data_A1I59 # _chem_comp.id A1I59 _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-[4-azanyl-5-[(1~{S})-1-azanyl-3,3-bis(oxidanyl)propyl]-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H21 N4 O10 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-03-17 _chem_comp.pdbx_modified_date 2025-10-31 _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 412.290 _chem_comp.one_letter_code C _chem_comp.three_letter_code A1I59 _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 9QF6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A1I59 C1 C1 C 0 1 N N N N N N 217.740 246.208 269.876 4.860 -1.367 0.457 C1 A1I59 1 A1I59 "C1'" C2 C 0 1 N N R N N N 213.399 242.433 269.300 -0.311 1.235 0.534 "C1'" A1I59 2 A1I59 C2 C3 C 0 1 N N N N N N 213.738 244.145 267.658 0.814 0.629 -1.536 C2 A1I59 3 A1I59 "C2'" C4 C 0 1 N N R N N N 214.229 241.236 268.839 -0.833 2.597 0.024 "C2'" A1I59 4 A1I59 C3 C5 C 0 1 N N N N N N 218.603 247.265 270.565 6.258 -1.543 1.055 C3 A1I59 5 A1I59 "C3'" C6 C 0 1 N N S N N N 215.142 241.037 270.039 -2.370 2.457 0.086 "C3'" A1I59 6 A1I59 C4 C7 C 0 1 N N N N N N 215.020 246.005 267.979 3.060 0.097 -1.638 C4 A1I59 7 A1I59 "C4'" C8 C 0 1 N N R N N N 214.217 241.340 271.206 -2.595 1.027 0.627 "C4'" A1I59 8 A1I59 C5 C9 C 0 1 N N N N N N 215.302 245.574 269.248 3.170 0.305 -0.248 C5 A1I59 9 A1I59 "C5'" C10 C 0 1 N N N N N N 214.885 241.757 272.490 -3.809 0.387 -0.051 "C5'" A1I59 10 A1I59 C6 C11 C 0 1 N N N N N N 214.760 244.382 269.687 2.069 0.674 0.449 C6 A1I59 11 A1I59 O1 O1 O 0 1 N N N N N N 218.936 246.834 271.863 6.555 -2.936 1.168 O1 A1I59 12 A1I59 CM5 C12 C 0 1 N N S N N N 216.222 246.414 270.183 4.492 0.118 0.451 CM5 A1I59 13 A1I59 N1 N1 N 0 1 N N N N N N 213.991 243.714 268.858 0.887 0.835 -0.209 N1 A1I59 14 A1I59 O4 O2 O 0 1 N N N N N N 217.883 248.472 270.647 7.221 -0.918 0.205 O4 A1I59 15 A1I59 N3 N2 N 0 1 N N N N N N 214.239 245.272 267.214 1.887 0.265 -2.236 N3 A1I59 16 A1I59 N4 N3 N 0 1 N N N N N N 215.584 247.284 267.470 4.162 -0.279 -2.371 N4 A1I59 17 A1I59 O2 O3 O 0 1 N N N N N N 213.038 243.504 266.947 -0.254 0.773 -2.108 O2 A1I59 18 A1I59 "O2'" O4 O 0 1 N N N N N N 213.361 240.125 268.679 -0.391 3.654 0.878 "O2'" A1I59 19 A1I59 "O3'" O5 O 0 1 N N N N N N 215.724 239.747 270.110 -2.925 3.423 0.981 "O3'" A1I59 20 A1I59 "O4'" O6 O 0 1 N N N N N N 213.375 242.415 270.713 -1.390 0.309 0.283 "O4'" A1I59 21 A1I59 "O5'" O7 O 0 1 N N N N N N 215.899 242.723 272.258 -4.069 -0.886 0.544 "O5'" A1I59 22 A1I59 OP2 O8 O 0 1 N N N N N N 217.526 242.002 274.036 -5.193 -3.241 0.867 OP1 A1I59 23 A1I59 OP3 O9 O 0 1 N Y N N N N 217.681 244.369 272.913 -6.684 -1.127 0.400 OP2 A1I59 24 A1I59 P P1 P 0 1 N N N N N N 216.841 243.218 273.441 -5.278 -1.842 0.076 P A1I59 25 A1I59 N5 N4 N 0 1 N N N N N N 215.965 246.037 271.557 4.387 0.603 1.834 N5 A1I59 26 A1I59 H1 H1 H 0 1 N N N N N N 218.044 245.212 270.231 4.851 -1.748 -0.564 H1 A1I59 27 A1I59 H2 H2 H 0 1 N N N N N N 217.896 246.273 268.789 4.136 -1.918 1.057 H2 A1I59 28 A1I59 "H1'" H3 H 0 1 N N N N N N 212.380 242.338 268.895 -0.095 1.287 1.601 H3 A1I59 29 A1I59 "H2'" H4 H 0 1 N N N N N N 214.803 241.471 267.930 -0.507 2.771 -1.001 H4 A1I59 30 A1I59 "H3'" H5 H 0 1 N N N N N N 215.931 241.803 270.009 -2.804 2.565 -0.908 H5 A1I59 31 A1I59 "H4'" H6 H 0 1 N N N N N N 213.599 240.451 271.402 -2.732 1.047 1.708 H6 A1I59 32 A1I59 "H5'" H7 H 0 1 N N N N N N 214.129 242.187 273.163 -4.678 1.032 0.075 H7 A1I59 33 A1I59 "H5''" H8 H 0 1 N N N N N N 215.336 240.872 272.962 -3.605 0.256 -1.114 H8 A1I59 34 A1I59 H6 H9 H 0 1 N N N N N N 214.962 244.011 270.681 2.128 0.839 1.515 H9 A1I59 35 A1I59 H10 H10 