data_1RN # _chem_comp.id 1RN _chem_comp.name "(E)-N-{[4-oxo-1-(5-O-phosphono-beta-D-arabinofuranosyl)-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl]methylidene}glycine" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H16 N3 O10 P S" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-05-09 _chem_comp.pdbx_modified_date 2013-05-24 _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 425.308 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1RN _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 4JYZ _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 1RN N1 N1 N 0 1 N N N 62.348 17.067 -13.404 0.606 1.747 0.408 N1 1RN 1 1RN C2 C2 C 0 1 N N N 62.900 18.147 -14.068 1.477 2.752 0.593 C2 1RN 2 1RN S2 S2 S 0 1 N N N 62.434 19.284 -14.003 0.889 4.359 0.646 S2 1RN 3 1RN N3 N3 N 0 1 N N N 64.018 17.848 -14.812 2.796 2.537 0.739 N3 1RN 4 1RN C4 C4 C 0 1 N N N 64.619 16.607 -14.959 3.292 1.282 0.702 C4 1RN 5 1RN O4 O4 O 0 1 N N N 65.626 16.500 -15.656 4.485 1.082 0.834 O4 1RN 6 1RN C5 C5 C 0 1 N N N 63.980 15.546 -14.252 2.359 0.162 0.500 C5 1RN 7 1RN C6 C6 C 0 1 N N N 62.899 15.805 -13.512 1.016 0.452 0.358 C6 1RN 8 1RN "C1'" "C1'" C 0 1 N N R 61.159 17.304 -12.579 -0.819 2.053 0.264 "C1'" 1RN 9 1RN "O2'" "O2'" O 0 1 N N N 60.352 15.651 -13.979 -0.407 1.570 -2.107 "O2'" 1RN 10 1RN "C2'" "C2'" C 0 1 N N S 59.881 16.649 -13.097 -1.158 2.391 -1.211 "C2'" 1RN 11 1RN "O3'" "O3'" O 0 1 N N N 58.602 17.568 -11.134 -3.454 3.232 -1.128 "O3'" 1RN 12 1RN "C3'" "C3'" C 0 1 N N S 59.122 16.438 -11.816 -2.667 2.050 -1.283 "C3'" 1RN 13 1RN "C4'" "C4'" C 0 1 N N R 60.224 15.875 -10.937 -2.895 1.091 -0.098 "C4'" 1RN 14 1RN "O4'" "O4'" O 0 1 N N N 61.363 16.729 -11.292 -1.620 0.883 0.534 "O4'" 1RN 15 1RN "C5'" "C5'" C 0 1 N N N 60.591 14.441 -11.213 -3.447 -0.242 -0.607 "C5'" 1RN 16 1RN "O5'" "O5'" O 0 1 N N N 59.507 13.585 -10.892 -3.764 -1.081 0.505 "O5'" 1RN 17 1RN P P P 0 1 N N N 58.956 12.540 -11.959 -4.370 -2.564 0.340 P 1RN 18 1RN OP1 OP1 O 0 1 N N N 59.777 12.650 -13.190 -5.833 -2.474 -0.326 OP1 1RN 19 1RN OP2 OP2 O 0 1 N N N 58.817 11.221 -11.287 -3.481 -3.366 -0.529 OP2 1RN 20 1RN C3 C3 C 0 1 N N N 64.484 14.247 -14.333 2.842 -1.225 0.451 C3 1RN 21 1RN N2 N2 N 0 1 N N N 63.701 13.290 -13.799 4.106 -1.477 0.587 N2 1RN 22 1RN C7 C7 C 0 1 N N N 64.114 12.133 -13.848 4.587 -2.859 0.539 C7 1RN 23 1RN C1 C1 C 0 1 N N N 63.580 11.333 -14.735 5.472 -3.041 -0.668 C1 1RN 24 1RN O2 O2 O 0 1 N N N 64.039 10.169 -14.799 5.678 -2.112 -1.411 O2 1RN 25 1RN O1 O1 O 0 1 N N N 62.723 11.824 -15.503 6.029 -4.237 -0.917 O1 1RN 26 1RN H1 H1 H 0 1 N N N 62.435 14.992 -12.974 0.299 -0.342 0.209 H1 1RN 27 1RN H2 H2 H 0 1 N N N 60.987 18.387 -12.486 -1.103 2.876 0.921 H2 1RN 28 1RN H3 H3 H 0 1 N N N 59.614 15.185 -14.354 -0.584 1.744 -3.042 H3 1RN 29 1RN H4 H4 H 0 1 N N N 59.340 17.408 -13.681 -0.987 3.447 -1.417 H4 1RN 30 1RN H5 H5 H 0 1 N N N 58.151 17.284 -10.348 -3.307 3.896 -1.815 H5 1RN 31 1RN H6 H6 H 0 1 N N N 58.344 15.675 -11.966 -2.902 1.557 -2.226 H6 1RN 32 1RN H7 H7 H 0 1 N N N 59.960 16.001 -9.877 -3.592 1.537 0.611 H7 1RN 33 1RN H8 H8 H 0 1 N N N 60.839 14.329 -12.279 -4.347 -0.062 -1.194 H8 1RN 34 1RN H9 H9 H 0 1 N N N 61.464 14.166 -10.603 -2.699 -0.731 -1.230 H9 1RN 35 1RN H10 H10 H 0 1 N N N 60.137 11.798 -13.408 -6.470 -1.962 0.191 H10 1RN 36 1RN H12 H12 H 0 1 N N N 65.436 14.025 -14.792 2.143 -2.035 0.302 H12 1RN 37 1RN H13 H13 H 0 1 N N N 65.194 12.178 -14.054 5.156 -3.078 1.442 H13 1RN 38 1RN H14 H14 H 0 1 N N N 63.948 11.683 -12.858 3.737 -3.538 0.472 H14 1RN 39 1RN H15 H15 H 0 1 N N N 62.468 11.176 -16.150 6.589 -4.305 -1.703 H15 1RN 40 1RN H16 H16 H 0 1 N N N 64.444 18.609 -15.301 3.395 3.288 0.871 H16 1RN 41 1RN OP3 OP3 O 0 1 N Y N ? ? ? -4.480 -3.263 1.786 OP3 1RN 42 1RN H18 H18 H 0 1 N N N ? ? ? -4.838 -4.161 1.763 H18 1RN 43 # 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 1RN N1 C2 SING N N 1 1RN N1 C6 SING N N 2 1RN N1 "C1'" SING N N 3 1RN C2 S2 DOUB N N 4 1RN C2 N3 SING N N 5 1RN N3 C4 SING N N 6 1RN C4 O4 DOUB N N 7 1RN C4 C5 SING N N 8 1RN C5 C6 DOUB N N 9 1RN C5 C3 SING N N 10 1RN "C1'" "C2'" SING N N 11 1RN "C1'" "O4'" SING N N 12 1RN "O2'" "C2'" SING N N 13 1RN "C2'" "C3'" SING N N 14 1RN "O3'" "C3'" SING N N 15 1RN "C3'" "C4'" SING N N 16 1RN "C4'" "O4'" SING N N 17 1RN "C4'" "C5'" SING N N 18 1RN "C5'" "O5'" SING N N 19 1RN "O5'" P SING N N 20 1RN P OP1 SING N N 21 1RN P OP2 DOUB N N 22 1RN C3 N2 DOUB N N 23 1RN N2 C7 SING N N 24 1RN C7 C1 SING N N 25 1RN C1 O2 DOUB N N 26 1RN C1 O1 SING N N 27 1RN C6 H1 SING N N 28 1RN "C1'" H2 SING N N 29 1RN "O2'" H3 SING N N 30 1RN "C2'" H4 SING N N 31 1RN "O3'" H5 SING N N 32 1RN "C3'" H6 SING N N 33 1RN "C4'" H7 SING N N 34 1RN "C5'" H8 SING N N 35 1RN "C5'" H9 SING N N 36 1RN OP1 H10 SING N N 37 1RN C3 H12 SING N N 38 1RN C7 H13 SING N N 39 1RN C7 H14 SING N N 40 1RN O1 H15 SING N N 41 1RN N3 H16 SING N N 42 1RN P OP3 SING N N 43 1RN OP3 H18 SING N N 44 # 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 1RN SMILES ACDLabs 12.01 "O=C(O)C/N=C/C=1C(=O)NC(=S)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O" 1RN InChI InChI 1.03 "InChI=1S/C12H16N3O10PS/c16-7(17)2-13-1-5-3-15(12(27)14-10(5)20)11-9(19)8(18)6(25-11)4-24-26(21,22)23/h1,3,6,8-9,11,18-19H,2,4H2,(H,16,17)(H,14,20,27)(H2,21,22,23)/b13-1+/t6-,8-,9+,11-/m1/s1" 1RN InChIKey InChI 1.03 OIOFJGQNCGWJPT-PDCDXKGCSA-N 1RN SMILES_CANONICAL CACTVS 3.370 "O[C@H]1[C@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C=NCC(O)=O)C(=O)NC2=S" 1RN SMILES CACTVS 3.370 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C=NCC(O)=O)C(=O)NC2=S" 1RN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=C(C(=O)NC(=S)N1[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)/C=N/CC(=O)O" 1RN SMILES "OpenEye OEToolkits" 1.7.6 "C1=C(C(=O)NC(=S)N1C2C(C(C(O2)COP(=O)(O)O)O)O)C=NCC(=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 1RN "SYSTEMATIC NAME" ACDLabs 12.01 "(E)-N-{[4-oxo-1-(5-O-phosphono-beta-D-arabinofuranosyl)-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl]methylidene}glycine" 1RN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "2-[(E)-[1-[(2R,3S,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-4-oxidanylidene-2-sulfanylidene-pyrimidin-5-yl]methylideneamino]ethanoic 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 1RN "Create component" 2013-05-09 RCSB 1RN "Modify linking type" 2013-05-22 RCSB 1RN "Initial release" 2013-05-29 RCSB #