data_UD0 # _chem_comp.id UD0 _chem_comp.name ;(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(S)-{[(S)-{[(2S,3R,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H34 N5 O22 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-07-13 _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 849.479 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UD0 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 3NUB _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 UD0 P P P 0 1 N N N -20.215 -59.242 16.852 1.311 -5.851 -0.160 P UD0 1 UD0 C1 C1 C 0 1 N N R -15.000 -63.403 13.558 2.901 3.455 -0.236 C1 UD0 2 UD0 N1 N1 N 0 1 Y N N -19.684 -63.885 20.966 6.689 -4.341 -0.416 N1 UD0 3 UD0 O1 O1 O 0 1 N N N -14.813 -61.954 13.463 3.269 4.023 1.023 O1 UD0 4 UD0 C2 C2 C 0 1 N N R -15.648 -63.876 14.868 3.792 2.245 -0.528 C2 UD0 5 UD0 C3 C3 C 0 1 N N R -16.992 -63.162 15.147 3.652 1.231 0.612 C3 UD0 6 UD0 C4 C4 C 0 1 N N S -16.960 -61.642 14.909 4.012 1.913 1.935 C4 UD0 7 UD0 C5 C5 C 0 1 N N S -15.951 -61.098 13.868 3.112 3.136 2.132 C5 UD0 8 UD0 C6 C6 C 0 1 N N N -15.452 -59.761 14.464 3.500 3.846 3.403 C6 UD0 9 UD0 PA PA P 0 1 N N N -15.191 -64.654 11.110 0.312 4.004 -0.603 PA UD0 10 UD0 PB PB P 0 1 N N N -12.653 -65.767 10.458 -2.522 3.383 -1.212 PB UD0 11 UD0 "C1'" "C1'" C 0 1 Y N N -19.309 -64.868 20.125 7.200 -3.133 -0.294 "C1'" UD0 12 UD0 "O1'" "O1'" O 0 1 N N N -18.580 -65.540 17.938 6.915 -0.791 0.053 "O1'" UD0 13 UD0 "C1'A" C1* C 0 0 N N R -12.404 -65.910 5.076 -6.573 -0.454 -0.416 C1* UD0 14 UD0 C1A C1A C 0 1 N N N -19.287 -66.311 20.639 8.692 -2.943 -0.397 C1A UD0 15 UD0 "C2'" "C2'" C 0 1 Y N N -18.952 -64.567 18.807 6.383 -2.034 -0.072 "C2'" UD0 16 UD0 "C2'A" C2* C 0 0 N N S -13.230 -67.198 4.881 -7.765 0.311 0.213 C2* UD0 17 UD0 "O2'" O2* O 0 1 N N N -13.050 -67.758 3.572 -7.948 -0.055 1.582 O2* UD0 18 UD0 C2A C2A C 0 1 N N N -16.073 -66.200 15.677 3.856 2.094 -2.959 C2A UD0 19 UD0 N2A N2A N 0 1 N N N -15.859 -65.323 14.701 3.379 1.625 -1.789 N2A UD0 20 UD0 O2A O2A O 0 1 N N N -16.147 -65.936 16.873 4.627 3.030 -2.967 O2A UD0 21 UD0 C2B C2B C 0 1 N N N -16.242 -67.627 15.185 3.431 1.457 -4.256 C2B UD0 22 UD0 "C3'" "C3'" C 0 1 Y N N -18.977 -63.247 18.361 4.995 -2.229 0.021 "C3'" UD0 23 UD0 "C3'A" C3* C 0 0 N N R -12.686 -68.131 5.975 -7.274 1.778 0.086 C3* UD0 24 UD0 "O3'" O3* O 0 1 N N N -11.576 -68.914 5.492 -7.845 2.596 1.110 O3* UD0 25 UD0 N3A N3A N 0 1 N N N -17.444 -63.393 16.543 4.558 0.103 0.379 N3A UD0 26 UD0 "C4'" "C4'" C 0 1 N N N -18.614 -62.969 17.030 4.083 -1.093 0.255 "C4'" UD0 27 UD0 "C4'A" C4* C 0 0 N N S -12.218 -67.175 7.080 -5.750 1.632 0.285 C4* UD0 28 UD0 "O4'" O4* O 0 1 N N N -12.359 -65.807 6.540 -5.404 0.273 -0.007 O4* UD0 29 UD0 O4A O4A O 0 1 N N N -18.277 -61.245 14.515 3.816 0.996 3.014 O4A UD0 30 UD0 "C5'" "C5'" C 0 1 Y N N -19.378 -62.249 19.257 4.503 -3.533 -0.116 "C5'" UD0 31 UD0 "C5'A" C5* C 0 0 N N N -13.071 -67.361 8.347 -5.009 2.573 -0.667 C5* UD0 32 UD0 "O5'" O5* O 0 1 N N N -13.286 -66.100 8.996 -3.607 2.517 -0.396 O5* UD0 33 UD0 "C6'" "C6'" C 0 1 Y N N -19.721 -62.621 20.568 5.391 -4.565 -0.335 "C6'" UD0 34 UD0 O6A O6A O 0 1 N N N -14.260 -59.444 14.246 3.958 4.963 3.355 O6A UD0 35 UD0 O6B O6B O 0 1 N N N -16.256 -59.052 15.132 3.338 3.238 4.588 O6B UD0 36 UD0 "C7'" "C7'" C 0 1 N N N -19.458 -60.752 18.924 3.023 -3.804 -0.026 "C7'" UD0 37 UD0 OA1 OA1 O 0 1 N N N -15.796 -64.017 12.491 1.534 3.040 -0.191 OA1 UD0 38 UD0 OA2 OA2 O 0 1 N N N -16.373 -65.629 10.587 0.229 5.236 0.430 OA2 UD0 39 UD0 OA3 OA3 O 0 1 N N N -14.879 -63.587 10.119 0.531 4.521 -1.972 OA3 UD0 40 UD0 OAE OAE O 0 1 N N N -7.308 -65.602 2.827 -6.419 -5.539 1.394 OAE UD0 41 UD0 OAF OAF O 0 1 N N N -11.834 -65.761 2.271 -6.824 -2.640 -1.944 OAF UD0 42 UD0 CAT CAT C 0 1 N N N -8.589 -65.740 4.705 -6.301 -3.313 1.901 CAT UD0 43 UD0 CAU CAU C 0 1 N N N -9.866 -65.814 5.260 -6.338 -2.047 1.431 CAU UD0 44 UD0 OB1 OB1 O 0 1 N N N -12.002 -64.272 10.351 -2.887 4.816 -1.152 OB1 UD0 45 UD0 OB2 OB2 O 0 1 N N N -11.652 -66.765 10.927 -2.495 2.900 -2.747 OB2 UD0 46 UD0 OB4 OB4 O 0 1 N N N -13.925 -65.618 11.486 -1.066 3.172 -0.557 OB4 UD0 47 UD0 NBB NBB N 0 1 N N N -9.568 -65.679 2.484 -6.624 -4.130 -0.318 NBB UD0 48 UD0 CBO CBO C 0 1 N N N -8.435 -65.669 3.320 -6.449 -4.389 0.994 CBO UD0 49 UD0 CBP CBP C 0 1 N N N -10.864 -65.755 3.032 -6.667 -2.859 -0.758 CBP UD0 50 UD0 NBZ NBZ N 0 1 N N N -11.029 -65.833 4.443 -6.522 -1.827 0.093 NBZ UD0 51 UD0 OP1 OP1 O 0 1 N N N -19.638 -58.010 17.655 1.405 -7.418 -0.518 OP1 UD0 52 UD0 OP2 OP2 O 0 1 N N N -19.116 -59.638 15.759 0.446 -5.170 -1.149 OP2 UD0 53 UD0 OP3 OP3 O 0 1 N N N -21.471 -58.949 16.113 0.684 -5.674 1.313 OP3 UD0 54 UD0 OP4 OP4 O 0 1 N N N -20.350 -60.527 17.825 2.784 -5.202 -0.198 OP4 