data_A1IDZ
# 
_chem_comp.id                                    A1IDZ 
_chem_comp.name                                  "[[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H17 N2 O14 P3 Se" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-06-07 
_chem_comp.pdbx_modified_date                    2024-11-08 
_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                        597.160 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IDZ 
_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        9FM3 
_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 
A1IDZ C2   C1  C  0 1 N N N N N N 29.152 7.504  10.116 4.087  0.679  2.189  C2   A1IDZ 1  
A1IDZ C4   C2  C  0 1 N N N N N N 30.759 5.900  9.140  2.400  -0.868 1.714  C4   A1IDZ 2  
A1IDZ C8   C3  C  0 1 N N N N N N 30.377 4.595  6.193  2.256  -3.407 0.075  C8   A1IDZ 3  
A1IDZ C9   C4  C  0 1 N N S N N N 29.644 5.141  4.977  1.010  -4.083 -0.547 C9   A1IDZ 4  
A1IDZ O5   O1  O  0 1 N N N N N N 31.552 4.983  9.309  1.430  -1.498 2.088  O5   A1IDZ 5  
A1IDZ C12  C5  C  0 1 N N N N N N 29.992 7.287  3.630  -1.266 -3.103 -0.119 C12  A1IDZ 6  
A1IDZ C11  C6  C  0 1 N N S N N N 30.612 6.204  4.477  0.060  -2.909 -0.858 C11  A1IDZ 7  
A1IDZ O1   O2  O  0 1 N N N N N N 28.618 7.898  11.150 4.642  1.435  2.964  O1   A1IDZ 8  
A1IDZ C7   C7  C  0 1 N N S N N N 31.131 5.808  6.727  2.125  -1.950 -0.437 C7   A1IDZ 9  
A1IDZ C27  C8  C  0 1 N N N N N N 29.590 7.459  7.739  3.922  -0.351 -0.016 C27  A1IDZ 10 
A1IDZ C28  C9  C  0 1 N N N N N N 28.912 8.019  8.782  4.582  0.517  0.812  C28  A1IDZ 11 
A1IDZ C29  C10 C  0 1 Y N N N N N 27.983 9.118  8.534  5.753  1.269  0.338  C29  A1IDZ 12 
A1IDZ C30  C11 C  0 1 Y N N N N N 27.826 9.877  7.390  6.523  2.161  1.006  C30  A1IDZ 13 
A1IDZ C31  C12 C  0 1 Y N N N N N 26.847 10.879 7.469  7.640  2.806  0.381  C31  A1IDZ 14 
A1IDZ C32  C13 C  0 1 Y N N N N N 26.212 10.949 8.645  7.983  2.566  -0.891 C32  A1IDZ 15 
A1IDZ N3   N1  N  0 1 N N N N N N 30.072 6.472  10.180 3.007  -0.034 2.575  N3   A1IDZ 16 
A1IDZ N6   N2  N  0 1 N N N N N N 30.483 6.426  7.893  2.832  -1.025 0.452  N6   A1IDZ 17 
A1IDZ O10  O3  O  0 1 N N N N N N 29.458 4.114  4.004  1.361  -4.773 -1.748 O10  A1IDZ 18 
A1IDZ O13  O4  O  0 1 N N N N N N 28.921 7.914  4.359  -2.180 -2.075 -0.504 O13  A1IDZ 19 
A1IDZ O15  O5  O  0 1 N N N N N N 28.149 8.899  2.188  -3.628 -1.931 1.559  O15  A1IDZ 20 
A1IDZ O16  O6  O  0 1 N N N N N N 27.204 9.726  4.400  -4.531 -3.247 -0.397 O16  A1IDZ 21 
A1IDZ O17  O7  O  0 1 N N N N N N 26.635 7.427  3.535  -4.372 -0.624 -0.468 O17  A1IDZ 22 
A1IDZ O19  O8  O  0 1 N N N N N N 26.780 4.924  3.631  -5.558 0.457  1.481  O19  A1IDZ 23 
A1IDZ O20  O9  O  0 1 N N N N N N 27.323 6.152  1.474  -6.996 -0.492 -0.363 O20  A1IDZ 24 
A1IDZ O21  O10 O  0 1 N N N N N N 24.960 6.047  2.351  -5.583 1.697  -0.717 O21  A1IDZ 25 
