data_X0F # _chem_comp.id X0F _chem_comp.name ;2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H16 N5 O14 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-05-25 _chem_comp.pdbx_modified_date 2023-12-22 _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 523.180 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X0F _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 8SY5 _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 X0F C14 C1 C 0 1 N N N N N N 133.272 146.192 132.409 -0.178 -2.565 -0.192 C14 X0F 1 X0F C15 C2 C 0 1 N N R N N N 131.882 146.238 133.068 -1.445 -2.192 0.580 C15 X0F 2 X0F C16 C3 C 0 1 N N S N N N 132.050 146.543 134.596 -2.546 -3.252 0.352 C16 X0F 3 X0F C17 C4 C 0 1 N N R N N N 130.852 145.773 135.256 -3.852 -2.429 0.288 C17 X0F 4 X0F C18 C5 C 0 1 N N R N N N 130.692 144.725 134.526 -3.386 -0.970 0.485 C18 X0F 5 X0F C20 C6 C 0 1 N N N N N N 132.294 142.855 134.394 -4.197 -0.039 -1.719 C20 X0F 6 X0F C22 C7 C 0 1 N N N N N N 132.144 142.044 136.406 -5.561 1.516 -1.066 C22 X0F 7 X0F C23 C8 C 0 1 N N N N N N 132.258 141.251 137.730 -6.476 2.560 -0.914 C23 X0F 8 X0F C26 C9 C 0 1 N N N N N N 130.586 142.760 138.766 -6.280 2.332 1.418 C26 X0F 9 X0F C29 C10 C 0 1 N N N N N N 131.302 143.105 136.316 -5.031 0.909 0.090 C29 X0F 10 X0F N19 N1 N 0 1 N N N N N N 131.399 143.605 135.069 -4.177 -0.064 -0.353 N19 X0F 11 X0F N21 N2 N 0 1 N N N N N N 132.752 141.895 135.221 -5.008 0.887 -2.136 N21 X0F 12 X0F N24 N3 N 0 1 N N N N N N 133.158 140.118 137.826 -7.018 3.180 -2.007 N24 X0F 13 X0F N25 N4 N 0 1 N N N N N N 131.478 141.633 138.865 -6.817 2.947 0.349 N25 X0F 14 X0F N28 N5 N 0 1 N N N N N N 130.480 143.505 137.513 -5.409 1.338 1.291 N28 X0F 15 X0F O02 O1 O 0 1 N N N N N N 131.831 145.181 129.447 2.241 -1.737 -1.989 O02 X0F 16 X0F O03 O2 O 0 1 N N N N N N 134.187 144.560 129.126 3.056 -3.081 -0.013 O03 X0F 17 X0F O04 O3 O 0 1 N N N N N N 133.595 147.039 129.571 3.205 -0.456 -0.039 O04 X0F 18 X0F O06 O4 O 0 1 N N N N N N 134.846 148.972 130.724 5.499 -0.767 -1.046 O06 X0F 19 X0F O07 O5 O 0 1 N N N N N N 135.943 146.775 130.584 4.151 1.215 -1.836 O07 X0F 20 X0F O08 O6 O 0 1 N N N N N N 135.751 148.205 128.438 5.199 1.144 0.575 O08 X0F 21 X0F O10 O7 O 0 1 N N N N N N 137.392 147.684 126.518 7.695 0.923 0.277 O10 X0F 22 X0F O11 O8 O 0 1 N N N N N N 136.461 145.800 127.798 6.693 3.217 -0.046 O11 X0F 23 X0F O12 O9 O 0 1 N N N N N N 135.029 147.067 126.239 6.880 2.128 2.340 O12 X0F 24 X0F O13 O10 O 0 1 N N N N N N 133.350 145.136 131.499 0.862 -1.638 0.123 O13 X0F 25 X0F O27 O11 O 0 1 N N N N N N 129.938 143.078 139.703 -6.602 2.699 2.537 O27 X0F 26 X0F O30 O12 O 0 1 N N N N N N 131.299 145.079 133.005 -2.004 -0.964 0.066 O30 X0F 27 X0F O31 O13 O 0 1 N N N N N N 129.633 146.620 135.223 -4.740 -2.817 1.338 O31 X0F 28 X0F O32 O14 O 0 1 N N N N N N 131.946 147.840 134.817 -2.587 -4.173 1.444 O32 X0F 29 X0F P01 P1 P 0 1 N N N N N N 133.243 145.459 129.887 2.339 -1.728 -0.512 P01 X0F 30 X0F P05 P2 P 0 1 N N N N N N 135.050 147.752 129.860 4.535 0.261 -0.596 P05 X0F 31 X0F P09 P3 P 0 1 N N N N N N 136.166 147.166 127.227 6.640 1.833 0.776 P09 X0F 32 X0F H1 H1 H 0 1 N N N N N N 133.453 147.139 131.880 0.135 -3.571 0.087 H1 X0F 33 X0F H2 H2 H 0 1 N N N N N N 134.037 146.055 133.188 -0.382 -2.533 -1.263 H2 X0F 34 X0F H3 H3 H 0 1 N N N N N N 131.289 147.042 132.608 -1.226 -2.095 1.643 H3 X0F 35 X0F H4 H4 H 0 1 N N N N N N 132.999 146.116 134.952 -2.380 -3.779 -0.587 H4 X0F 36 