data_A1A7T
# 
_chem_comp.id                                    A1A7T 
_chem_comp.name                                  "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[3-(thiophen-2-ylcarbonylamino)pyridin-1-yl]oxolan-2-yl]methyl hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H30 N7 O14 P2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2024-09-17 
_chem_comp.pdbx_modified_date                    2024-11-22 
_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                        746.557 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1A7T 
_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        9DMU 
_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 
A1A7T C13 C1  C 0 1 N N R N N N 180.224 131.496 123.525 5.364   0.885  -1.944 C13 A1A7T 1  
A1A7T C24 C2  C 0 1 N N N N N N 177.453 135.532 119.922 -1.839  -3.407 0.909  C24 A1A7T 2  
A1A7T C02 C3  C 0 1 Y N N N N N 186.484 131.225 126.896 10.494  1.748  2.920  C02 A1A7T 3  
A1A7T C04 C4  C 0 1 Y N N N N N 185.514 129.041 126.550 9.884   3.829  2.129  C04 A1A7T 4  
A1A7T C06 C5  C 0 1 Y N N N N N 184.097 130.800 126.198 8.776   2.018  1.250  C06 A1A7T 5  
A1A7T C07 C6  C 0 1 Y N N N N N 185.149 131.723 126.528 9.543   1.167  2.063  C07 A1A7T 6  
A1A7T C09 C7  C 0 1 Y N N N N N 183.315 132.924 126.039 8.207   -0.084 0.900  C09 A1A7T 7  
A1A7T C11 C8  C 0 1 N N R N N N 181.569 131.113 125.482 6.951   1.630  -0.461 C11 A1A7T 8  
A1A7T C14 C9  C 0 1 N N N N N N 180.462 132.714 122.425 4.688   -0.365 -2.509 C14 A1A7T 9  
A1A7T C25 C10 C 0 1 N N R N N N 178.343 135.340 118.593 -2.847  -2.504 1.623  C25 A1A7T 10 
A1A7T C27 C11 C 0 1 N N R N N N 179.709 136.715 117.151 -4.744  -1.244 1.332  C27 A1A7T 11 
A1A7T C29 C12 C 0 1 Y N N N N N 181.584 138.612 117.060 -5.801  -1.424 -0.817 C29 A1A7T 12 
A1A7T C30 C13 C 0 1 Y N N N N N 182.153 139.864 117.470 -6.723  -1.042 -1.773 C30 A1A7T 13 
A1A7T C31 C14 C 0 1 Y N N N N N 181.495 140.651 118.438 -7.590  0.003  -1.498 C31 A1A7T 14 
A1A7T C32 C15 C 0 1 Y N N N N N 180.242 140.238 119.049 -7.496  0.632  -0.259 C32 A1A7T 15 
A1A7T C34 C16 C 0 1 N N N N N N 178.065 141.087 120.374 -9.606  1.718  -0.420 C34 A1A7T 16 
A1A7T C36 C17 C 0 1 Y N N N N N 177.436 142.005 121.497 -10.462 2.883  -0.177 C36 A1A7T 17 
A1A7T C37 C18 C 0 1 Y N N N N N 178.051 142.929 122.299 -11.749 3.027  -0.614 C37 A1A7T 18 
A1A7T C38 C19 C 0 1 Y N N N N N 177.161 143.636 123.273 -12.318 4.221  -0.243 C38 A1A7T 19 
A1A7T C39 C20 C 0 1 Y N N N N N 175.852 143.271 123.240 -11.528 5.029  0.474  C39 A1A7T 20 
A1A7T C41 C21 C 0 1 Y N N N N N 179.738 138.971 118.585 -6.543  0.191  0.649  C41 A1A7T 21 
A1A7T C42 C22 C 0 1 N N R N N N 180.547 135.475 117.696 -5.241  -2.505 2.073  C42 A1A7T 22 
A1A7T C44 C23 C 0 1 N N S N N N 179.766 134.968 118.980 -3.965  -3.353 2.269  C44 A1A7T 23 
A1A7T C46 C24 C 0 1 N N S N N N 179.479 131.942 124.868 6.547   1.311  -2.842 C46 A1A7T 24 
A1A7T C48 C25 C 0 1 N N R N N N 180.570 132.192 125.968 7.615   1.812  -1.844 C48 A1A7T 25 
A1A7T N01 N1  N 0 1 N N N N N N 187.595 132.038 127.239 11.279  0.961  3.744  N01 A1A7T 26 
A1A7T N03 N2  N 0 1 Y N N N N N 186.610 129.841 126.889 10.625  3.070  2.916  N03 A1A7T 27 
A1A7T N05 N3  N 0 1 Y N N N N N 184.266 129.427 126.204 8.982   3.329  1.311  N05 A1A7T 28 