A1IDZ O23  O11 O  0 1 N N N N N N 23.613 6.713  0.255  -7.630 2.942  0.077  O23  A1IDZ 26 
A1IDZ O24  O12 O  0 1 N N N N N N 23.751 8.305  2.207  -5.380 3.888  0.721  O24  A1IDZ 27 
A1IDZ O25  O13 O  0 1 N N N N N N 25.747 7.972  0.712  -6.262 4.016  -1.752 O25  A1IDZ 28 
A1IDZ O26  O14 O  0 1 N N N N N N 31.173 6.772  5.678  0.702  -1.707 -0.402 O26  A1IDZ 29 
A1IDZ P14  P1  P  0 1 N N N N N N 27.716 8.609  3.571  -3.677 -1.968 0.080  P14  A1IDZ 30 
A1IDZ P18  P2  P  0 1 N N N N N N 26.521 6.054  2.718  -5.626 0.264  0.015  P18  A1IDZ 31 
A1IDZ P22  P3  P  0 1 N N N N N N 24.501 7.346  1.303  -6.244 3.132  -0.407 P22  A1IDZ 32 
A1IDZ SE33 SE1 SE 0 0 Y N N N N N 26.802 9.697  9.848  6.623  1.235  -1.442 SE33 A1IDZ 33 
A1IDZ H8A  H1  H  0 1 N N N N N N 31.074 3.794  5.905  2.215  -3.442 1.163  H8A  A1IDZ 34 
A1IDZ H8B  H2  H  0 1 N N N N N N 29.667 4.212  6.941  3.173  -3.869 -0.293 H8B  A1IDZ 35 
A1IDZ H9   H3  H  0 1 N N N N N N 28.690 5.600  5.277  0.551  -4.768 0.166  H9   A1IDZ 36 
A1IDZ H12A H4  H  0 0 N N N N N N 30.755 8.039  3.381  -1.685 -4.076 -0.375 H12A A1IDZ 37 
A1IDZ H12B H5  H  0 0 N N N N N N 29.596 6.846  2.704  -1.093 -3.053 0.956  H12B A1IDZ 38 
A1IDZ H11  H6  H  0 1 N N N N N N 31.405 5.711  3.896  -0.119 -2.852 -1.932 H11  A1IDZ 39 
A1IDZ H7   H7  H  0 1 N N N N N N 32.152 5.499  6.997  2.504  -1.866 -1.456 H7   A1IDZ 40 
A1IDZ H27  H8  H  0 1 N N N N N N 29.417 7.846  6.746  4.256  -0.495 -1.032 H27  A1IDZ 41 
A1IDZ H30  H9  H  0 1 N N N N N N 28.414 9.711  6.500  6.289  2.392  2.035  H30  A1IDZ 42 
A1IDZ H31  H10 H  0 1 N N N N N N 26.624 11.541 6.646  8.224  3.511  0.955  H31  A1IDZ 43 
A1IDZ H32  H11 H  0 1 N N N N N N 25.435 11.667 8.862  8.795  2.987  -1.466 H32  A1IDZ 44 
A1IDZ H3   H12 H  0 1 N N N N N N 30.257 6.100  11.090 2.668  0.056  3.480  H3   A1IDZ 45 
A1IDZ H10  H13 H  0 1 N N N N N N 28.568 4.147  3.674  2.003  -5.485 -1.618 H10  A1IDZ 46 
A1IDZ H1   H14 H  0 1 N N N N N N 27.225 10.531 3.896  -4.605 -3.335 -1.357 H1   A1IDZ 47 
A1IDZ H2   H15 H  0 1 N N N N N N 27.934 5.426  1.433  -7.108 -0.652 -1.311 H2   A1IDZ 48 
A1IDZ H4   H16 H  0 1 N N N N N N 22.838 8.337  1.947  -4.459 4.046  0.472  H4   A1IDZ 49 
A1IDZ H5   H17 H  0 1 N N N N N N 25.746 7.852  -0.230 -6.648 4.896  -1.640 H5   A1IDZ 50 
# 
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 
A1IDZ O1   C2   DOUB N N 1  
A1IDZ C2   N3   SING N N 2  
A1IDZ N3   C4   SING N N 3  
A1IDZ C4   O5   DOUB N N 4  
A1IDZ C4   N6   SING N N 5  
A1IDZ N6   C7   SING N N 6  
A1IDZ C7   C8   SING N N 7  
A1IDZ C8   C9   SING N N 8  
A1IDZ C9   O10  SING N N 9  
A1IDZ C9   C11  SING N N 10 
A1IDZ C11  C12  SING N N 11 
A1IDZ C12  O13  SING N N 12 
A1IDZ O13  P14  SING N N 13 
A1IDZ P14  O15  DOUB N N 14 
A1IDZ P14  O16  SING N N 15 
A1IDZ P14  O17  SING N N 16 
A1IDZ O17  P18  SING N N 17 
A1IDZ P18  O19  DOUB N N 18 
