UP1 "C3'" "C4'"  SING N N 20 
UP1 "C3'" "O3'"  SING N N 21 
UP1 "C3'" "H3'"  SING N N 22 
UP1 "C4'" "O4'"  SING N N 23 
UP1 "C4'" "C5'"  SING N N 24 
UP1 "C4'" "H4'"  SING N N 25 
UP1 "O3'" HB     SING N N 26 
UP1 "C5'" "O5'"  SING N N 27 
UP1 "C5'" "H5'1" SING N N 28 
UP1 "C5'" "H5'2" SING N N 29 
UP1 "O5'" PA     SING N N 30 
UP1 PA    O1A    DOUB N N 31 
UP1 PA    O2A    SING N N 32 
UP1 PA    O3A    SING N N 33 
UP1 O2A   H2A    SING N N 34 
UP1 O3A   PB     SING N N 35 
UP1 PB    O1B    SING N N 36 
UP1 PB    O2B    DOUB N N 37 
UP1 PB    O3B    SING N N 38 
UP1 O1B   H1B    SING N N 39 
UP1 O3B   C1     SING N N 40 
UP1 C1    C23    SING N N 41 
UP1 C1    O5     SING N N 42 
UP1 C1    H1     SING N N 43 
UP1 C23   C3     SING N N 44 
UP1 C23   F2     SING N N 45 
UP1 C23   H2     SING N N 46 
UP1 C3    C45    SING N N 47 
UP1 C3    O3     SING N N 48 
UP1 C3    H33    SING N N 49 
UP1 C45   C56    SING N N 50 
UP1 C45   O45    SING N N 51 
UP1 C45   H4     SING N N 52 
UP1 C56   C67    SING N N 53 
UP1 C56   O5     SING N N 54 
UP1 C56   H56    SING N N 55 
UP1 C67   O6     SING N N 56 
UP1 C67   H61    SING N N 57 
UP1 C67   H62    SING N N 58 
UP1 O3    HC     SING N N 59 
UP1 O45   HD     SING N N 60 
UP1 O6    H66    SING N N 61 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
UP1 SMILES           ACDLabs              10.04 "O=P(OC1OC(C(O)C(O)C1F)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O" 
UP1 SMILES_CANONICAL CACTVS               3.341 "OC[C@H]1O[C@H](O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@H]2O)N3C=CC(=O)NC3=O)[C@@H](F)[C@H](O)[C@H]1O" 
UP1 SMILES           CACTVS               3.341 "OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](F)[CH](O)[CH]1O" 
UP1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H](C(O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@H]([C@@H]([C@H]([C@H](O3)CO)O)O)F)O)O" 
UP1 SMILES           "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)F)O)O" 
UP1 InChI            InChI                1.03  
"InChI=1S/C15H23FN2O16P2/c16-8-11(23)9(21)5(3-19)32-14(8)33-36(28,29)34-35(26,27)30-4-6-10(22)12(24)13(31-6)18-2-1-7(20)17-15(18)25/h1-2,5-6,8-14,19,21-24H,3-4H2,(H,26,27)(H,28,29)(H,17,20,25)/t5-,6-,8+,9+,10+,11+,12-,13-,14-/m1/s1" 
UP1 InChIKey         InChI                1.03  NGTCPFGWXMBZEP-ASADWNOXSA-N 
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
UP1 "SYSTEMATIC NAME" ACDLabs              10.04 
"[(2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5R,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" 
UP1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3S,4R,5R,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-hydroxy-phosphoryl] hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
UP1 "Create component"  2006-12-22 PDBJ 
UP1 "Modify descriptor" 2011-06-04 RCSB 
# 
