data_UPA
# 
_chem_comp.id                                    UPA 
_chem_comp.name                                  "URIDYLYL-2'-5'-PHOSPHO-ADENOSINE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H24 N7 O12 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_chem_comp.pdbx_modified_date                    2008-10-14 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        573.407 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UPA 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        11BA 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
UPA N1U    N1U  N 0 1 N N N 6.258  -15.472 14.105 1.741  -0.179 -3.972 N1U    UPA 1  
UPA C2U    C2U  C 0 1 N N N 6.009  -14.487 15.022 1.661  1.125  -4.290 C2U    UPA 2  
UPA O2U    O2U  O 0 1 N N N 5.949  -13.283 14.731 0.712  1.527  -4.935 O2U    UPA 3  
UPA N3U    N3U  N 0 1 N N N 5.851  -14.882 16.324 2.611  1.992  -3.895 N3U    UPA 4  
UPA O4U    O4U  O 0 1 N N N 5.820  -16.386 18.016 4.532  2.346  -2.826 O4U    UPA 5  
UPA C4U    C4U  C 0 1 N N N 5.947  -16.158 16.798 3.670  1.562  -3.179 C4U    UPA 6  
UPA C5U    C5U  C 0 1 N N N 6.226  -17.110 15.786 3.769  0.190  -2.842 C5U    UPA 7  
UPA C6U    C6U  C 0 1 N N N 6.357  -16.760 14.501 2.799  -0.656 -3.247 C6U    UPA 8  
UPA C5D    C5*U C 0 1 N N N 6.485  -18.071 10.490 -1.288 -0.861 -7.407 C5D    UPA 9  
UPA O5D    O5*U O 0 1 N N N 6.288  -18.781 11.712 -0.444 -1.144 -8.525 O5D    UPA 10 
UPA C4D    C4*U C 0 1 N N R 6.644  -16.564 10.804 -0.747 -1.573 -6.166 C4D    UPA 11 
UPA O4D    O4*U O 0 1 N N N 5.757  -16.158 11.918 0.565  -1.080 -5.850 O4D    UPA 12 
UPA C3D    C3*U C 0 1 N N R 8.002  -16.395 11.473 -1.651 -1.274 -4.954 C3D    UPA 13 
UPA O3D    O3*U O 0 1 N N N 8.947  -16.347 10.400 -2.203 -2.483 -4.429 O3D    UPA 14 
UPA C2D    C2*U C 0 1 N N R 7.768  -14.981 12.064 -0.700 -0.619 -3.923 C2D    UPA 15 
UPA O2D    O2*U O 0 1 N N N 7.731  -14.050 11.003 -0.971 -1.098 -2.604 O2D    UPA 16 
UPA C1D    C1*U C 0 1 N N R 6.384  -15.077 12.677 0.689  -1.099 -4.412 C1D    UPA 17 
UPA P      P    P 0 1 N N S 8.838  -13.001 10.663 -1.261 0.195  -1.690 P      UPA 18 
UPA O1P    O1P  O 0 1 N N N 8.217  -11.645 10.534 -0.074 1.079  -1.695 O1P    UPA 19 
UPA O2P    O2P  O 0 1 N N N 9.762  -13.070 11.866 -2.528 0.995  -2.279 O2P    UPA 20 
UPA O5B    O5*A O 0 1 N N N 9.552  -13.528 9.432  -1.575 -0.272 -0.182 O5B    UPA 21 
UPA C5B    C5*A C 0 1 N N N 10.362 -12.813 8.518  -1.822 0.913  0.574  C5B    UPA 22 
UPA C4B    C4*A C 0 1 N N R 11.266 -13.720 7.766  -2.129 0.537  2.025  C4B    UPA 23 
UPA O4B    O4*A O 0 1 N N N 12.178 -14.376 8.678  -1.000 -0.139 2.619  O4B    UPA 24 
UPA C3B    C3*A C 0 1 N N S 10.543 -14.899 7.062  -2.324 1.807  2.883  C3B    UPA 25 
UPA O3B    O3*A O 0 1 N N N 10.624 -14.664 5.691  -3.715 2.096  3.041  O3B    UPA 26 
UPA C2B    C2*A C 0 1 N N R 11.501 -16.116 7.321  -1.688 1.443  4.245  C2B    UPA 27 
UPA O2B    O2*A O 0 1 N N N 11.881 -16.713 6.061  -2.666 1.498  5.285  O2B    UPA 28 
UPA C1B    C1*A C 0 1 N N R 12.750 -15.409 7.829  -1.182 -0.002 4.045  C1B    UPA 29 
UPA N9A    N9A  N 0 1 Y N N 13.646 -16.193 8.698  0.091  -0.197 4.743  N9A    UPA 30 