UD0 55 UD0 H1 H1 H 0 1 N N N -13.953 -63.732 13.483 3.030 4.199 -1.022 H1 UD0 56 UD0 H2 H2 H 0 1 N N N -15.003 -63.642 15.728 4.831 2.567 -0.602 H2 UD0 57 UD0 H3 H3 H 0 1 N N N -17.692 -63.606 14.424 2.624 0.870 0.654 H3 UD0 58 UD0 H4 H4 H 0 1 N N N -16.613 -61.212 15.860 5.055 2.228 1.910 H4 UD0 59 UD0 H5 H5 H 0 1 N N N -16.488 -61.019 12.911 2.072 2.815 2.197 H5 UD0 60 UD0 "HO1'" "HO1'" H 0 0 N N N -17.659 -65.442 17.727 6.994 -0.312 -0.783 "HO1'" UD0 61 UD0 "H1'" H1* H 0 1 N N N -12.877 -65.071 4.544 -6.656 -0.457 -1.503 H1* UD0 62 UD0 H1A H1A H 0 1 N N N -19.603 -66.330 21.692 8.964 -2.757 -1.436 H1A UD0 63 UD0 H1AA H1AA H 0 0 N N N -19.975 -66.924 20.039 8.993 -2.093 0.215 H1AA UD0 64 UD0 H1AB H1AB H 0 0 N N N -18.267 -66.715 20.555 9.198 -3.842 -0.044 H1AB UD0 65 UD0 "H2'" H2* H 0 1 N N N -14.313 -67.025 4.960 -8.679 0.152 -0.360 H2* UD0 66 UD0 "HO2'" HO2* H 0 0 N N N -12.618 -67.123 3.012 -8.683 0.399 2.016 HO2* UD0 67 UD0 HN2A HN2A H 0 0 N N N -15.840 -65.679 13.767 2.762 0.876 -1.782 HN2A UD0 68 UD0 H2B H2B H 0 1 N N N -16.424 -68.292 16.042 3.915 1.967 -5.088 H2B UD0 69 UD0 H2BA H2BA H 0 0 N N N -17.096 -67.678 14.494 3.720 0.406 -4.256 H2BA UD0 70 UD0 H2BB H2BB H 0 0 N N N -15.328 -67.945 14.662 2.349 1.535 -4.362 H2BB UD0 71 UD0 "H3'" H3* H 0 1 N N N -13.443 -68.852 6.318 -7.499 2.179 -0.902 H3* UD0 72 UD0 "HO3'" HO3* H 0 0 N N N -11.261 -69.480 6.187 -8.810 2.647 1.080 HO3* UD0 73 UD0 "H4'" "H4'" H 0 1 N N N -19.286 -62.409 16.397 3.018 -1.261 0.324 "H4'" UD0 74 UD0 "H4'A" H4* H 0 0 N N N -11.175 -67.374 7.367 -5.488 1.868 1.317 H4* UD0 75 UD0 HO4A HO4A H 0 0 N N N -18.584 -60.551 15.087 4.025 1.362 3.884 HO4A UD0 76 UD0 "H5'" H5* H 0 1 N N N -14.043 -67.793 8.067 -5.193 2.266 -1.696 H5* UD0 77 UD0 "H5'A" H5*A H 0 0 N N N -12.547 -68.038 9.038 -5.367 3.592 -0.522 H5*A UD0 78 UD0 "H6'" "H6'" H 0 1 N N N -20.023 -61.857 21.270 5.018 -5.573 -0.442 "H6'" UD0 79 UD0 HO6B HO6B H 0 0 N N N -15.814 -58.265 15.429 3.601 3.733 5.376 HO6B UD0 80 UD0 "H7'" "H7'" H 0 1 N N N -19.827 -60.207 19.805 2.655 -3.490 0.951 "H7'" UD0 81 UD0 "H7'A" "H7'A" H 0 0 N N N -18.455 -60.389 18.654 2.503 -3.248 -0.806 "H7'A" UD0 82 UD0 HOA2 HOA2 H 0 0 N N N -16.663 -65.344 9.728 0.086 4.971 1.348 HOA2 UD0 83 UD0 HAT HAT H 0 1 N N N -7.720 -65.738 5.346 -6.156 -3.501 2.954 HAT UD0 84 UD0 HAU HAU H 0 1 N N N -9.974 -65.858 6.334 -6.223 -1.214 