data_A1ID5 # _chem_comp.id A1ID5 _chem_comp.name ;N3-propargyl adenosine-5'-monophosphate ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H17 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms "[(2R,3S,4R,5R)-5-(6-azanyl-3-prop-2-ynyl-purin-3-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2024-06-13 _chem_comp.pdbx_modified_date 2025-01-31 _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 386.277 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1ID5 _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 9FN3 _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 A1ID5 C2 C1 C 0 1 Y N N N N N 24.699 42.098 36.548 4.932 0.282 0.455 C2 A1ID5 1 A1ID5 "C1'" C2 C 0 1 N N R N N N 21.707 44.482 34.076 0.492 0.640 -0.097 "C1'" A1ID5 2 A1ID5 "C2'" C3 C 0 1 N N R N N N 20.424 45.225 33.726 0.269 1.361 -1.451 "C2'" A1ID5 3 A1ID5 "C3'" C4 C 0 1 N N S N N N 20.874 46.042 32.517 -1.132 1.991 -1.256 "C3'" A1ID5 4 A1ID5 "C4'" C5 C 0 1 N N R N N N 22.357 46.319 32.808 -1.764 1.162 -0.121 "C4'" A1ID5 5 A1ID5 "C5'" C6 C 0 1 N N N N N N 22.690 47.747 33.177 -3.066 0.521 -0.608 "C5'" A1ID5 6 A1ID5 C1P C7 C 0 1 N N N N N N 24.469 43.033 34.323 3.151 1.892 0.617 C1P A1ID5 7 A1ID5 C2P C8 C 0 1 N N N N N N 25.812 42.360 34.041 2.720 1.972 2.022 C2P A1ID5 8 A1ID5 C3P C9 C 0 1 N N N N N N 26.879 41.863 33.886 2.376 2.035 3.143 C3P A1ID5 9 A1ID5 C4 C10 C 0 1 Y N N N N N 22.751 43.248 36.032 2.796 -0.406 -0.042 C4 A1ID5 10 A1ID5 C5 C11 C 0 1 Y N N N N N 22.313 42.990 37.317 3.286 -1.696 -0.310 C5 A1ID5 11 A1ID5 C6 C12 C 0 1 Y N N N N N 23.124 42.265 38.196 4.666 -1.923 -0.171 C6 A1ID5 12 A1ID5 C8 C13 C 0 1 Y N N N N N 20.781 44.107 36.331 1.143 -1.738 -0.637 C8 A1ID5 13 A1ID5 N1 N1 N 0 1 Y N N N N N 24.301 41.838 37.784 5.438 -0.913 0.214 N1 A1ID5 14 A1ID5 N3 N2 N 1 1 Y N N N N N 23.966 42.782 35.671 3.647 0.543 0.334 N3 A1ID5 15 A1ID5 N6 N3 N 0 1 N N N N N N 22.671 41.987 39.546 5.206 -3.173 -0.421 N6 A1ID5 16 A1ID5 N7 N4 N 0 1 Y N N N N N 21.100 43.530 37.473 2.225 -2.459 -0.668 N7 A1ID5 17 A1ID5 N9 N5 N 0 1 Y N N N N N 21.758 43.962 35.449 1.441 -0.465 -0.251 N9 A1ID5 18 A1ID5 "O2'" O1 O 0 1 N N N N N N 19.359 44.337 33.460 1.258 2.370 -1.660 "O2'" A1ID5 19 A1ID5 "O3'" O2 O 0 1 N N N N N N 20.753 45.238 31.347 -1.017 3.362 -0.869 "O3'" A1ID5 20 A1ID5 "O4'" O3 O 0 1 N N N N N N 22.726 45.436 33.904 -0.820 0.139 0.242 "O4'" A1ID5 21 A1ID5 "O5'" O4 O 0 1 N N N N N N 21.674 48.333 33.983 -3.704 -0.148 0.482 "O5'" A1ID5 22 A1ID5 OP1 O5 O 0 1 N N N N N N 20.679 49.627 32.082 -4.985 -1.941 -0.749 OP1 A1ID5 23 A1ID5 OP2 O6 O 0 1 N N N N N N 19.865 49.991 34.539 -5.453 -1.673 1.717 OP2 A1ID5 24 A1ID5 P P1 P 0 1 N N N N N N 20.978 49.702 33.558 -5.100 -0.935 0.331 P A1ID5 25 A1ID5 H2 H1 H 0 1 N N N N N N 25.668 41.737 36.235 5.596 1.075 0.766 H2 A1ID5 26 A1ID5 "H1'" H2 H 0 1 N N N N N N 21.838 43.652 33.366 0.842 1.342 0.659 "H1'" A1ID5 27 A1ID5 "H2'" H3 H 0 1 N N N N N N 20.166 45.909 34.548 0.263 0.648 -2.275 "H2'" A1ID5 28 A1ID5 "H3'" H4 H 0 1 N N N N N N 20.307 46.982 32.444 -1.720 1.899 -2.169 "H3'" A1ID5 29 A1ID5 "H4'" H5 H 0 1 N N N N N N 22.937 46.047 31.914 -1.965 1.802 0.738 "H4'" A1ID5 30 A1ID5 "H5''" H6 H 0 0 N N N N N N 23.638 47.759 33.734 -3.728 1.295 -0.997 "H5''" A1ID5 31 A1ID5 "H5'" H7 H 0 1 N N N N N N 22.799 48.337 32.255 -2.844 -0.198 -1.396 "H5'" A1ID5 32 A1ID5 H1 H8 H 0 1 N N N N N N 24.589 44.119 34.192 2.306 2.112 -0.035 H1 A1ID5 33 A1ID5 H3 H9 H 0 1 N N N N N N 23.731 42.656 33.600 3.946 2.616 0.439 H3 A1ID5 34 A1ID5 H4 H10 H 0 1 N N N N N N 27.832 41.419 33.748 2.069 2.092 4.146 H4 A1ID5 35 A1ID5 H8 H11 H 0 1 N N N N N N 19.853 44.625 36.142 0.153 -2.096 -0.878 H8 A1ID5 36 A1ID5 H62 H12 H 0 1 N N N N N N 23.370 41.462 40.031 4.630 -3.904 -0.695 H62 A1ID5 37 A1ID5 H61 H13 H 0 1 N N N N N N 22.507 42.849 40.027 6.160 -3.317 -0.322 H61 A1ID5 38 A1ID5 "HO2'" H14 H 0 0 N N N N N N 19.134 43.865 34.253 1.161 2.850 -2.494 "HO2'" A1ID5 39 A1ID5 "HO3'" H15 H 0 0 N Y N N N N 19.835 45.070 31.171 -0.625 3.930 -1.547 "HO3'" A1ID5 40 A1ID5 HOP2 H17 H 0 0 N N N N N N 19.047 50.099 34.068 -6.284 -2.168 1.699 HOP2 A1ID5 41 A1ID5 OP3 O7 O 0 1 N Y N N N N 22.121 50.808 33.771 -6.269 0.111 -0.033 OP3 A1ID5 42 A1ID5 HOP3 H18 H 0 0 N Y N N N N 22.365 51.178 32.931 -6.400 0.801 0.632 HOP3 A1ID5 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 A1ID5 "O3'" "C3'" SING N N 1 A1ID5 OP1 P DOUB N N 2 A1ID5 "C3'" "C4'" SING N N 3 A1ID5 "C3'" "C2'" SING N N 4 A1ID5 "C4'" "C5'" SING N N 5 A1ID5 "C4'" "O4'" SING N N 6 A1ID5 "C5'" "O5'" SING N N 7 A1ID5 "O2'" "C2'" SING N N 8 A1ID5 P "O5'" SING N N 9 A1ID5 P OP2 SING N N 10 A1ID5 "C2'" "C1'" SING N N 11 A1ID5 C3P C2P TRIP N N 12 A1ID5 "O4'" "C1'" SING N N 13 A1ID5 C2P C1P SING N N 14 A1ID5 "C1'" N9 SING N N 15 A1ID5 C1P N3 SING N N 16 A1ID5 N9 C4 SING Y N 17 A1ID5 N9 C8 SING Y N 18 A1ID5 N3 C4 SING Y N 19 A1ID5 N3 C2 DOUB Y N 20 A1ID5 C4 C5 DOUB Y N 21 A1ID5 C8 N7 DOUB Y N 22 A1ID5 C2 N1 SING Y N 23 A1ID5 C5 N7 SING Y N 24 A1ID5 C5 C6 SING Y N 25 A1ID5 N1 C6 DOUB Y N 26 A1ID5 C6 N6 SING N N 27 A1ID5 C2 H2 SING N N 28 A1ID5 "C1'" "H1'" SING N N 29 A1ID5 "C2'" "H2'" SING N N 30 A1ID5 "C3'" "H3'" SING N N 31 A1ID5 "C4'" "H4'" SING N N 32 A1ID5 "C5'" "H5''" SING N N 33 A1ID5 "C5'" "H5'" SING N N 34 A1ID5 C1P H1 SING N N 35 A1ID5 C1P H3 SING N N 36 A1ID5 C3P H4 SING N N 37 A1ID5 C8 H8 SING N N 38 A1ID5 N6 H62 SING N N 39 A1ID5 N6 H61 SING N N 40 A1ID5 "O2'" "HO2'" SING N N 41 A1ID5 "O3'" "HO3'" SING N N 42 A1ID5 OP2 HOP2 SING N N 43 A1ID5 P OP3 SING N N 44 A1ID5 OP3 HOP3 SING N N 45 # 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 A1ID5 InChI InChI 1.06 "InChI=1S/C13H16N5O7P/c1-2-3-17-5-16-11(14)8-12(17)18(6-15-8)13-10(20)9(19)7(25-13)4-24-26(21,22)23/h1,5-7,9-10,13-14,19-20H,3-4H2,(H2,21,22,23)/p+1/t7-,9-,10-,13-/m1/s1" A1ID5 InChIKey InChI 1.06 STQVXBAAZLTCOR-QYVSTXNMSA-O A1ID5 SMILES_CANONICAL CACTVS 3.385 "Nc1nc[n+](CC#C)c2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O" A1ID5 SMILES CACTVS 3.385 "Nc1nc[n+](CC#C)c2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O" A1ID5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#CC[n+]1cnc(c2c1n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N" A1ID5 SMILES "OpenEye OEToolkits" 2.0.7 "C#CC[n+]1cnc(c2c1n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N" # _pdbx_chem_comp_identifier.comp_id A1ID5 _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-(6-azanyl-3-prop-2-ynyl-purin-3-ium-9-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 A1ID5 "Create component" 2024-06-13 PDBE A1ID5 "Modify name" 2024-08-30 PDBE A1ID5 "Initial release" 2025-02-05 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1ID5 _pdbx_chem_comp_synonyms.name "[(2R,3S,4R,5R)-5-(6-azanyl-3-prop-2-ynyl-purin-3-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? #