data_URU # _chem_comp.id URU _chem_comp.name "((2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-(2- ((((2R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)- 3,4-dihydroxytetrahydrofuran-2-yl)methyl)amino)-2-oxoethyl)-4- hydroxytetrahydrofuran-2-yl)methyl phosphate" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C20 H26 N5 O14 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-01-07 _chem_comp.pdbx_modified_date 2014-07-03 _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 591.419 _chem_comp.one_letter_code ? _chem_comp.three_letter_code URU _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4O41 _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 URU P P P 0 1 N N N 8.858 -1.049 9.850 -5.936 3.625 0.733 P URU 1 URU OP1 OP1 O 0 1 N N N 9.016 0.138 8.973 -6.589 3.395 -0.575 OP1 URU 2 URU "O5'" "O5'" O 0 1 N N N 7.303 -1.392 10.016 -4.976 2.380 1.080 "O5'" URU 3 URU "C5'" "C5'" C 0 1 N N N 6.408 -1.433 8.886 -3.943 1.925 0.204 "C5'" URU 4 URU "C4'" "C4'" C 0 1 N N S 5.039 -1.832 9.363 -3.227 0.730 0.837 "C4'" URU 5 URU "C3'" "C3'" C 0 1 N N S 4.442 -1.058 10.531 -2.091 0.223 -0.086 "C3'" URU 6 URU "C6'" "C6'" C 0 1 N N N 3.887 0.313 10.144 -0.795 0.997 0.166 "C6'" URU 7 URU "C2'" "C2'" C 0 1 N N R 3.442 -2.055 11.096 -1.946 -1.253 0.357 "C2'" URU 8 URU "O2'" "O2'" O 0 1 N N N 2.245 -2.012 10.296 -0.868 -1.394 1.284 "O2'" URU 9 URU "C1'" "C1'" C 0 1 N N R 4.209 -3.373 10.920 -3.291 -1.576 1.038 "C1'" URU 10 URU "O4'" "O4'" O 0 1 N N N 5.100 -3.202 9.858 -4.116 -0.404 0.932 "O4'" URU 11 URU N1 N1 N 0 1 N N N 4.942 -3.681 12.156 -3.936 -2.702 0.358 N1 URU 12 URU C6 C6 C 0 1 N N N 6.284 -3.423 12.301 -4.120 -3.882 1.027 C6 URU 13 URU C5 C5 C 0 1 N N N 6.953 -3.690 13.433 -4.714 -4.920 0.400 C5 URU 14 URU C4 C4 C 0 1 N N N 6.257 -4.269 14.544 -5.137 -4.764 -0.942 C4 URU 15 URU N3 N3 N 0 1 N N N 4.921 -4.486 14.311 -4.937 -3.585 -1.566 N3 URU 16 URU C2 C2 C 0 1 N N N 4.221 -4.222 13.192 -4.346 -2.565 -0.916 C2 URU 17 URU O2 O2 O 0 1 N N N 3.034 -4.448 13.090 -4.177 -1.507 -1.489 O2 URU 18 URU O4 O4 O 0 1 N N N 6.779 -4.545 15.614 -5.675 -5.686 -1.528 O4 URU 19 URU OP2 OP2 O 0 1 N N N 9.421 -1.049 11.228 -5.060 4.974 0.664 OP2 URU 20 URU C C C 0 1 N N N 3.263 0.997 11.337 0.250 0.565 -0.830 C URU 21 URU O3 O3 O 0 1 N N N 3.511 0.720 12.501 -0.014 -0.280 -1.659 O3 URU 22 URU "NZ'" "NZ'" N 0 1 N N N 2.330 1.996 11.027 1.479 1.117 -0.798 "NZ'" URU 23 URU "CZ'" "CZ'" C 0 1 N N N 1.656 2.802 12.030 2.496 0.696 -1.766 "CZ'" URU 24 URU "CY'" "CY'" C 0 1 N N R 0.190 2.339 12.049 3.791 1.471 -1.514 "CY'" URU 25 URU "CX'" "CX'" C 0 1 N N S -0.502 2.774 13.335 4.833 1.115 -2.592 "CX'" URU 26 URU "OX'" "OX'" O 0 1 N N N -0.849 4.136 13.211 5.218 2.283 -3.321 "OX'" URU 27 URU "CW'" "CW'" C 0 1 N N R -1.617 1.746 13.448 6.033 0.557 -1.791 "CW'" URU 28 URU "OW'" "OW'" O 0 1 N N N -2.634 2.136 12.569 7.270 1.029 -2.329 "OW'" URU 29 URU "CV'" "CV'" C 0 1 N N R -0.964 0.463 12.928 5.783 1.145 -0.379 "CV'" URU 30 URU "OY'" "OY'" O 0 1 N