A1A7T N08 N4  N 0 1 Y N N N N N 184.607 133.037 126.413 9.146   -0.101 1.801  N08 A1A7T 29 
A1A7T N10 N5  N 0 1 Y N N N N N 182.946 131.567 125.894 7.943   1.201  0.528  N10 A1A7T 30 
A1A7T N28 N6  N 1 1 Y N N N N N 180.402 138.195 117.619 -5.737  -0.807 0.347  N28 A1A7T 31 
A1A7T N33 N7  N 0 1 N N N N N N 179.537 141.050 120.067 -8.349  1.692  0.065  N33 A1A7T 32 
A1A7T O12 O1  O 0 1 N N N N N N 181.453 130.958 124.065 5.960   0.598  -0.660 O12 A1A7T 33 
A1A7T O15 O2  O 0 1 N N N N N N 179.892 133.891 122.801 3.530   -0.674 -1.732 O15 A1A7T 34 
A1A7T O17 O3  O 0 1 N N N N N N 182.190 135.193 122.312 3.382   -3.171 -2.071 O17 A1A7T 35 
A1A7T O18 O4  O 0 1 N N N N N N 180.814 135.808 124.385 1.862   -1.722 -3.473 O18 A1A7T 36 
A1A7T O19 O5  O 0 1 N N N N N N 180.078 136.658 121.953 1.450   -2.048 -0.897 O19 A1A7T 37 
A1A7T O21 O6  O 0 1 N N N N N N 177.704 136.097 122.959 -0.006  -4.003 -1.552 O21 A1A7T 38 
A1A7T O22 O7  O 0 1 N N N N N N 178.239 138.503 122.326 1.322   -4.217 0.584  O22 A1A7T 39 
A1A7T O23 O8  O 0 1 N N N N N N 177.580 136.767 120.431 -0.755  -2.615 0.418  O23 A1A7T 40 
A1A7T O26 O9  O 0 1 N N N N N N 178.505 136.629 117.781 -3.530  -1.660 0.670  O26 A1A7T 41 
A1A7T O35 O10 O 0 1 N N N N N N 177.357 140.358 119.705 -10.031 0.774  -1.060 O35 A1A7T 42 
A1A7T O43 O11 O 0 1 N N N N N N 180.470 134.454 116.762 -5.807  -2.152 3.338  O43 A1A7T 43 
A1A7T O45 O12 O 0 1 N N N N N N 179.823 133.606 119.251 -3.703  -3.550 3.660  O45 A1A7T 44 
A1A7T O47 O13 O 0 1 N N N N N N 178.667 130.921 125.340 6.152   2.364  -3.724 O47 A1A7T 45 
A1A7T O49 O14 O 0 1 N N N N N N 180.195 131.938 127.290 7.912   3.189  -2.079 O49 A1A7T 46 
A1A7T P16 P1  P 0 1 N N N N N N 180.874 135.454 122.944 2.574   -1.931 -2.044 P16 A1A7T 47 
A1A7T P20 P2  P 0 1 N N N N N N 178.459 137.051 122.096 0.492   -3.238 -0.387 P20 A1A7T 48 
A1A7T S40 S1  S 0 1 Y N N N N N 175.687 142.015 121.974 -10.000 4.315  0.731  S40 A1A7T 49 
A1A7T H1  H1  H 0 1 N N N N N N 179.632 130.707 123.038 4.643   1.698  -1.855 H1  A1A7T 50 
A1A7T H2  H2  H 0 1 N N N N N N 176.396 135.357 119.672 -1.458  -4.151 1.608  H2  A1A7T 51 
A1A7T H3  H3  H 0 1 N N N N N N 177.777 134.800 120.677 -2.328  -3.909 0.074  H3  A1A7T 52 
A1A7T H4  H4  H 0 1 N N N N N N 185.688 127.975 126.567 10.024  4.899  2.158  H4  A1A7T 53 
A1A7T H5  H5  H 0 1 N N N N N N 182.651 133.759 125.873 7.711   -0.958 0.505  H5  A1A7T 54 
A1A7T H6  H6  H 0 1 N N N N N N 181.335 130.165 125.988 6.476   2.558  -0.143 H6  A1A7T 55 
A1A7T H7  H7  H 0 1 N N N N N N 181.544 132.871 122.305 4.394   -0.184 -3.543 H7  A1A7T 56 
A1A7T H8  H8  H 0 1 N N N N N N 180.028 132.406 121.462 5.385   -1.203 -2.471 H8  A1A7T 57 
A1A7T H9  H9  H 0 1 N N N N N N 177.897 134.551 117.970 -2.346  -1.899 2.378  H9  A1A7T 58 
A1A7T H10 H10 H 0 1 N N N N N N 179.644 136.680 116.053 -4.535  -0.444 2.042  H10 A1A7T 59 
A1A7T H11 H11 H 0 1 N N N N N N 182.081 138.004 116.319 -5.126  -2.241 -1.024 H11 A1A7T 60 
A1A7T H12 H12 H 0 1 N N N N N N 183.083 140.203 117.038 -6.767  -1.553 -2.724 H12 A1A7T 61 
A1A7T H13 H13 H 0 1 N N N N N N 181.936 141.591 118.735 -8.321  0.322  -2.227 H13 A1A7T 62 
A1A7T H14 H14 H 0 1 N N N N N N 179.109 143.134 122.233 -12.266 2.277  -1.195 H14 A1A7T 63 
