data_A1CC9 # _chem_comp.id A1CC9 _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(3~{S},4~{S},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H26 N4 O23 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-05-19 _chem_comp.pdbx_modified_date 2025-08-29 _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 790.307 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1CC9 _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 9OMX _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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 A1CC9 C10 C1 C 0 1 N N N N N N 22.392 -17.882 15.306 -5.507 5.253 -0.845 C10 A1CC9 1 A1CC9 C11 C2 C 0 1 N N N N N N 20.153 -18.764 16.645 -5.938 2.661 -1.556 C11 A1CC9 2 A1CC9 C07 C3 C 0 1 N N R N N N 18.693 -17.517 15.182 -6.177 2.006 0.773 C07 A1CC9 3 A1CC9 C16 C4 C 0 1 N N R N N N 18.579 -15.987 15.100 -7.593 1.393 0.622 C16 A1CC9 4 A1CC9 C18 C5 C 0 1 N N S N N N 18.516 -15.681 13.590 -7.421 0.010 1.297 C18 A1CC9 5 A1CC9 O26 O1 O 0 1 N N N N N N 17.328 -17.379 7.873 3.093 -2.879 0.092 O26 A1CC9 6 A1CC9 C04 C6 C 0 1 N N N N N N 18.738 -17.220 11.628 -5.605 -1.534 0.500 C04 A1CC9 7 A1CC9 C05 C7 C 0 1 N N R N N N 18.022 -17.005 12.974 -5.901 -0.241 1.263 C05 A1CC9 8 A1CC9 C09 C8 C 0 1 N N N N N N 21.171 -17.495 14.923 -5.725 4.320 0.106 C09 A1CC9 9 A1CC9 C13 C9 C 0 1 N N N N N N 22.518 -18.762 16.413 -5.506 4.863 -2.206 C13 A1CC9 10 A1CC9 N08 N1 N 0 1 N N N N N N 20.054 -17.921 15.581 -5.941 3.019 -0.259 N08 A1CC9 11 A1CC9 N12 N2 N 0 1 N N N N N N 21.395 -19.193 17.073 -5.717 3.570 -2.524 N12 A1CC9 12 A1CC9 O01 O2 O 0 1 N N N N N N 22.436 -17.092 10.969 -4.224 -4.334 0.351 O01 A1CC9 13 A1CC9 O03 O3 O 0 1 N N N N N N 20.083 -16.739 11.716 -4.207 -1.820 0.573 O03 A1CC9 14 A1CC9 O06 O4 O 0 1 N N N N N N 18.385 -18.052 13.886 -5.296 0.877 0.588 O06 A1CC9 15 A1CC9 O14 O5 O 0 1 N N N N N N 23.676 -19.152 16.798 -5.317 5.688 -3.082 O14 A1CC9 16 A1CC9 O15 O6 O 0 1 N N N N N N 19.138 -19.133 17.214 -6.127 1.498 -1.857 O15 A1CC9 17 A1CC9 O17 O7 O 0 1 N N N N N N 17.335 -15.540 15.662 -8.565 2.181 1.312 O17 A1CC9 18 A1CC9 O19 O8 O 0 1 N N N N N N 17.532 -14.664 13.345 -7.894 0.050 2.645 O19 A1CC9 19 A1CC9 O20 O9 O 0 1 N N N N N N 20.538 -17.704 9.328 -1.979 -3.184 0.274 O20 A1CC9 20 A1CC9 O22 O10 O 0 1 N N N N N N 20.180 -17.066 6.879 -0.930 -4.990 -1.143 O22 A1CC9 21 A1CC9 O23 O11 O 0 1 N N N N N N 19.130 -15.537 8.655 0.602 -3.674 0.371 O23 A1CC9 