data_A1H3D
# 
_chem_comp.id                                    A1H3D 
_chem_comp.name                                  "3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]benzoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H19 N5 O5 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-02-01 
_chem_comp.pdbx_modified_date                    2024-02-09 
_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                        417.439 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1H3D 
_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        8RVA 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
A1H3D C1   C1  C 0 1 N N S N N N 53.979 -66.898 -29.538 2.764  2.100  -0.493 C1   A1H3D 1  
A1H3D C11  C2  C 0 1 Y N N N N N 51.246 -64.697 -28.954 4.640  -0.437 0.512  C11  A1H3D 2  
A1H3D C12  C3  C 0 1 Y N N N N N 50.448 -64.064 -29.895 5.191  -1.556 -0.134 C12  A1H3D 3  
A1H3D C14  C4  C 0 1 Y N N N N N 52.408 -64.496 -30.783 3.229  -1.216 -0.993 C14  A1H3D 4  
A1H3D C16  C5  C 0 1 Y N N N N N 49.505 -64.581 -27.402 6.546  -0.255 1.783  C16  A1H3D 5  
A1H3D C18  C6  C 0 1 Y N N N N N 49.148 -63.697 -29.542 6.474  -1.981 0.252  C18  A1H3D 6  
A1H3D C2   C7  C 0 1 N N R N N N 55.420 -67.075 -29.093 1.374  2.686  -0.828 C2   A1H3D 7  
A1H3D C20  C8  C 0 1 N N N N N N 58.383 -65.478 -27.293 -3.419 0.374  -1.475 C20  A1H3D 8  
A1H3D C21  C9  C 0 1 Y N N N N N 59.375 -66.290 -26.544 -4.524 -0.493 -0.929 C21  A1H3D 9  
A1H3D C22  C10 C 0 1 Y N N N N N 59.928 -67.461 -27.038 -4.526 -1.852 -1.185 C22  A1H3D 10 
A1H3D C23  C11 C 0 1 Y N N N N N 60.848 -68.149 -26.255 -5.536 -2.655 -0.687 C23  A1H3D 11 
A1H3D C24  C12 C 0 1 Y N N N N N 61.207 -67.680 -24.995 -6.550 -2.104 0.069  C24  A1H3D 12 
A1H3D C25  C13 C 0 1 Y N N N N N 60.627 -66.497 -24.574 -6.555 -0.733 0.332  C25  A1H3D 13 
A1H3D C26  C14 C 0 1 Y N N N N N 59.714 -65.812 -25.320 -5.528 0.071  -0.169 C26  A1H3D 14 
A1H3D C27  C15 C 0 1 N N N N N N 60.912 -65.848 -23.295 -7.637 -0.136 1.140  C27  A1H3D 15 
A1H3D C3   C16 C 0 1 N N S N N N 55.871 -65.678 -28.667 0.382  1.679  -0.204 C3   A1H3D 16 
A1H3D C5   C17 C 0 1 N N R N N N 53.558 -65.623 -28.828 2.447  0.809  0.294  C5   A1H3D 17 
A1H3D C9   C18 C 0 1 N N N N N N 57.009 -65.184 -29.556 -0.846 1.516  -1.101 C9   A1H3D 18 
A1H3D N13  N1  N 0 1 Y N N N N N 51.188 -63.948 -31.023 4.279  -1.984 -1.040 N13  A1H3D 19 
A1H3D N15  N2  N 0 1 Y N N N N N 50.759 -64.942 -27.714 5.348  0.179  1.453  N15  A1H3D 20 
A1H3D N17  N3  N 0 1 Y N N N N N 48.703 -63.969 -28.290 7.103  -1.304 1.207  N17  A1H3D 21 
A1H3D N19  N4  N 0 1 N N N N N N 48.325 -63.077 -30.426 7.067  -3.077 -0.348 N19  A1H3D 22 
A1H3D N8   N5  N 0 1 Y N N N N N 52.434 -64.948 -29.520 3.403  -0.246 -0.051 N8   A1H3D 23 
