data_A1I2I # _chem_comp.id A1I2I _chem_comp.name "[[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H18 N3 O13 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-02-17 _chem_comp.pdbx_modified_date 2025-04-25 _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 481.184 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1I2I _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 9HFT _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 A1I2I "C1'" C1 C 0 1 N N R N N N 89.179 76.890 85.722 -3.925 -0.482 1.324 "C1'" A1I2I 1 A1I2I C2 C2 C 0 1 N N N N N N 90.225 78.233 84.008 -4.910 0.354 -0.737 C2 A1I2I 2 A1I2I "C2'" C3 C 0 1 N N N N N N 87.729 76.909 86.155 -4.507 -1.906 1.220 "C2'" A1I2I 3 A1I2I "C3'" C4 C 0 1 N N S N N N 87.617 75.732 87.008 -3.374 -2.731 0.562 "C3'" A1I2I 4 A1I2I C4 C5 C 0 1 N N N N N N 89.519 78.139 81.766 -6.348 2.161 -0.802 C4 A1I2I 5 A1I2I "C4'" C6 C 0 1 N N R N N N 88.772 74.846 86.737 -2.125 -1.862 0.859 "C4'" A1I2I 6 A1I2I C5 C7 C 0 1 N N N N N N 88.574 77.207 82.124 -6.240 2.295 0.597 C5 A1I2I 7 A1I2I "C5'" C8 C 0 1 N N N N N N 88.285 73.555 86.047 -1.023 -2.134 -0.167 "C5'" A1I2I 8 A1I2I C5A C9 C 0 1 N N N N N N 87.624 76.615 81.043 -6.999 3.375 1.324 C5A A1I2I 9 A1I2I C6 C10 C 0 1 N N N N N N 88.463 76.796 83.430 -5.443 1.437 1.278 C6 A1I2I 10 A1I2I N1 N1 N 0 1 N N N N N N 89.289 77.310 84.364 -4.781 0.459 0.598 N1 A1I2I 11 A1I2I N3 N2 N 0 1 N N N N N N 90.334 78.645 82.693 -5.681 1.196 -1.422 N3 A1I2I 12 A1I2I N4 N3 N 0 1 N N N N N N 89.628 78.573 80.374 -7.151 3.018 -1.519 N4 A1I2I 13 A1I2I O1A O1 O 0 1 N N N N N N 84.980 71.820 87.168 2.120 -2.954 -0.621 O1A A1I2I 14 A1I2I O1B O2 O 0 1 N N N N N N 88.129 70.038 84.947 4.673 -0.674 -1.436 O1B A1I2I 15 A1I2I O1G O3 O 0 1 N N N N N N 84.845 67.446 82.124 6.463 2.807 0.292 O1G A1I2I 16 A1I2I O2 O4 O 0 1 N N N N N N 90.958 78.691 84.828 -4.307 -0.525 -1.331 O2 A1I2I 17 A1I2I O2A O5 O 0 1 N N N N N N 85.153 73.837 85.759 1.228 -1.087 -2.066 O2A A1I2I 18 A1I2I O2B O6 O 0 1 N N N N N N 86.057 69.359 86.094 3.486 1.553 -1.509 O2B A1I2I 19 A1I2I O2G O7 O 0 1 N N N N N N 83.727 68.476 84.079 6.822 1.135 2.288 O2G A1I2I 20 A1I2I "O3'" O8 O 0 1 N N N N N N 87.643 76.147 88.420 -3.258 -4.017 1.174 "O3'" A1I2I 21 A1I2I O3A O9 O 0 1 N N N N N N 86.073 71.600 84.811 2.583 -0.432 -0.041 O3A A1I2I 22 A1I2I O3B O10 O 0 1 N N N N N N 86.138 69.213 83.509 4.820 0.781 0.622 O3B A1I2I 23 A1I2I O3G O11 O 0 1 N N N N N N 85.565 66.861 84.423 7.211 0.429 -0.104 O3G A1I2I 24 A1I2I "O4'" O12 O 0 1 N N N N N N 89.692 75.528 85.871 -2.616 -0.511 0.731 "O4'" A1I2I 25 A1I2I "O5'" O13 O 0 1 N N N N N N 87.315 72.918 86.855 0.154 -1.411 0.195 "O5'" A1I2I 26 A1I2I PA P1 P 0 1 N N N N N N 85.838 72.557 86.165 1.515 -1.463 -0.664 PA A1I2I 27 A1I2I PB P2 P 0 1 N N N N N N 86.624 70.041 84.873 3.907 0.286 -0.609 PB A1I2I 28 A1I2I PG P3 P 0 1 N N N N N N 85.047 67.972 83.535 6.348 1.270 0.756 PG A1I2I 29 A1I2I "H1'" H1 H 0 1 N N N N N N 89.751 77.569 86.372 -3.852 -0.188 2.371 "H1'" A1I2I 30 A1I2I "H2'1" H2 H 0 0 N N N N N N 87.498 77.826 86.717 -4.737 -2.297 2.211 "H2'1" A1I2I 31 A1I2I "H2'2" H3 H 0 0 N N N N N N 87.058 76.832 85.287 -5.397 -1.910 0.591 "H2'2" A1I2I 32 A1I2I "H3'" H4 H 0 1 N N N N N N 86.680 75.198 86.793 -3.535 -2.826 -0.512 "H3'" A1I2I 33 A1I2I "H4'" H5 H 0 1 N N N N