22 A1CC9 O25 O12 O 0 1 N N N N N N 16.885 -14.851 7.579 2.117 -4.685 -1.377 O25 A1CC9 23 A1CC9 O28 O13 O 0 1 N N N N N N 16.393 -19.408 6.569 4.846 -0.980 -0.386 O28 A1CC9 24 A1CC9 O29 O14 O 0 1 N N N N N N 15.813 -17.122 5.758 4.589 -2.953 -1.939 O29 A1CC9 25 A1CC9 O46 O15 O 0 1 N N N N N N 14.809 -18.023 7.833 5.665 -3.381 0.304 O46 A1CC9 26 A1CC9 O47 O16 O 0 1 N N N N N N 16.840 -15.800 9.845 2.576 -5.280 1.033 O47 A1CC9 27 A1CC9 O48 O17 O 0 1 N N N N N N 21.700 -15.682 8.242 -1.106 -5.424 1.338 O48 A1CC9 28 A1CC9 O49 O18 O 0 1 N N N N N N 21.002 -19.061 11.418 -3.683 -2.995 -1.719 O49 A1CC9 29 A1CC9 P02 P1 P 0 1 N N N N N N 21.028 -17.646 10.894 -3.538 -3.110 -0.120 P02 A1CC9 30 A1CC9 P21 P2 P 0 1 N N N N N N 20.412 -16.475 8.248 -0.855 -4.332 0.181 P21 A1CC9 31 A1CC9 P24 P3 P 0 1 N N N N N N 17.519 -15.871 8.496 2.098 -4.142 -0.001 P24 A1CC9 32 A1CC9 P27 P4 P 0 1 N N N N N N 16.072 -18.001 7.003 4.549 -2.557 -0.514 P27 A1CC9 33 A1CC9 H1 H1 H 0 1 N N N N N N 23.268 -17.531 14.782 -5.339 6.285 -0.572 H1 A1CC9 34 A1CC9 H2 H2 H 0 1 N N N N N N 17.969 -17.885 15.924 -6.048 2.434 1.766 H2 A1CC9 35 A1CC9 H3 H3 H 0 1 N N N N N N 19.450 -15.501 15.564 -7.859 1.283 -0.429 H3 A1CC9 36 A1CC9 H4 H4 H 0 1 N N N N N N 19.509 -15.411 13.201 -7.948 -0.758 0.731 H4 A1CC9 37 A1CC9 H5 H5 H 0 1 N N N N N N 18.204 -16.671 10.838 -6.167 -2.355 0.945 H5 A1CC9 38 A1CC9 H6 H6 H 0 1 N N N N N N 18.748 -18.293 11.386 -5.898 -1.416 -0.543 H6 A1CC9 39 A1CC9 H7 H7 H 0 1 N N N N N N 16.934 -16.964 12.819 -5.514 -0.313 2.279 H7 A1CC9 40 A1CC9 H8 H8 H 0 1 N N N N N N 21.067 -16.832 14.077 -5.728 4.599 1.149 H8 A1CC9 41 A1CC9 H9 H9 H 0 1 N N N N N N 21.474 -19.811 17.855 -5.718 3.295 -3.454 H9 A1CC9 42 A1CC9 H10 H10 H 0 1 N N N N N N 17.330 -15.710 16.597 -9.467 1.838 1.247 H10 A1CC9 43 A1CC9 H11 H11 H 0 1 N N N N N N 17.825 -13.842 13.720 -8.834 0.262 2.726 H11 A1CC9 44 A1CC9 H13 H13 H 0 1 N N N N N N 14.142 -17.496 7.409 5.695 -3.172 1.247 H13 A1CC9 45 A1CC9 H14 H14 H 0 1 N N N N N N 16.164 -15.132 9.825 2.588 -4.992 1.956 H14 A1CC9 46 A1CC9 H15 H15 H 0 1 N N N N N N 22.093 -15.722 7.378 -1.071 -5.062 2.234 H15 A1CC9 47 A1CC9 H16 H16 H 0 1 N N N N N N 21.877 -19.315 11.688 -3.256 -2.215 -2.098 H16 A1CC9 48 A1CC9 C1 C10 C 0 1 N N S N N N ? ? ? 6.015 -0.362 -0.928 C1 A1CC9 49 A1CC9 C2 C11 C 0 1 N N N N N N ? ? ? 5.984 1.139 -0.629 C2 A1CC9 50 A1CC9 O1 O19 O 0 1 N N N N N N ? ? ? 