data_A1D8A
# 
_chem_comp.id                                    A1D8A 
_chem_comp.name                                  "[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H24 N5 O17 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-05-15 
_chem_comp.pdbx_modified_date                    2024-11-01 
_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                        639.296 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D8A 
_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        8ZF0 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_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 
A1D8A "C1'" C1  C 0 1 N N R N N N 105.625 123.142 113.416 0.253  -0.124 1.486  "C1'" A1D8A 1  
A1D8A "C2'" C2  C 0 1 N N R N N N 106.854 124.197 113.790 -0.273 -1.260 0.572  "C2'" A1D8A 2  
A1D8A "C3'" C3  C 0 1 N N R N N N 107.586 123.629 114.626 0.960  -2.192 0.472  "C3'" A1D8A 3  
A1D8A "C4'" C4  C 0 1 N N R N N N 106.782 122.379 115.162 2.150  -1.285 0.842  "C4'" A1D8A 4  
A1D8A "C5'" C5  C 0 1 N N N N N N 106.606 122.462 116.571 3.156  -1.252 -0.311 "C5'" A1D8A 5  
A1D8A "O2'" O1  O 0 1 N N N N N N 107.646 124.501 112.570 -1.375 -1.936 1.181  "O2'" A1D8A 6  
A1D8A "O5'" O2  O 0 1 N N N N N N 107.743 123.028 117.119 4.308  -0.504 0.084  "O5'" A1D8A 7  
A1D8A C2    C6  C 0 1 Y N N N N N 102.248 122.249 110.710 -3.614 1.482  3.104  C2    A1D8A 8  
A1D8A C26   C7  C 0 1 N N S N N N 107.066 125.648 111.873 -2.313 -2.476 0.248  C26   A1D8A 9  
A1D8A C28   C8  C 0 1 N N R N N N 106.706 125.174 109.445 -4.241 -1.984 -0.936 C28   A1D8A 10 
A1D8A C29   C9  C 0 1 N N N N N N 106.568 123.786 108.761 -5.360 -0.941 -0.887 C29   A1D8A 11 
A1D8A C35   C10 C 0 1 N N S N N N 107.959 125.439 109.698 -4.600 -3.182 -0.030 C35   A1D8A 12 
A1D8A C37   C11 C 0 1 N N R N N N 107.971 126.238 111.154 -3.434 -3.249 0.987  C37   A1D8A 13 
A1D8A C4    C12 C 0 1 Y N N N N N 103.459 123.471 112.242 -1.691 1.457  1.845  C4    A1D8A 14 
A1D8A C5    C13 C 0 1 Y N N N N N 102.492 124.441 112.232 -2.028 2.718  1.326  C5    A1D8A 15 
A1D8A C6    C14 C 0 1 Y N N N N N 101.363 124.263 111.404 -3.215 3.324  1.771  C6    A1D8A 16 
A1D8A C8    C15 C 0 1 Y N N N N N 104.056 125.021 113.589 -0.146 2.130  0.423  C8    A1D8A 17 
A1D8A N1    N1  N 0 1 Y N N N N N 101.284 123.176 110.675 -3.969 2.670  2.648  N1    A1D8A 18 
A1D8A N3    N2  N 0 1 Y N N N N N 103.317 122.383 111.473 -2.506 0.882  2.723  N3    A1D8A 19 
A1D8A N6    N3  N 0 1 N N N N N N 100.283 125.286 111.354 -3.598 4.566  1.296  N6    A1D8A 20 
A1D8A N7    N4  N 0 1 Y N N N N N 102.893 125.386 113.077 -1.043 3.071  0.465  N7    A1D8A 21 
A1D8A N9    N5  N 0 1 Y N N N N N 104.415 123.867 113.094 -0.501 1.112  1.258  N9    A1D8A 22 
A1D8A O1A   O3  O 0 1 N N N N N N 108.083 123.575 119.599 5.120  0.628  -2.145 O1A   A1D8A 23 
A1D8A O1B   O4  O 0 1 N N N N N N 108.554 120.386 121.200 8.476  1.977  -1.375 O1B   A1D8A 24 
A1D8A O27   O5  O 0 1 N N N N N N 105.985 125.159 110.837 -3.021 -1.416 -0.430 O27   A1D8A 25 
A1D8A O2A   O6  O 0 1 N N N N N N 109.686 122.118 118.487 6.082  -1.569 -1.361 O2A   A1D8A 26 
A1D8A O2B   O7  O 0 1 N N N N N N 106.613 121.810 121.401 9.024  1.128  1.053  O2B   A1D8A 27 
A1D8A "O3'" O8  O 0 1 N N N N N N 108.891 123.162 113.953 0.847  -3.272 1.401  "O3'" A1D8A 28 
A1D8A O30   O9  O 0 1 N N N N N N 107.842 123.393 108.258 -5.075 0.107  -1.815 O30   A1D8A 29 
A1D8A O32   O10 O 0 1 N N N N N N 109.432 121.357 108.565 -5.351 2.414  -3.047 O32   A1D8A 30 
A1D8A O33   O11 O 0 1 N N N N N N 106.991 120.923 108.565 -7.449 0.882  -2.639 O33   A1D8A 31 