A1H3D O28  O1  O 0 1 N N N N N N 60.254 -64.813 -23.069 -8.623 -0.914 1.626  O28  A1H3D 24 
A1H3D O29  O2  O 0 1 N N N N N N 61.752 -66.353 -22.539 -7.638 1.058  1.367  O29  A1H3D 25 
A1H3D O4   O3  O 0 1 N N N N N N 54.737 -64.814 -28.801 1.116  0.438  -0.125 O4   A1H3D 26 
A1H3D O6   O4  O 0 1 N N N N N N 55.498 -67.992 -27.991 1.219  3.977  -0.238 O6   A1H3D 27 
A1H3D O7   O5  O 0 1 N N N N N N 53.163 -68.017 -29.150 3.512  3.010  0.316  O7   A1H3D 28 
A1H3D S10  S1  S 0 1 N N N N N N 58.444 -65.994 -28.950 -2.058 0.447  -0.278 S10  A1H3D 29 
A1H3D H1   H1  H 0 1 N N N N N N 53.943 -66.746 -30.627 3.310  1.866  -1.407 H1   A1H3D 30 
A1H3D H4   H2  H 0 1 N N N N N N 53.221 -64.557 -31.491 2.350  -1.330 -1.609 H4   A1H3D 31 
A1H3D H16  H4  H 0 1 N N N N N N 49.130 -64.788 -26.411 7.093  0.266  2.556  H16  A1H3D 32 
A1H3D H2   H5  H 0 1 N N N N N N 56.032 -67.421 -29.939 1.233  2.741  -1.908 H2   A1H3D 33 
A1H3D H202 H6  H 0 0 N N N N N N 57.375 -65.642 -26.884 -3.056 -0.048 -2.412 H202 A1H3D 34 
A1H3D H201 H7  H 0 0 N N N N N N 58.638 -64.410 -27.221 -3.800 1.380  -1.654 H201 A1H3D 35 
A1H3D H22  H8  H 0 1 N N N N N N 59.649 -67.832 -28.013 -3.734 -2.289 -1.776 H22  A1H3D 36 
A1H3D H23  H9  H 0 1 N N N N N N 61.290 -69.060 -26.630 -5.532 -3.716 -0.891 H23  A1H3D 37 
A1H3D H24  H10 H 0 1 N N N N N N 61.908 -68.216 -24.373 -7.339 -2.732 0.457  H24  A1H3D 38 
A1H3D H26  H11 H 0 1 N N N N N N 59.268 -64.904 -24.943 -5.523 1.131  0.034  H26  A1H3D 39 
A1H3D H3   H12 H 0 1 N N N N N N 56.213 -65.710 -27.622 0.083  2.009  0.791  H3   A1H3D 40 
A1H3D H5   H13 H 0 1 N N N N N N 53.252 -65.875 -27.802 2.467  1.004  1.366  H5   A1H3D 41 
A1H3D H92  H14 H 0 1 N N N N N N 57.118 -64.092 -29.474 -1.292 2.493  -1.289 H92  A1H3D 42 
A1H3D H91  H15 H 0 1 N N N N N N 56.826 -65.456 -30.606 -0.548 1.065  -2.047 H91  A1H3D 43 
A1H3D HN19 H17 H 0 0 N N N N N N 47.443 -62.898 -29.991 6.597  -3.563 -1.044 HN19 A1H3D 44 
A1H3D H7   H18 H 0 1 N N N N N N 48.736 -62.212 -30.714 7.953  -3.361 -0.072 H7   A1H3D 45 
A1H3D H8   H19 H 0 1 N N N N N N 60.495 -64.463 -22.219 -9.309 -0.479 2.150  H8   A1H3D 46 
A1H3D HO6  H20 H 0 1 N N N N N N 55.214 -68.853 -28.274 1.858  4.633  -0.552 HO6  A1H3D 47 
A1H3D HO7  H21 H 0 1 N N N N N N 52.270 -67.875 -29.443 3.738  3.838  -0.129 HO7  A1H3D 48 
# 
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 
A1H3D O29 C27  DOUB N N 1  
A1H3D C27 O28  SING N N 2  
A1H3D C25 C27  SING N N 3  
A1H3D C25 C24  DOUB Y N 4  
A1H3D C26 C25  SING Y N 5  
A1H3D C24 C23  SING Y N 6  
A1H3D C23 C22  DOUB Y N 7  
A1H3D C22 C21  SING Y N 8  
A1H3D C21 C26  DOUB Y N 9  
A1H3D C20 C21  SING N N 10 
A1H3D S10 C20  SING N N 11 
A1H3D C9  S10  SING N N 12 