X0F H5 H5 H 0 1 N N N N N N 131.115 145.537 136.298 -4.332 -2.549 -0.683 H5 X0F 37 X0F H6 H6 H 0 1 N N N N N N 129.630 144.469 134.394 -3.467 -0.683 1.533 H6 X0F 38 X0F H8 H8 H 0 1 N N N N N N 132.593 142.999 133.366 -3.619 -0.691 -2.359 H8 X0F 39 X0F H9 H9 H 0 1 N N N N N N 133.105 139.727 138.745 -6.768 2.896 -2.900 H9 X0F 40 X0F H10 H10 H 0 1 N N N N N N 132.895 139.426 137.154 -7.653 3.904 -1.888 H10 X0F 41 X0F H12 H12 H 0 1 N N N N N N 133.691 144.010 128.531 3.154 -3.143 0.947 H12 X0F 42 X0F H13 H13 H 0 1 N N N N N N 136.187 147.134 131.429 3.521 1.914 -1.613 H13 X0F 43 X0F H14 H14 H 0 1 N N N N N N 137.355 145.556 127.590 6.027 3.863 0.228 H14 X0F 44 X0F H15 H15 H 0 1 N Y N N N N 135.327 147.351 125.383 7.731 2.544 2.536 H15 X0F 45 X0F H17 H17 H 0 1 N N N N N N 128.910 146.151 135.623 -5.016 -3.743 1.298 H17 X0F 46 X0F H18 H18 H 0 1 N N N N N N 132.049 148.013 135.745 -3.261 -4.861 1.353 H18 X0F 47 X0F H7 H7 H 0 1 N N N N N N 131.551 141.122 139.721 -7.451 3.670 0.477 H7 X0F 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 X0F C14 C15 SING N N 1 X0F C14 O13 SING N N 2 X0F C15 C16 SING N N 3 X0F C15 O30 SING N N 4 X0F C16 C17 SING N N 5 X0F C16 O32 SING N N 6 X0F C17 C18 SING N N 7 X0F C17 O31 SING N N 8 X0F C18 N19 SING N N 9 X0F C20 N19 SING N N 10 X0F C20 N21 DOUB N N 11 X0F C22 C23 DOUB N N 12 X0F C22 C29 SING N N 13 X0F C22 N21 SING N N 14 X0F C23 N24 SING N N 15 X0F C23 N25 SING N N 16 X0F C26 N25 SING N N 17 X0F C26 N28 SING N N 18 X0F C26 O27 DOUB N N 19 X0F C29 N19 SING N N 20 X0F C29 N28 DOUB N N 21 X0F O02 P01 DOUB N N 22 X0F O03 P01 SING N N 23 X0F O04 P01 SING N N 24 X0F O04 P05 SING N N 25 X0F O06 P05 DOUB N N 26 X0F O07 P05 SING N N 27 X0F O08 P05 SING N N 28 X0F O08 P09 SING N N 29 X0F O10 P09 DOUB N N 30 X0F O11 P09 SING N N 31 X0F O12 P09 SING N N 32 X0F O13 P01 SING N N 33 X0F C14 H1 SING N N 34 X0F C14 H2 SING N N 35 X0F C15 H3 SING N N 36 X0F C16 H4 SING N N 37 X0F C17 H5 SING N N 38 X0F C18 H6 SING N N 39 X0F C20 H8 SING N N 40 X0F N24 H9 SING N N 41 X0F N24 H10 SING N N 42 X0F O03 H12 SING N N 43 X0F O07 H13 SING N N 44 X0F O11 H14 SING N N 45 X0F O12 H15 SING N N 46 X0F O31 H17 SING N N 47 X0F O32 H18 SING N N 48 X0F O30 C18 SING N N 49 X0F N25 H7 SING N N 50 # 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 X0F SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(N2C=NC3=C(N)NC(=O)N=C32)C(O)C1O" X0F InChI InChI 1.06 "InChI=1S/C10H16N5O14P3/c11-7-4-8(14-10(18)13-7)15(2-12-4)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1" X0F InChIKey InChI 1.06 DJHOBIUAJLDRDQ-UUOKFMHZSA-N X0F SMILES_CANONICAL CACTVS 3.385 "NC1=C2N=CN([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)C2=NC(=O)N1" X0F SMILES CACTVS 3.385 "NC1=C2N=CN([CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O)C2=NC(=O)N1" X0F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=NC2=C(NC(=O)N=C2N1C3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N" X0F SMILES "OpenEye OEToolkits" 2.0.7 "C1=NC2=C(NC(=O)N=C2N1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N" # 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 X0F "SYSTEMATIC NAME" ACDLabs 12.01 ;2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate) ; X0F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R})-5-(6-azanyl-2-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(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 X0F "Create component" 2023-05-25 RCSB X0F "Initial release" 2023-12-27 RCSB #