UPA C8A    C8A  C 0 1 Y N N 13.371 -17.274 9.485  1.334  0.037  4.234  C8A    UPA 31 
UPA N7A    N7A  N 0 1 Y N N 14.361 -17.657 10.236 2.239  -0.243 5.125  N7A    UPA 32 
UPA C6A    C6A  C 0 1 Y N N 16.700 -16.640 10.367 2.093  -1.105 7.517  C6A    UPA 33 
UPA N6A    N6A  N 0 1 N N N 17.213 -17.481 11.264 3.446  -1.150 7.803  N6A    UPA 34 
UPA C5A    C5A  C 0 1 Y N N 15.375 -16.755 9.898  1.637  -0.669 6.261  C5A    UPA 35 
UPA C4A    C4A  C 0 1 Y N N 14.948 -15.842 8.972  0.252  -0.650 6.028  C4A    UPA 36 
UPA N3A    N3A  N 0 1 Y N N 15.655 -14.795 8.431  -0.571 -1.033 6.998  N3A    UPA 37 
UPA C2A    C2A  C 0 1 Y N N 16.872 -14.791 8.926  -0.099 -1.429 8.161  C2A    UPA 38 
UPA N1A    N1A  N 0 1 Y N N 17.408 -15.629 9.820  1.193  -1.469 8.425  N1A    UPA 39 
UPA H3U    H3U  H 0 1 N N N 5.641  -14.154 17.007 2.536  2.931  -4.130 H3U    UPA 40 
UPA H5U    H5U  H 0 1 N N N 6.348  -18.182 16.011 4.609  -0.172 -2.269 H5U    UPA 41 
UPA H6U    H6U  H 0 1 N N N 6.550  -17.548 13.754 2.858  -1.706 -2.999 H6U    UPA 42 
UPA H5U1   1H5U H 0 0 N N N 7.339  -18.473 9.897  -2.298 -1.214 -7.617 H5U1   UPA 43 
UPA H5U2   2H5U H 0 0 N N N 5.675  -18.267 9.749  -1.308 0.213  -7.230 H5U2   UPA 44 
UPA HOU5   5HOU H 0 0 N N N 6.190  -19.706 11.519 -0.819 -0.678 -9.284 HOU5   UPA 45 
UPA "H4U'" *H4U H 0 0 N N N 6.462  -16.001 9.858  -0.707 -2.648 -6.343 "H4U'" UPA 46 
UPA "H3U'" *H3U H 0 0 N N N 8.350  -17.156 12.209 -2.446 -0.583 -5.233 "H3U'" UPA 47 
UPA HOU3   3HOU H 0 0 N N N 9.793  -16.241 10.817 -2.784 -2.845 -5.111 HOU3   UPA 48 
UPA "H2U'" *H2U H 0 0 N N N 8.553  -14.666 12.790 -0.773 0.467  -3.963 "H2U'" UPA 49 
UPA "H1U'" *H1U H 0 0 N N N 5.949  -14.051 12.636 0.892  -2.110 -4.057 "H1U'" UPA 50 
UPA HOP2   2HOP H 0 0 N N N 10.435 -12.432 11.659 -3.278 0.385  -2.258 HOP2   UPA 51 
UPA H5A1   1H5A H 0 0 N N N 9.746  -12.188 7.829  -2.674 1.445  0.149  H5A1   UPA 52 
UPA H5A2   2H5A H 0 0 N N N 10.930 -12.000 9.026  -0.941 1.554  0.544  H5A2   UPA 53 
UPA "H4A'" *H4A H 0 0 N N N 11.755 -13.057 7.014  -3.018 -0.092 2.073  "H4A'" UPA 54 
UPA "H3A'" *H3A H 0 0 N N N 9.490  -15.041 7.401  -1.807 2.655  2.433  "H3A'" UPA 55 
UPA HOA3   3HOA H 0 0 N N N 10.181 -15.385 5.260  -3.774 2.895  3.582  HOA3   UPA 56 
UPA "H2A'" *H2A H 0 0 N N N 11.055 -16.894 7.983  -0.855 2.110  4.468  "H2A'" UPA 57 
UPA HOA2   2HOA H 0 0 N N N 12.460 -17.449 6.217  -2.986 2.410  5.320  HOA2   UPA 58 
UPA "H1A'" *H1A H 0 0 N N N 13.378 -15.112 6.957  -1.923 -0.717 4.403  "H1A'" UPA 59 
UPA H8A    H8A  H 0 1 N N N 12.405 -17.806 9.512  1.536  0.401  3.237  H8A    UPA 60 
UPA H6A1   1H6A H 0 0 N N N 18.171 -17.397 11.603 3.748  -1.450 8.675  H6A1   UPA 61 
UPA H6A2   2H6A H 0 0 N N N 17.093 -18.427 10.903 4.093  -0.886 7.130  H6A2   UPA 62 
UPA H2A    H2A  H 0 1 N N N 17.522 -13.986 8.544  -0.796 -1.733 8.928  H2A    UPA 63 
# 
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 
UPA N1U C2U    SING N N 1  
UPA N1U C6U    SING N N 2  
UPA N1U C1D    SING N N 3  
UPA C2U O2U    DOUB N N 4  
UPA C2U N3U    SING N N 5  
UPA N3U C4U    SING N N 6  
UPA N3U H3U    SING N N 7  