A1D8A O34   O12 O 0 1 N N N N N N 108.167 121.530 106.434 -6.277 2.043  -0.728 O34   A1D8A 32 
A1D8A O36   O13 O 0 1 N N N N N N 108.499 126.286 108.670 -4.666 -4.386 -0.795 O36   A1D8A 33 
A1D8A O38   O14 O 0 1 N N N N N N 107.622 127.634 110.957 -3.046 -4.603 1.229  O38   A1D8A 34 
A1D8A O3A   O15 O 0 1 N N N N N N 107.401 121.198 119.025 6.732  0.501  -0.072 O3A   A1D8A 35 
A1D8A O3B   O16 O 0 1 N N N N N N 106.328 119.493 120.694 8.911  -0.465 -0.902 O3B   A1D8A 36 
A1D8A "O4'" O17 O 0 1 N N N N N N 105.430 122.441 114.466 1.627  0.034  1.072  "O4'" A1D8A 37 
A1D8A P31   P1  P 0 1 N N N N N N 108.119 121.761 107.953 -6.043 1.376  -2.029 P31   A1D8A 38 
A1D8A PA    P2  P 0 1 N N N N N N 108.258 122.487 118.579 5.572  -0.265 -0.884 PA    A1D8A 39 
A1D8A PB    P3  P 0 1 N N N N N N 107.220 120.719 120.628 8.299  0.758  -0.337 PB    A1D8A 40 
A1D8A H1    H1  H 0 1 N N N N N N 105.952 122.544 112.553 0.200  -0.419 2.534  H1    A1D8A 41 
A1D8A H2    H2  H 0 1 N N N N N N 106.391 125.121 114.168 -0.549 -0.874 -0.409 H2    A1D8A 42 
A1D8A H3    H3  H 0 1 N N N N N N 107.841 124.267 115.485 1.070  -2.571 -0.544 H3    A1D8A 43 
A1D8A H4    H4  H 0 1 N N N N N N 107.311 121.458 114.876 2.633  -1.657 1.745  H4    A1D8A 44 
A1D8A H5    H5  H 0 1 N N N N N N 105.731 123.089 116.800 3.452  -2.270 -0.563 H5    A1D8A 45 
A1D8A H6    H6  H 0 1 N N N N N N 106.455 121.455 116.987 2.697  -0.781 -1.180 H6    A1D8A 46 
A1D8A H7    H7  H 0 1 N N N N N N 102.149 121.366 110.096 -4.254 0.988  3.820  H7    A1D8A 47 
A1D8A H8    H8  H 0 1 N N N N N N 106.583 126.325 112.593 -1.810 -3.122 -0.470 H8    A1D8A 48 
A1D8A H9    H9  H 0 1 N N N N N N 106.231 125.935 108.808 -4.095 -2.325 -1.961 H9    A1D8A 49 
A1D8A H10   H10 H 0 1 N N N N N N 105.848 123.852 107.932 -6.307 -1.412 -1.150 H10   A1D8A 50 
A1D8A H11   H11 H 0 1 N N N N N N 106.216 123.046 109.495 -5.427 -0.527 0.119  H11   A1D8A 51 
A1D8A H12   H12 H 0 1 N N N N N N 108.570 124.532 109.810 -5.544 -3.003 0.484  H12   A1D8A 52 
A1D8A H13   H13 H 0 1 N N N N N N 108.982 126.150 111.578 -3.702 -2.751 1.919  H13   A1D8A 53 
A1D8A H14   H14 H 0 1 N N N N N N 104.624 125.592 114.309 0.748  2.152  -0.182 H14   A1D8A 54 
A1D8A H15   H15 H 0 1 N N N N N N 99.572  124.990 110.716 -3.045 5.029  0.647  H15   A1D8A 55 
A1D8A H16   H16 H 0 1 N N N N N N 99.887  125.397 112.266 -4.420 4.974  1.611  H16   A1D8A 56 
A1D8A H17   H17 H 0 1 N N N N N N 108.928 123.799 119.972 4.774  1.499  -1.906 H17   A1D8A 57 
A1D8A H18   H18 H 0 1 N N N N N N 108.560 119.479 121.483 8.097  2.812  -1.069 H18   A1D8A 58 
A1D8A H19   H19 H 0 1 N N N N N N 105.792 121.514 121.777 9.973  1.296  0.969  H19   A1D8A 59 
A1D8A H20   H20 H 0 1 N N N N N N 109.442 122.731 114.595 1.593  -3.887 1.382  H20   A1D8A 60 
A1D8A H21   H21 H 0 1 N N N N N N 110.016 121.044 107.884 -5.879 3.204  -3.222 H21   A1D8A 61 
A1D8A H22   H22 H 0 1 N N N N N N 106.553 120.432 107.880 -7.372 0.436  -3.493 H22   A1D8A 62 
A1D8A H23   H23 H 0 1 N N N N N N 109.410 126.474 108.861 -4.887 -5.171 -0.276 H23   A1D8A 63 
A1D8A H24   H24 H 0 1 N N N N N N 107.631 128.084 111.794 -2.319 -4.698 1.859  H24   A1D8A 64 
# 
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 
A1D8A O34   P31   DOUB N N 1  
A1D8A P31   O30   SING N N 2  
A1D8A P31   O33   SING N N 3  
A1D8A P31   O32   SING N N 4  
A1D8A O30   C29   SING N N 5  
A1D8A O36   C35   SING N N 6  
A1D8A C29   C28   SING N N 7  
A1D8A C28   C35   SING N N 8  
A1D8A C28   O27   SING N N 9  
A1D8A C35   C37   SING N N 10 
A1D8A N1    C2    DOUB Y N 11 
A1D8A N1    C6    SING Y N 12 
A1D8A C2    N3    SING Y N 13 