2.107 HAU UD0 85 UD0 HOB2 HOB2 H 0 0 N N N -10.819 -66.333 11.075 -2.262 1.968 -2.863 HOB2 UD0 86 UD0 HOP1 HOP1 H 0 0 N N N -18.781 -57.783 17.315 0.553 -7.874 -0.514 HOP1 UD0 87 UD0 HOP3 HOP3 H 0 0 N N N -21.325 -59.065 15.181 1.200 -6.096 2.013 HOP3 UD0 88 UD0 HNBB HNBB H 0 0 N N N -9.452 -65.632 1.492 -6.730 -4.862 -0.945 HNBB UD0 89 # 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 UD0 OP2 P DOUB N N 1 UD0 OP3 P SING N N 2 UD0 P OP1 SING N N 3 UD0 P OP4 SING N N 4 UD0 OA1 C1 SING N N 5 UD0 O1 C1 SING N N 6 UD0 C1 C2 SING N N 7 UD0 C1 H1 SING N N 8 UD0 "C1'" N1 DOUB Y N 9 UD0 "C6'" N1 SING Y N 10 UD0 O1 C5 SING N N 11 UD0 N2A C2 SING N N 12 UD0 C2 C3 SING N N 13 UD0 C2 H2 SING N N 14 UD0 C4 C3 SING N N 15 UD0 C3 N3A SING N N 16 UD0 C3 H3 SING N N 17 UD0 C5 C4 SING N N 18 UD0 O4A C4 SING N N 19 UD0 C4 H4 SING N N 20 UD0 C5 C6 SING N N 21 UD0 C5 H5 SING N N 22 UD0 O6A C6 DOUB N N 23 UD0 C6 O6B SING N N 24 UD0 OA3 PA DOUB N N 25 UD0 OA2 PA SING N N 26 UD0 PA OB4 SING N N 27 UD0 PA OA1 SING N N 28 UD0 "O5'" PB SING N N 29 UD0 OB1 PB DOUB N N 30 UD0 PB OB2 SING N N 31 UD0 PB OB4 SING N N 32 UD0 "C2'" "C1'" SING Y N 33 UD0 "C1'" C1A SING N N 34 UD0 "O1'" "C2'" SING N N 35 UD0 "O1'" "HO1'" SING N N 36 UD0 NBZ "C1'A" SING N N 37 UD0 "C2'A" "C1'A" SING N N 38 UD0 "C1'A" "O4'" SING N N 39 UD0 "C1'A" "H1'" SING N N 40 UD0 C1A H1A SING N N 41 UD0 C1A H1AA SING N N 42 UD0 C1A H1AB SING N N 43 UD0 "C3'" "C2'" DOUB Y N 44 UD0 "O2'" "C2'A" SING N N 45 UD0 "C2'A" "C3'A" SING N N 46 UD0 "C2'A" "H2'" SING N N 47 UD0 "O2'" "HO2'" SING N N 48 UD0 N2A C2A SING N N 49 UD0 C2B C2A SING N N 50 UD0 C2A O2A DOUB N N 51 UD0 N2A HN2A SING N N 52 UD0 C2B H2B SING N N 53 UD0 C2B H2BA SING N N 54 UD0 C2B H2BB SING N N 55 UD0 "C4'" "C3'" SING N N 56 UD0 "C3'" "C5'" SING Y N 57 UD0 "O3'" "C3'A" SING N N 58 UD0 "C3'A" "C4'A" SING N N 59 UD0 "C3'A" "H3'" SING N N 60 UD0 "O3'" "HO3'" SING N N 61 UD0 N3A "C4'" DOUB N N 62 UD0 "C4'" "H4'" SING N N 63 UD0 "O4'" "C4'A" SING N N 64 UD0 "C4'A" "C5'A" SING N N 65 UD0 "C4'A" "H4'A" SING N N 66 UD0 O4A HO4A SING N N 67 UD0 "C7'" "C5'" SING N N 68 UD0 "C5'" "C6'" DOUB Y N 69 UD0 "C5'A" "O5'" SING N N 70 UD0 "C5'A" "H5'" SING N N 71 UD0 "C5'A" "H5'A" SING N N 72 UD0 "C6'" "H6'" SING N N 73 UD0 O6B HO6B SING N N 74 UD0 OP4 "C7'" SING N N 75 UD0 "C7'" "H7'" SING N N 76 UD0 "C7'" "H7'A" SING N N 77 UD0 OA2 HOA2 