A1H3D C3  C9   SING N N 13 
A1H3D C3  C2   SING N N 14 
A1H3D O4  C3   SING N N 15 
A1H3D O6  C2   SING N N 16 
A1H3D C2  C1   SING N N 17 
A1H3D C5  O4   SING N N 18 
A1H3D C1  C5   SING N N 19 
A1H3D N8  C5   SING N N 20 
A1H3D O7  C1   SING N N 21 
A1H3D N8  C14  SING Y N 22 
A1H3D C11 N8   SING Y N 23 
A1H3D C14 N13  DOUB Y N 24 
A1H3D N13 C12  SING Y N 25 
A1H3D C11 N15  DOUB Y N 26 
A1H3D C12 C11  SING Y N 27 
A1H3D N15 C16  SING Y N 28 
A1H3D C16 N17  DOUB Y N 29 
A1H3D N17 C18  SING Y N 30 
A1H3D C18 C12  DOUB Y N 31 
A1H3D N19 C18  SING N N 32 
A1H3D C1  H1   SING N N 33 
A1H3D C14 H4   SING N N 34 
A1H3D C16 H16  SING N N 35 
A1H3D C2  H2   SING N N 36 
A1H3D C20 H202 SING N N 37 
A1H3D C20 H201 SING N N 38 
A1H3D C22 H22  SING N N 39 
A1H3D C23 H23  SING N N 40 
A1H3D C24 H24  SING N N 41 
A1H3D C26 H26  SING N N 42 
A1H3D C3  H3   SING N N 43 
A1H3D C5  H5   SING N N 44 
A1H3D C9  H92  SING N N 45 
A1H3D C9  H91  SING N N 46 
A1H3D N19 HN19 SING N N 47 
A1H3D N19 H7   SING N N 48 
A1H3D O28 H8   SING N N 49 
A1H3D O6  HO6  SING N N 50 
A1H3D O7  HO7  SING N N 51 
# 
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 
A1H3D InChI            InChI                1.06  "InChI=1S/C18H19N5O5S/c19-15-12-16(21-7-20-15)23(8-22-12)17-14(25)13(24)11(28-17)6-29-5-9-2-1-3-10(4-9)18(26)27/h1-4,7-8,11,13-14,17,24-25H,5-6H2,(H,26,27)(H2,19,20,21)" 
A1H3D InChIKey         InChI                1.06  FRBGIZZDIAVFAN-UHFFFAOYSA-N                                                                                                                                               
A1H3D SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCc4cccc(c4)C(O)=O)[C@H](O)[C@@H]3O"                                                                                                      
A1H3D SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSCc4cccc(c4)C(O)=O)[CH](O)[CH]3O"                                                                                                            
A1H3D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(cc(c1)C(=O)O)CSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O"                                                                                                    
A1H3D SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(cc(c1)C(=O)O)CSCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O"                                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           A1H3D 
_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        "3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]benzoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1H3D "Create component" 2024-02-01 PDBE 
A1H3D "Initial release"  2024-02-14 RCSB 
# 