A1D8A O27   C26   SING N N 14 
A1D8A O38   C37   SING N N 15 
A1D8A C37   C26   SING N N 16 
A1D8A N6    C6    SING N N 17 
A1D8A C6    C5    DOUB Y N 18 
A1D8A N3    C4    DOUB Y N 19 
A1D8A C26   "O2'" SING N N 20 
A1D8A C5    C4    SING Y N 21 
A1D8A C5    N7    SING Y N 22 
A1D8A C4    N9    SING Y N 23 
A1D8A "O2'" "C2'" SING N N 24 
A1D8A N7    C8    DOUB Y N 25 
A1D8A N9    "C1'" SING N N 26 
A1D8A N9    C8    SING Y N 27 
A1D8A "C1'" "C2'" SING N N 28 
A1D8A "C1'" "O4'" SING N N 29 
A1D8A "C2'" "C3'" SING N N 30 
A1D8A "O3'" "C3'" SING N N 31 
A1D8A "O4'" "C4'" SING N N 32 
A1D8A "C3'" "C4'" SING N N 33 
A1D8A "C4'" "C5'" SING N N 34 
A1D8A "C5'" "O5'" SING N N 35 
A1D8A "O5'" PA    SING N N 36 
A1D8A O2A   PA    DOUB N N 37 
A1D8A PA    O3A   SING N N 38 
A1D8A PA    O1A   SING N N 39 
A1D8A O3A   PB    SING N N 40 
A1D8A PB    O3B   DOUB N N 41 
A1D8A PB    O1B   SING N N 42 
A1D8A PB    O2B   SING N N 43 
A1D8A "C1'" H1    SING N N 44 
A1D8A "C2'" H2    SING N N 45 
A1D8A "C3'" H3    SING N N 46 
A1D8A "C4'" H4    SING N N 47 
A1D8A "C5'" H5    SING N N 48 
A1D8A "C5'" H6    SING N N 49 
A1D8A C2    H7    SING N N 50 
A1D8A C26   H8    SING N N 51 
A1D8A C28   H9    SING N N 52 
A1D8A C29   H10   SING N N 53 
A1D8A C29   H11   SING N N 54 
A1D8A C35   H12   SING N N 55 
A1D8A C37   H13   SING N N 56 
A1D8A C8    H14   SING N N 57 
A1D8A N6    H15   SING N N 58 
A1D8A N6    H16   SING N N 59 
A1D8A O1A   H17   SING N N 60 
A1D8A O1B   H18   SING N N 61 
A1D8A O2B   H19   SING N N 62 
A1D8A "O3'" H20   SING N N 63 
A1D8A O32   H21   SING N N 64 
A1D8A O33   H22   SING N N 65 
A1D8A O36   H23   SING N N 66 
A1D8A O38   H24   SING N N 67 
# 
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 
A1D8A InChI            InChI                1.06  "InChI=1S/C15H24N5O17P3/c16-12-7-13(18-3-17-12)20(4-19-7)14-11(9(22)6(34-14)2-33-40(30,31)37-39(27,28)29)36-15-10(23)8(21)5(35-15)1-32-38(24,25)26/h3-6,8-11,14-15,21-23H,1-2H2,(H,30,31)(H2,16,17,18)(H2,24,25,26)(H2,27,28,29)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1" 
A1D8A InChIKey         InChI                1.06  GOABUQLPPRUQSR-ZQSHOCFMSA-N                                                                                                                                                                                                                                          
A1D8A SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O"                                                                                                                                                
A1D8A SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O"                                                                                                                                                            
A1D8A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)N"                                                                                                                                              
A1D8A SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)OC4C(C(C(O4)COP(=O)(O)O)O)O)N"                                                                                                                                                                                  
# 
_pdbx_chem_comp_identifier.comp_id           A1D8A 
_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~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl 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 
A1D8A "Create component" 2024-05-15 PDBC 
A1D8A "Initial release"  2024-11-06 RCSB 
# 