N N 89.265 74.579 87.684 -1.762 -2.045 1.870 "H4'" A1I2I 34 A1I2I "H5'2" H6 H 0 0 N N N N N N 87.841 73.807 85.073 -0.802 -3.201 -0.189 "H5'2" A1I2I 35 A1I2I "H5'1" H7 H 0 0 N N N N N N 89.138 72.877 85.897 -1.358 -1.813 -1.154 "H5'1" A1I2I 36 A1I2I H5A3 H8 H 0 0 N N N N N N 86.941 75.891 81.511 -7.579 3.956 0.607 H5A3 A1I2I 37 A1I2I H5A2 H9 H 0 0 N N N N N N 87.040 77.426 80.584 -7.671 2.920 2.052 H5A2 A1I2I 38 A1I2I H5A1 H10 H 0 0 N N N N N N 88.220 76.109 80.269 -6.296 4.030 1.839 H5A1 A1I2I 39 A1I2I H1 H11 H 0 1 N N N N N N 87.718 76.065 83.707 -5.343 1.520 2.351 H1 A1I2I 40 A1I2I HN42 H12 H 0 0 N N N N N N 90.315 79.251 80.114 -7.644 3.717 -1.061 HN42 A1I2I 41 A1I2I HN41 H13 H 0 0 N N N N N N 89.015 78.191 79.682 -7.223 2.924 -2.481 HN41 A1I2I 42 A1I2I H2 H14 H 0 1 N N N N N N 84.188 72.317 87.334 2.332 -3.267 0.269 H2 A1I2I 43 A1I2I H4 H15 H 0 1 N N N N N N 85.086 66.528 82.090 5.922 3.417 0.812 H4 A1I2I 44 A1I2I H3 H16 H 0 1 N N N N N N 86.768 69.070 86.655 2.980 2.224 -1.031 H3 A1I2I 45 A1I2I H5 H17 H 0 1 N N N N N N 83.501 67.990 84.863 7.735 1.412 2.443 H5 A1I2I 46 A1I2I "HO3'" H18 H 0 0 N N N N N N 87.570 75.381 88.977 -4.051 -4.564 1.093 "HO3'" A1I2I 47 # 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 A1I2I N1 C2 SING N N 1 A1I2I N1 C6 SING N N 2 A1I2I N1 "C1'" SING N N 3 A1I2I C2 N3 SING N N 4 A1I2I C2 O2 DOUB N N 5 A1I2I N3 C4 DOUB N N 6 A1I2I C4 C5 SING N N 7 A1I2I C4 N4 SING N N 8 A1I2I C5 C6 DOUB N N 9 A1I2I C5 C5A SING N N 10 A1I2I "C1'" "C2'" SING N N 11 A1I2I "C1'" "O4'" SING N N 12 A1I2I "C2'" "C3'" SING N N 13 A1I2I "C3'" "C4'" SING N N 14 A1I2I "C3'" "O3'" SING N N 15 A1I2I "C4'" "O4'" SING N N 16 A1I2I "C4'" "C5'" SING N N 17 A1I2I "C5'" "O5'" SING N N 18 A1I2I "O5'" PA SING N N 19 A1I2I PA O1A SING N N 20 A1I2I PA O2A DOUB N N 21 A1I2I PA O3A SING N N 22 A1I2I O3A PB SING N N 23 A1I2I PB O1B DOUB N N 24 A1I2I PB O2B SING N N 25 A1I2I PB O3B SING N N 26 A1I2I O3B PG SING N N 27 A1I2I PG O1G SING N N 28 A1I2I PG O2G SING N N 29 A1I2I PG O3G DOUB N N 30 A1I2I "C1'" "H1'" SING N N 31 A1I2I "C2'" "H2'1" SING N N 32 A1I2I "C2'" "H2'2" SING N N 33 A1I2I "C3'" "H3'" SING N N 34 A1I2I "C4'" "H4'" SING N N 35 A1I2I "C5'" "H5'2" SING N N 36 A1I2I "C5'" "H5'1" SING N N 37 A1I2I C5A H5A3 SING N N 38 A1I2I C5A H5A2 SING N N 39 A1I2I C5A H5A1 SING N N 40 A1I2I C6 H1 SING N N 41 A1I2I N4 HN42 SING N N 42 A1I2I N4 HN41 SING N N 43 A1I2I O1A H2 SING N N 44 A1I2I O1G H4 SING N N 45 A1I2I O2B H3 SING N N 46 A1I2I O2G H5 SING N N 47 A1I2I "O3'" "HO3'" SING N N 48 # 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 A1I2I InChI InChI 1.06 "InChI=1S/C10H18N3O13P3/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,14H,2,4H2,1H3,(H,19,20)(H,21,22)(H2,11,12,15)(H2,16,17,18)" A1I2I InChIKey InChI 1.06 NGYHUCPPLJOZIX-UHFFFAOYSA-N A1I2I SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)N=C1N" A1I2I SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)N=C1N" A1I2I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" A1I2I SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id A1I2I _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},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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 A1I2I "Create component" 2025-02-17 PDBE A1I2I "Initial release" 2025-04-30 RCSB #