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 2011-06-04 _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 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" UPA InChI InChI 1.03 "InChI=1S/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" UPA InChIKey InChI 1.03 QARCCHXXGAIRFS-KPKSGTNCSA-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" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UPA "Create component" 1999-07-08 RCSB UPA "Modify descriptor" 2011-06-04 RCSB #