A1A7T H15 H15 H 0 1 N N N N N N 177.534 144.385 123.956 -13.330 4.489  -0.511 H15 A1A7T 64 
A1A7T H16 H16 H 0 1 N N N N N N 175.060 143.664 123.860 -11.820 6.001  0.843  H16 A1A7T 65 
A1A7T H17 H17 H 0 1 N N N N N N 178.811 138.601 118.997 -6.461  0.672  1.613  H17 A1A7T 66 
A1A7T H18 H18 H 0 1 N N N N N N 181.573 135.776 117.952 -5.968  -3.044 1.466  H18 A1A7T 67 
A1A7T H19 H19 H 0 1 N N N N N N 180.082 135.567 119.847 -4.060  -4.311 1.759  H19 A1A7T 68 
A1A7T H20 H20 H 0 1 N N N N N N 178.920 132.871 124.683 6.922   0.458  -3.407 H20 A1A7T 69 
A1A7T H21 H21 H 0 1 N N N N N N 181.005 133.194 125.841 8.519   1.207  -1.916 H21 A1A7T 70 
A1A7T H22 H22 H 0 1 N N N N N N 188.382 131.457 127.446 11.176  -0.004 3.735  H22 A1A7T 71 
A1A7T H23 H23 H 0 1 N N N N N N 187.817 132.639 126.472 11.932  1.373  4.331  H23 A1A7T 72 
A1A7T H24 H24 H 0 1 N N N N N N 180.113 141.651 120.621 -8.036  2.408  0.638  H24 A1A7T 73 
A1A7T H25 H25 H 0 1 N N N N N N 181.693 135.823 124.745 1.315   -0.927 -3.527 H25 A1A7T 74 
A1A7T H26 H26 H 0 1 N N N N N N 177.613 138.621 123.031 1.680   -3.782 1.370  H26 A1A7T 75 
A1A7T H27 H27 H 0 1 N N N N N N 180.965 133.704 117.070 -6.135  -2.906 3.846  H27 A1A7T 76 
A1A7T H28 H28 H 0 1 N N N N N N 180.710 133.368 119.493 -4.373  -4.077 4.116  H28 A1A7T 77 
A1A7T H29 H29 H 0 1 N N N N N N 178.233 131.203 126.137 6.857   2.670  -4.311 H29 A1A7T 78 
A1A7T H30 H30 H 0 1 N N N N N N 179.583 132.604 127.580 8.331   3.361  -2.934 H30 A1A7T 79 
# 
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 
A1A7T C13 C14 SING N N 1  
A1A7T C13 C46 SING N N 2  
A1A7T C13 O12 SING N N 3  
A1A7T C24 C25 SING N N 4  
A1A7T C24 O23 SING N N 5  
A1A7T C02 C07 DOUB Y N 6  
A1A7T C02 N01 SING N N 7  
A1A7T C02 N03 SING Y N 8  
A1A7T C04 N03 DOUB Y N 9  
A1A7T C04 N05 SING Y N 10 
A1A7T C06 C07 SING Y N 11 
A1A7T C06 N05 DOUB Y N 12 
A1A7T C06 N10 SING Y N 13 
A1A7T C07 N08 SING Y N 14 
A1A7T C09 N08 DOUB Y N 15 
A1A7T C09 N10 SING Y N 16 
A1A7T C11 C48 SING N N 17 
A1A7T C11 N10 SING N N 18 
A1A7T C11 O12 SING N N 19 
A1A7T C14 O15 SING N N 20 
A1A7T C25 C44 SING N N 21 
A1A7T C25 O26 SING N N 22 
A1A7T C27 C42 SING N N 23 
A1A7T C27 O26 SING N N 24 
A1A7T C29 C30 DOUB Y N 25 
A1A7T C29 N28 SING Y N 26 
A1A7T C30 C31 SING Y N 27 
A1A7T C31 C32 DOUB Y N 28 
A1A7T C32 C41 SING Y N 29 
A1A7T C32 N33 SING N N 30 
A1A7T C34 C36 SING N N 31 
A1A7T C34 N33 SING N N 32 
A1A7T C34 O35 DOUB N N 33 
A1A7T C36 C37 DOUB Y N 34 
A1A7T C36 S40 SING Y N 35 
A1A7T C37 C38 SING Y N 36 
A1A7T C38 C39 DOUB Y N 37 
A1A7T C39 S40 SING Y N 38 
A1A7T C41 N28 DOUB Y N 39 
A1A7T C42 C44 SING N N 40 
A1A7T C42 O43 SING N N 41 
A1A7T C44 O45 SING N N 42 
A1A7T C46 C48 SING N N 43 
A1A7T C46 O47 SING N N 44 
A1A7T C48 O49 SING N N 45 
A1A7T O15 P16 SING N N 46 
A1A7T O17 P16 DOUB N N 47 
A1A7T O18 P16 SING N N 48 
A1A7T O19 P16 SING N N 49 
A1A7T O19 P20 SING N N 50 
A1A7T O21 P20 DOUB N N 51 
A1A7T O22 P20 SING N N 52 
A1A7T O23 P20 SING N N 53 
A1A7T C27 N28 SING N N 54 
A1A7T C13 H1  SING N N 55 
A1A7T C24 H2  SING N N 56 
A1A7T C24 H3  SING N N 57 
A1A7T C04 H4  SING N N 58 
A1A7T C09 H5  SING N N 59 
A1A7T C11 H6  SING N N 60 
A1A7T C14 H7  SING N N 61 
A1A7T C14 H8  SING N N 62 
A1A7T C25 H9  SING N N 63 
A1A7T C27 H10 SING N N 64 