UPA O4U C4U    DOUB N N 8  
UPA C4U C5U    SING N N 9  
UPA C5U C6U    DOUB N N 10 
UPA C5U H5U    SING N N 11 
UPA C6U H6U    SING N N 12 
UPA C5D O5D    SING N N 13 
UPA C5D C4D    SING N N 14 
UPA C5D H5U1   SING N N 15 
UPA C5D H5U2   SING N N 16 
UPA O5D HOU5   SING N N 17 
UPA C4D O4D    SING N N 18 
UPA C4D C3D    SING N N 19 
UPA C4D "H4U'" SING N N 20 
UPA O4D C1D    SING N N 21 
UPA C3D O3D    SING N N 22 
UPA C3D C2D    SING N N 23 
UPA C3D "H3U'" SING N N 24 
UPA O3D HOU3   SING N N 25 
UPA C2D O2D    SING N N 26 
UPA C2D C1D    SING N N 27 
UPA C2D "H2U'" SING N N 28 
UPA O2D P      SING N N 29 
UPA C1D "H1U'" SING N N 30 
UPA P   O1P    DOUB N N 31 
UPA P   O2P    SING N N 32 
UPA P   O5B    SING N N 33 
UPA O2P HOP2   SING N N 34 
UPA O5B C5B    SING N N 35 
UPA C5B C4B    SING N N 36 
UPA C5B H5A1   SING N N 37 
UPA C5B H5A2   SING N N 38 
UPA C4B O4B    SING N N 39 
UPA C4B C3B    SING N N 40 
UPA C4B "H4A'" SING N N 41 
UPA O4B C1B    SING N N 42 
UPA C3B O3B    SING N N 43 
UPA C3B C2B    SING N N 44 
UPA C3B "H3A'" SING N N 45 
UPA O3B HOA3   SING N N 46 
UPA C2B O2B    SING N N 47 
UPA C2B C1B    SING N N 48 
UPA C2B "H2A'" SING N N 49 
UPA O2B HOA2   SING N N 50 
UPA C1B N9A    SING N N 51 
UPA C1B "H1A'" SING N N 52 
UPA N9A C8A    SING Y N 53 
UPA N9A C4A    SING Y N 54 
UPA C8A N7A    DOUB Y N 55 
UPA C8A H8A    SING N N 56 
UPA N7A C5A    SING Y N 57 
UPA C6A N6A    SING N N 58 
UPA C6A C5A    SING Y N 59 
UPA C6A N1A    DOUB Y N 60 
UPA N6A H6A1   SING N N 61 
UPA N6A H6A2   SING N N 62 
UPA C5A C4A    DOUB Y N 63 
UPA C4A N3A    SING Y N 64 
UPA N3A C2A    DOUB Y N 65 
UPA C2A N1A    SING Y N 66 
UPA C2A H2A    SING N N 67 
# 
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 
UPA SMILES           ACDLabs              10.04 O=C1C=CN(C(=O)N1)C5OC(CO)C(O)C5OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4O 
UPA InChI            InChI                1.02b 
;InChI=1/C19H24N7O12P/c20-15-10-16(22-5-21-15)26(6-23-10)17-13(31)11(29)8(37-17)4-35-39(33,34)38-14-12(30)7(3-27)36-18(14)25-2-1-9(28)24-19(25)32/h1-2,5-8,11-14,17-18,27,29-31H,3-4H2,(H,33,34)(H2,20,21,22)(H,24,28,32)/t7-,8-,11-,12-,13-,14-,17-,18-/m1/s1/f/h24,33H,20H2
;
UPA InChIKey         InChI                1.02b QARCCHXXGAIRFS-UUDRXOJBDX 
UPA SMILES_CANONICAL CACTVS               3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[C@@H]4[C@H](O)[C@@H](CO)O[C@H]4N5C=CC(=O)NC5=O)[C@@H](O)[C@H]3O 
UPA SMILES           CACTVS               3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[CH]4[CH](O)[CH](CO)O[CH]4N5C=CC(=O)NC5=O)[CH](O)[CH]3O 
UPA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4N5C=CC(=O)NC5=O)CO)O)O)O)N 
UPA SMILES           "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(C(OC4N5C=CC(=O)NC5=O)CO)O)O)O)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 
UPA "SYSTEMATIC NAME" ACDLabs              10.04 
"[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl hydrogen (S)-phosphate (non-preferred name)" 
UPA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [(2R,3R,4R,5R)-2-(2,4-dioxopyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate" 
# 