6.101 1.377 0.790 O1 A1CC9 51 A1CC9 C4 C12 C 0 1 N N R N N N ? ? ? 6.568 2.727 0.951 C4 A1CC9 52 A1CC9 C5 C13 C 0 1 N N R N N N ? ? ? 7.357 3.094 -0.320 C5 A1CC9 53 A1CC9 C6 C14 C 0 1 N N S N N N ? ? ? 7.235 1.839 -1.218 C6 A1CC9 54 A1CC9 N1 N3 N 0 1 N N N N N N ? ? ? 5.427 3.633 1.109 N1 A1CC9 55 A1CC9 O3 O20 O 0 1 N N N N N N ? ? ? 6.770 4.227 -0.963 O3 A1CC9 56 A1CC9 O2 O21 O 0 1 N N N N N N ? ? ? 8.391 1.008 -1.092 O2 A1CC9 57 A1CC9 C7 C15 C 0 1 N N N N N N ? ? ? 4.177 3.136 1.116 C7 A1CC9 58 A1CC9 N2 N4 N 0 1 N N N N N N ? ? ? 3.111 3.946 1.259 N2 A1CC9 59 A1CC9 C9 C16 C 0 1 N N N N N N ? ? ? 3.282 5.276 1.399 C9 A1CC9 60 A1CC9 C12 C17 C 0 1 N N N N N N ? ? ? 4.593 5.812 1.394 C12 A1CC9 61 A1CC9 C14 C18 C 0 1 N N N N N N ? ? ? 5.644 4.976 1.254 C14 A1CC9 62 A1CC9 O5 O22 O 0 1 N N N N N N ? ? ? 4.008 1.939 0.991 O5 A1CC9 63 A1CC9 O4 O23 O 0 1 N N N N N N ? ? ? 2.319 6.009 1.528 O4 A1CC9 64 A1CC9 H12 H12 H 0 1 N N N N N N ? ? ? 6.903 -0.803 -0.475 H12 A1CC9 65 A1CC9 H17 H17 H 0 1 N N N N N N ? ? ? 6.041 -0.517 -2.006 H17 A1CC9 66 A1CC9 H18 H18 H 0 1 N N N N N N ? ? ? 5.070 1.587 -1.020 H18 A1CC9 67 A1CC9 H19 H19 H 0 1 N N N N N N ? ? ? 7.219 2.792 1.823 H19 A1CC9 68 A1CC9 H20 H20 H 0 1 N N N N N N ? ? ? 8.401 3.290 -0.078 H20 A1CC9 69 A1CC9 H21 H21 H 0 1 N N N N N N ? ? ? 7.071 2.119 -2.258 H21 A1CC9 70 A1CC9 H22 H22 H 0 1 N N N N N N ? ? ? 7.227 4.502 -1.770 H22 A1CC9 71 A1CC9 H23 H23 H 0 1 N N N N N N ? ? ? 9.214 1.436 -1.364 H23 A1CC9 72 A1CC9 H24 H24 H 0 1 N N N N N N ? ? ? 2.217 3.571 1.262 H24 A1CC9 73 A1CC9 H25 H25 H 0 1 N N N N N N ? ? ? 4.749 6.875 1.504 H25 A1CC9 74 A1CC9 H26 H26 H 0 1 N N N N N N ? ? ? 6.651 5.367 1.248 H26 A1CC9 75 # 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 A1CC9 O29 P27 DOUB N N 1 A1CC9 O28 P27 SING N N 2 A1CC9 O22 P21 DOUB N N 3 A1CC9 P27 O46 SING N N 4 A1CC9 P27 O26 SING N N 5 A1CC9 O25 P24 DOUB N N 6 A1CC9 O26 P24 SING N N 7 A1CC9 O48 P21 SING N N 8 A1CC9 P21 O23 SING N N 9 A1CC9 P21 O20 SING N N 10 A1CC9 P24 O23 SING N N 11 A1CC9 P24 O47 SING N N 12 A1CC9 O20 P02 SING N N 13 A1CC9 P02 O01 DOUB N N 14 A1CC9 P02 O49 SING N N 15 A1CC9 P02 O03 SING N N 16 A1CC9 C04 O03 SING N N 17 A1CC9 C04 C05 SING N N 18 A1CC9 C05 C18 SING N N 19 A1CC9 C05 O06 SING N N 20 A1CC9 O19 C18 SING N N 21 A1CC9 C18 C16 SING N N 22 A1CC9 O06 C07 SING N N 23 A1CC9 C09 C10 DOUB N N 24 A1CC9 C09 N08 SING N N 25 A1CC9 C16 C07 SING N N 26 A1CC9 C16 O17 SING N N 27 A1CC9 C07 N08 SING N N 28 