H 0 1 N N N N N N 219.472 247.493 272.288 7.428 -3.123 1.541 H10 A1I59 36 A1I59 H11 H11 H 0 1 N N N N N N 215.983 247.478 270.038 5.263 0.682 -0.074 H11 A1I59 37 A1I59 H12 H12 H 0 1 N N N N N N 218.417 249.131 271.075 7.247 -1.278 -0.692 H12 A1I59 38 A1I59 H41 H13 H 0 1 N N N N N N 215.370 247.591 266.542 5.036 -0.310 -1.952 H13 A1I59 39 A1I59 H42 H14 H 0 1 N N N N N N 216.177 247.837 268.055 4.065 -0.512 -3.308 H14 A1I59 40 A1I59 "HO2'" H15 H 0 1 N N N N N N 213.862 239.370 268.392 -0.691 4.532 0.604 H15 A1I59 41 A1I59 "HO3'" H16 H 0 1 N Y N N N N 216.279 239.691 270.879 -2.760 4.340 0.721 H16 A1I59 42 A1I59 HOP2 H17 H 0 1 N N N N N N 217.253 241.895 274.940 -5.892 -3.868 0.635 H17 A1I59 43 A1I59 HOP3 H18 H 0 1 N N N N N N 217.382 245.183 273.300 -6.820 -0.933 1.337 H18 A1I59 44 A1I59 H19 H19 H 0 1 N N N N N N 216.552 246.572 272.165 4.113 1.574 1.857 H19 A1I59 45 A1I59 H20 H20 H 0 1 N N N N N N 215.006 246.215 271.778 3.748 0.034 2.369 H20 A1I59 46 A1I59 OP1 OP3 O 0 1 N N N N N N 215.816 244.052 274.450 -5.175 -2.091 -1.379 OP3 A1I59 47 A1I59 H22 H22 H 0 1 N N N N N N 219.516 247.410 269.969 6.291 -1.082 2.042 H22 A1I59 48 # 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 A1I59 O2 C2 DOUB N N 1 A1I59 N3 C2 SING N N 2 A1I59 N3 C4 DOUB N N 3 A1I59 N4 C4 SING N N 4 A1I59 C2 N1 SING N N 5 A1I59 C4 C5 SING N N 6 A1I59 "O2'" "C2'" SING N N 7 A1I59 "C2'" "C1'" SING N N 8 A1I59 "C2'" "C3'" SING N N 9 A1I59 N1 "C1'" SING N N 10 A1I59 N1 C6 SING N N 11 A1I59 C5 C6 DOUB N N 12 A1I59 C5 CM5 SING N N 13 A1I59 "C1'" "O4'" SING N N 14 A1I59 C1 CM5 SING N N 15 A1I59 C1 C3 SING N N 16 A1I59 "C3'" "O3'" SING N N 17 A1I59 "C3'" "C4'" SING N N 18 A1I59 CM5 N5 SING N N 19 A1I59 C3 O4 SING N N 20 A1I59 C3 O1 SING N N 21 A1I59 "O4'" "C4'" SING N N 22 A1I59 "C4'" "C5'" SING N N 23 A1I59 "O5'" "C5'" SING N N 24 A1I59 "O5'" P SING N N 25 A1I59 OP3 P SING N N 26 A1I59 P OP2 SING N N 27 A1I59 C1 H1 SING N N 28 A1I59 C1 H2 SING N N 29 A1I59 "C1'" "H1'" SING N N 30 A1I59 "C2'" "H2'" SING N N 31 A1I59 "C3'" "H3'" SING N N 32 A1I59 "C4'" "H4'" SING N N 33 A1I59 "C5'" "H5'" SING N N 34 A1I59 "C5'" "H5''" SING N N 35 A1I59 C6 H6 SING N N 36 A1I59 O1 H10 SING N N 37 A1I59 CM5 H11 SING N N 38 A1I59 O4 H12 SING N N 39 A1I59 N4 H41 SING N N 40 A1I59 N4 H42 SING N N 41 A1I59 "O2'" "HO2'" SING N N 42 A1I59 "O3'" "HO3'" SING N N 43 A1I59 OP2 HOP2 SING N N 44 A1I59 OP3 HOP3 SING N N 45 A1I59 N5 H19 SING N N 46 A1I59 N5 H20 SING N N 47 A1I59 P OP1 DOUB N N 48 A1I59 C3 H22 SING N N 49 # 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 A1I59 InChI InChI 1.06 "InChI=1S/C12H21N4O10P/c13-5(1-7(17)18)4-2-16(12(21)15-10(4)14)11-9(20)8(19)6(26-11)3-25-27(22,23)24/h2,5-9,11,17-20H,1,3,13H2,(H2,14,15,21)(H2,22,23,24)/t5-,6+,8+,9+,11+/m0/s1" A1I59 InChIKey InChI 1.06 MVVSSDOMXIJOEA-DANLAGSESA-N A1I59 SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CC(O)O)C1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N=C1N" A1I59 SMILES CACTVS 3.385 "N[CH](CC(O)O)C1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N=C1N" A1I59 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)[C@H](CC(O)O)N" A1I59 SMILES "OpenEye OEToolkits" 2.0.7 "C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)C(CC(O)O)N" # _pdbx_chem_comp_identifier.comp_id A1I59 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-5-[4-azanyl-5-[(1~{S})-1-azanyl-3,3-bis(oxidanyl)propyl]-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(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 A1I59 "Create component" 2025-03-17 PDBE A1I59 "Modify leaving atom flag" 2025-03-18 PDBE A1I59 "Initial release" 2025-11-05 RCSB #