N N 0.101 0.871 12.106 4.346 1.095 -0.243 "OY'" URU 31 URU N11 N11 N 0 1 N N N -0.428 -0.373 14.026 6.427 0.320 0.646 N11 URU 32 URU C16 C16 C 0 1 N N N 0.925 -0.569 14.218 7.452 0.840 1.389 C16 URU 33 URU C15 C15 C 0 1 N N N 1.370 -1.394 15.192 8.045 0.079 2.334 C15 URU 34 URU C14 C14 C 0 1 N N N 0.453 -2.060 16.050 7.592 -1.247 2.536 C14 URU 35 URU N13 N13 N 0 1 N N N -0.882 -1.810 15.795 6.580 -1.722 1.783 N13 URU 36 URU C12 C12 C 0 1 N N N -1.366 -0.998 14.816 6.003 -0.940 0.851 C12 URU 37 URU O12 O12 O 0 1 N N N -2.584 -0.837 14.661 5.088 -1.380 0.183 O12 URU 38 URU O14 O14 O 0 1 N N N 0.681 -2.835 16.975 8.112 -1.952 3.382 O14 URU 39 URU H2 H2 H 0 1 N N N 6.772 -2.168 8.153 -4.380 1.623 -0.748 H2 URU 40 URU H3 H3 H 0 1 N N N 6.360 -0.439 8.417 -3.228 2.730 0.037 H3 URU 41 URU H4 H4 H 0 1 N N N 4.340 -1.781 8.515 -2.837 0.995 1.820 H4 URU 42 URU H5 H5 H 0 1 N N N 5.233 -0.906 11.280 -2.383 0.287 -1.134 H5 URU 43 URU H6 H6 H 0 1 N N N 4.706 0.938 9.758 -0.983 2.065 0.054 H6 URU 44 URU H7 H7 H 0 1 N N N 3.124 0.185 9.362 -0.441 0.794 1.176 H7 URU 45 URU H8 H8 H 0 1 N N N 3.242 -1.856 12.159 -1.792 -1.898 -0.508 H8 URU 46 URU H9 H9 H 0 1 N N N 1.612 -2.631 10.639 -0.732 -2.300 1.595 H9 URU 47 URU H10 H10 H 0 1 N N N 3.491 -4.177 10.703 -3.126 -1.822 2.087 H10 URU 48 URU H11 H11 H 0 1 N N N 6.821 -2.988 11.471 -3.791 -3.983 2.050 H11 URU 49 URU H12 H12 H 0 1 N N N 8.008 -3.470 13.506 -4.866 -5.857 0.916 H12 URU 50 URU H13 H13 H 0 1 N N N 4.404 -4.890 15.066 -5.224 -3.471 -2.485 H13 URU 51 URU H14 H14 H 0 1 N N N 9.851 -0.218 11.395 -4.602 5.188 1.489 H14 URU 52 URU H15 H15 H 0 1 N N N 2.117 2.163 10.064 1.691 1.792 -0.135 H15 URU 53 URU H16 H16 H 0 1 N N N 2.117 2.645 13.016 2.684 -0.371 -1.655 H16 URU 54 URU H17 H17 H 0 1 N N N 1.715 3.868 11.763 2.142 0.900 -2.777 H17 URU 55 URU H18 H18 H 0 1 N N N -0.345 2.735 11.173 3.591 2.542 -1.528 H18 URU 56 URU H19 H19 H 0 1 N N N 0.194 2.634 14.175 4.438 0.356 -3.268 H19 URU 57 URU H20 H20 H 0 1 N Y N -1.283 4.426 14.005 5.872 2.117 -4.013 H20 URU 58 URU H21 H21 H 0 1 N N N -1.956 1.631 14.488 6.012 -0.533 -1.767 H21 URU 59 URU H22 H22 H 0 1 N N N -3.042 2.932 12.889 7.429 0.760 -3.244 H22 URU 60 URU H23 H23 H 0 1 N N N -1.706 -0.110 12.352 6.140 2.173 -0.323 H23 URU 61 URU H24 H24 H 0 1 N N N 1.635 -0.058 13.584 7.784 1.854 1.221 H24 URU 62 URU H25 H25 H 0 1 N N N 2.431 -1.548 15.319 8.856 0.477 2.927 H25 URU 63 URU H26 H26 H 0 1 N N N -1.551 -2.266 16.382 6.264 -2.629 1.915 H26 URU 64 URU OP3 OP3 O 0 1 N Y N ? ? ? -7.060 3.772 1.876 OP3 URU 65 URU H1 H1 H 0 1 N Y N ? ? ? -7.674 4.505 1.731 H1 URU 66 # 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 URU "C5'" "C4'" SING N N 1 URU "C5'" "O5'" SING N N 2 URU OP1 P DOUB N N 3 URU "C4'" "O4'" SING N N 4 URU "C4'" "C3'" SING N N 5 URU P "O5'" SING N N 6 URU P OP2 SING N N 7 URU "O4'" "C1'" SING N N 8 URU "C6'" "C3'" SING N N 9 URU "C6'" C SING N N 10 URU "O2'" "C2'" SING N N 11 URU "C3'" "C2'" SING N N 12 URU "C1'" "C2'" SING N N 13 URU "C1'" N1 