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 
# 