A1IDZ P18  O20  SING N N 19 
A1IDZ P18  O21  SING N N 20 
A1IDZ O21  P22  SING N N 21 
A1IDZ P22  O23  DOUB N N 22 
A1IDZ P22  O24  SING N N 23 
A1IDZ P22  O25  SING N N 24 
A1IDZ C11  O26  SING N N 25 
A1IDZ N6   C27  SING N N 26 
A1IDZ C27  C28  DOUB N N 27 
A1IDZ C28  C29  SING N N 28 
A1IDZ C29  C30  DOUB Y N 29 
A1IDZ C30  C31  SING Y N 30 
A1IDZ C31  C32  DOUB Y N 31 
A1IDZ C32  SE33 SING Y N 32 
A1IDZ O26  C7   SING N N 33 
A1IDZ C28  C2   SING N N 34 
A1IDZ SE33 C29  SING Y N 35 
A1IDZ C8   H8A  SING N N 36 
A1IDZ C8   H8B  SING N N 37 
A1IDZ C9   H9   SING N N 38 
A1IDZ C12  H12A SING N N 39 
A1IDZ C12  H12B SING N N 40 
A1IDZ C11  H11  SING N N 41 
A1IDZ C7   H7   SING N N 42 
A1IDZ C27  H27  SING N N 43 
A1IDZ C30  H30  SING N N 44 
A1IDZ C31  H31  SING N N 45 
A1IDZ C32  H32  SING N N 46 
A1IDZ N3   H3   SING N N 47 
A1IDZ O10  H10  SING N N 48 
A1IDZ O16  H1   SING N N 49 
A1IDZ O20  H2   SING N N 50 
A1IDZ O24  H4   SING N N 51 
A1IDZ O25  H5   SING N N 52 
# 
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 
A1IDZ InChI            InChI                1.06  "InChI=1S/C13H17N2O14P3Se/c16-8-4-11(15-5-7(10-2-1-3-33-10)12(17)14-13(15)18)27-9(8)6-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-3,5,8-9,11,16H,4,6H2,(H,22,23)(H,24,25)(H,14,17,18)(H2,19,20,21)/t8-,9?,11-/m0/s1" 
A1IDZ InChIKey         InChI                1.06  IFHZFLUXRCNTJE-QCZWPSDZSA-N                                                                                                                                                                                        
A1IDZ SMILES_CANONICAL CACTVS               3.385 "O[C@H]1C[C@H](O[C@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(C(=O)NC2=O)c3[se]ccc3"                                                                                                                             
A1IDZ SMILES           CACTVS               3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(C(=O)NC2=O)c3[se]ccc3"                                                                                                                                
A1IDZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc([se]c1)C2=CN(C(=O)NC2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O"                                                                                                                              
A1IDZ SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc([se]c1)C2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O"                                                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           A1IDZ 
_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-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-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 
A1IDZ "Create component" 2024-06-07 PDBE 
A1IDZ "Initial release"  2024-11-13 RCSB 
# 