SING N N 14 URU "NZ'" C SING N N 15 URU "NZ'" "CZ'" SING N N 16 URU C O3 DOUB N N 17 URU "CZ'" "CY'" SING N N 18 URU "CY'" "OY'" SING N N 19 URU "CY'" "CX'" SING N N 20 URU "OY'" "CV'" SING N N 21 URU N1 C6 SING N N 22 URU N1 C2 SING N N 23 URU C6 C5 DOUB N N 24 URU "OW'" "CW'" SING N N 25 URU "CV'" "CW'" SING N N 26 URU "CV'" N11 SING N N 27 URU O2 C2 DOUB N N 28 URU C2 N3 SING N N 29 URU "OX'" "CX'" SING N N 30 URU "CX'" "CW'" SING N N 31 URU C5 C4 SING N N 32 URU N11 C16 SING N N 33 URU N11 C12 SING N N 34 URU C16 C15 DOUB N N 35 URU N3 C4 SING N N 36 URU C4 O4 DOUB N N 37 URU O12 C12 DOUB N N 38 URU C12 N13 SING N N 39 URU C15 C14 SING N N 40 URU N13 C14 SING N N 41 URU C14 O14 DOUB N N 42 URU "C5'" H2 SING N N 43 URU "C5'" H3 SING N N 44 URU "C4'" H4 SING N N 45 URU "C3'" H5 SING N N 46 URU "C6'" H6 SING N N 47 URU "C6'" H7 SING N N 48 URU "C2'" H8 SING N N 49 URU "O2'" H9 SING N N 50 URU "C1'" H10 SING N N 51 URU C6 H11 SING N N 52 URU C5 H12 SING N N 53 URU N3 H13 SING N N 54 URU OP2 H14 SING N N 55 URU "NZ'" H15 SING N N 56 URU "CZ'" H16 SING N N 57 URU "CZ'" H17 SING N N 58 URU "CY'" H18 SING N N 59 URU "CX'" H19 SING N N 60 URU "OX'" H20 SING N N 61 URU "CW'" H21 SING N N 62 URU "OW'" H22 SING N N 63 URU "CV'" H23 SING N N 64 URU C16 H24 SING N N 65 URU C15 H25 SING N N 66 URU N13 H26 SING N N 67 URU P OP3 SING N N 68 URU OP3 H1 SING N N 69 # 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 URU SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C=CC(=O)NC1=O)C(O)C2CC(=O)NCC4OC(N3C(=O)NC(=O)C=C3)C(O)C4O" URU InChI InChI 1.03 ;InChI=1S/C20H26N5O14P/c26-11-1-3-24(19(32)22-11)17-14(29)8(10(39-17)7-37-40(34,35)36)5-13(28)21-6-9-15(30)16(31)18(38-9)25-4-2-12(27)23-20(25)33/h1-4,8-10,14-18,29-31H,5-7H2,(H,21,28)(H,22,26,32)(H,23,27,33)(H2,34,35,36)/t8-,9-,10-,14-,15-,16-,17-,18-/m1/s1 ; URU InChIKey InChI 1.03 WKTKVGCYUSOTBH-VKGBBMGNSA-N URU SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CNC(=O)C[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO[P](O)(O)=O)N3C=CC(=O)NC3=O)N4C=CC(=O)NC4=O" URU SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CNC(=O)C[CH]2[CH](O)[CH](O[CH]2CO[P](O)(O)=O)N3C=CC(=O)NC3=O)N4C=CC(=O)NC4=O" URU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)CC(=O)NC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)O" URU SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)CC(=O)NCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)O" # 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 URU "SYSTEMATIC NAME" ACDLabs 12.01 ;{(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-[2-({[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}amino)-2-oxoethyl]-4-hydroxytetrahydrofuran-2-yl}methyl dihydrogen phosphate (non-preferred name) ; URU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-[2-[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]-4-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 URU "Create component" 2014-01-07 RCSB URU "Initial release" 2014-07-08 RCSB #