A1A7T C29 H11 SING N N 65 
A1A7T C30 H12 SING N N 66 
A1A7T C31 H13 SING N N 67 
A1A7T C37 H14 SING N N 68 
A1A7T C38 H15 SING N N 69 
A1A7T C39 H16 SING N N 70 
A1A7T C41 H17 SING N N 71 
A1A7T C42 H18 SING N N 72 
A1A7T C44 H19 SING N N 73 
A1A7T C46 H20 SING N N 74 
A1A7T C48 H21 SING N N 75 
A1A7T N01 H22 SING N N 76 
A1A7T N01 H23 SING N N 77 
A1A7T N33 H24 SING N N 78 
A1A7T O18 H25 SING N N 79 
A1A7T O22 H26 SING N N 80 
A1A7T O43 H27 SING N N 81 
A1A7T O45 H28 SING N N 82 
A1A7T O47 H29 SING N N 83 
A1A7T O49 H30 SING N N 84 
# 
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 
A1A7T SMILES           ACDLabs              14.52 "O=C(Nc1ccc[n+](c1)C1OC(COP(=O)(O)OP(=O)(O)OCC2OC(n3cnc4c(N)ncnc43)C(O)C2O)C(O)C1O)c1cccs1"                                                                                                                                                                                                                  
A1A7T InChI            InChI                1.06  "InChI=1S/C25H29N7O14P2S/c26-21-16-22(28-10-27-21)32(11-29-16)25-20(36)18(34)14(45-25)9-43-48(40,41)46-47(38,39)42-8-13-17(33)19(35)24(44-13)31-5-1-3-12(7-31)30-23(37)15-4-2-6-49-15/h1-7,10-11,13-14,17-20,24-25,33-36H,8-9H2,(H4-,26,27,28,30,37,38,39,40,41)/p+1/t13-,14-,17-,18-,19-,20-,24-,25-/m1/s1" 
A1A7T InChIKey         InChI                1.06  DPLWQOAIFYMWQG-DLOVRGRYSA-O                                                                                                                                                                                                                                                                                  
A1A7T SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)[n+]5cccc(NC(=O)c6sccc6)c5)[C@@H](O)[C@H]3O"                                                                                                                                                                           
A1A7T SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)[n+]5cccc(NC(=O)c6sccc6)c5)[CH](O)[CH]3O"                                                                                                                                                                                      
A1A7T SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)NC(=O)c6cccs6"                                                                                                                                                                          
A1A7T SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)NC(=O)c6cccs6"                                                                                                                                                                                                              
# 
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 
A1A7T "SYSTEMATIC NAME" ACDLabs              14.52 "1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-3-[(thiophene-2-carbonyl)amino]pyridin-1-ium (non-preferred name)" 
A1A7T "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[3-(thiophen-2-ylcarbonylamino)pyridin-1-ium-1-yl]oxolan-2-yl]methyl 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 
A1A7T "Create component" 2024-09-17 RCSB 
A1A7T "Initial release"  2024-11-27 RCSB 
# 