A1CC9 C10 C13 SING N N 29 A1CC9 N08 C11 SING N N 30 A1CC9 C13 O14 DOUB N N 31 A1CC9 C13 N12 SING N N 32 A1CC9 C11 N12 SING N N 33 A1CC9 C11 O15 DOUB N N 34 A1CC9 C10 H1 SING N N 35 A1CC9 C07 H2 SING N N 36 A1CC9 C16 H3 SING N N 37 A1CC9 C18 H4 SING N N 38 A1CC9 C04 H5 SING N N 39 A1CC9 C04 H6 SING N N 40 A1CC9 C05 H7 SING N N 41 A1CC9 C09 H8 SING N N 42 A1CC9 N12 H9 SING N N 43 A1CC9 O17 H10 SING N N 44 A1CC9 O19 H11 SING N N 45 A1CC9 O46 H13 SING N N 46 A1CC9 O47 H14 SING N N 47 A1CC9 O48 H15 SING N N 48 A1CC9 O49 H16 SING N N 49 A1CC9 O28 C1 SING N N 50 A1CC9 C1 C2 SING N N 51 A1CC9 C2 O1 SING N N 52 A1CC9 O1 C4 SING N N 53 A1CC9 C4 C5 SING N N 54 A1CC9 C5 C6 SING N N 55 A1CC9 C6 C2 SING N N 56 A1CC9 C4 N1 SING N N 57 A1CC9 C5 O3 SING N N 58 A1CC9 C6 O2 SING N N 59 A1CC9 N1 C7 SING N N 60 A1CC9 C7 N2 SING N N 61 A1CC9 N2 C9 SING N N 62 A1CC9 C9 C12 SING N N 63 A1CC9 C12 C14 DOUB N N 64 A1CC9 C14 N1 SING N N 65 A1CC9 C7 O5 DOUB N N 66 A1CC9 C9 O4 DOUB N N 67 A1CC9 C1 H12 SING N N 68 A1CC9 C1 H17 SING N N 69 A1CC9 C2 H18 SING N N 70 A1CC9 C4 H19 SING N N 71 A1CC9 C5 H20 SING N N 72 A1CC9 C6 H21 SING N N 73 A1CC9 O3 H22 SING N N 74 A1CC9 O2 H23 SING N N 75 A1CC9 N2 H24 SING N N 76 A1CC9 C12 H25 SING N N 77 A1CC9 C14 H26 SING N N 78 # 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 A1CC9 InChI InChI 1.06 "InChI=1S/C18H26N4O23P4/c23-9-1-3-21(17(29)19-9)15-13(27)11(25)7(41-15)5-39-46(31,32)43-48(35,36)45-49(37,38)44-47(33,34)40-6-8-12(26)14(28)16(42-8)22-4-2-10(24)20-18(22)30/h1-4,7-8,11-16,25-28H,5-6H2,(H,31,32)(H,33,34)(H,35,36)(H,37,38)(H,19,23,29)(H,20,24,30)/t7-,8?,11-,12?,13-,14?,15-,16?/m1/s1" A1CC9 InChIKey InChI 1.06 NMLMACJWHPHKGR-JILDPCHGSA-N A1CC9 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OCC2OC(C(O)C2O)N3C=CC(=O)NC3=O)N4C=CC(=O)NC4=O" A1CC9 SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OCC2OC(C(O)C2O)N3C=CC(=O)NC3=O)N4C=CC(=O)NC4=O" A1CC9 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC3[C@H]([C@@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)O)O" A1CC9 SMILES "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id A1CC9 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 3.1.0.0 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(3~{S},4~{S},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] 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 A1CC9 "Create component" 2025-05-19 RCSB A1CC9 "Initial release" 2025-09-03 RCSB #