SING N N 78 UD0 OAE CBO DOUB N N 79 UD0 OAF CBP DOUB N N 80 UD0 CBO CAT SING N N 81 UD0 CAT CAU DOUB N N 82 UD0 CAT HAT SING N N 83 UD0 NBZ CAU SING N N 84 UD0 CAU HAU SING N N 85 UD0 OB2 HOB2 SING N N 86 UD0 NBB CBP SING N N 87 UD0 NBB CBO SING N N 88 UD0 CBP NBZ SING N N 89 UD0 OP1 HOP1 SING N N 90 UD0 OP3 HOP3 SING N N 91 UD0 NBB HNBB SING N N 92 # 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 UD0 SMILES ACDLabs 12.01 "O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC4OC(C(=O)O)C(O)C(/N=C/c3c(cnc(c3O)C)COP(=O)(O)O)C4NC(=O)C)O)O" UD0 SMILES_CANONICAL CACTVS 3.370 "CC(=O)N[C@H]1[C@H](O[C@@H]([C@@H](O)[C@@H]1N=Cc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[C@@H]3O[C@H]([C@@H](O)[C@H]3O)N4C=CC(=O)NC4=O" UD0 SMILES CACTVS 3.370 "CC(=O)N[CH]1[CH](O[CH]([CH](O)[CH]1N=Cc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=O)NC4=O" UD0 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H]2[C@H]([C@H](O[C@@H]([C@H]2O)C(=O)O)O[P@](=O)(O)O[P@@](=O)(O)OC[C@H]3[C@@H]([C@@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)NC(=O)C)O" UD0 SMILES "OpenEye OEToolkits" 1.7.0 "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(C(OC(C2O)C(=O)O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)NC(=O)C)O" UD0 InChI InChI 1.03 ;InChI=1S/C25H34N5O22P3/c1-9-17(33)12(11(5-26-9)7-47-53(40,41)42)6-27-15-16(28-10(2)31)24(50-21(19(15)35)23(37)38)51-55(45,46)52-54(43,44)48-8-13-18(34)20(36)22(49-13)30-4-3-14(32)29-25(30)39/h3-6,13,15-16,18-22,24,33-36H,7-8H2,1-2H3,(H,28,31)(H,37,38)(H,43,44)(H,45,46)(H,29,32,39)(H2,40,41,42)/b27-6+/t13-,15+,16+,18-,19-,20-,21-,22+,24+/m0/s1 ; UD0 InChIKey InChI 1.03 IGKBPIFLZAFLLV-VUZHIUKYSA-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 UD0 "SYSTEMATIC NAME" ACDLabs 12.01 ;(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(S)-{[(S)-{[(2S,3R,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxy-4-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid ; UD0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 ;(2S,3S,4R,5R,6R)-5-acetamido-6-[[[(2S,3R,4S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3-hydroxy-4-[(E)-[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxane-2-carboxylic acid ; # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UD0 "Create component" 2010-07-13 RCSB UD0 "Modify aromatic_flag" 2011-06-04 RCSB UD0 "Modify descriptor" 2011-06-04 RCSB #