data_A1H4D
# 
_chem_comp.id                                    A1H4D 
_chem_comp.name                                  "3-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-imidazol-1-yl-benzoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H21 N7 O5 S" 
_chem_comp.mon_nstd_parent_comp_id               ADE 
_chem_comp.pdbx_synonyms                         "3-(((((2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)thio)methyl)-5-(1H-imidazol-1-yl)benzoic acid" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-02-13 
_chem_comp.pdbx_modified_date                    2024-02-16 
_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                        483.500 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1H4D 
_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        8RZC 
_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 
A1H4D C10    C1  C 0 1 N N N N N N 87.712 -20.441 34.542 4.841  -3.527 0.514  C10 A1H4D 1  
A1H4D C13    C2  C 0 1 Y N N N N N 88.493 -18.066 35.112 5.729  -1.304 -0.173 C13 A1H4D 2  
A1H4D C14    C3  C 0 1 Y N N N N N 88.648 -16.701 34.791 5.628  0.076  -0.214 C14 A1H4D 3  
A1H4D C16    C4  C 0 1 Y N N N N N 89.017 -14.445 35.882 7.730  0.347  -1.495 C16 A1H4D 4  
A1H4D C17    C5  C 0 1 Y N N N N N 89.862 -14.017 36.899 8.399  1.411  -1.978 C17 A1H4D 5  
A1H4D C19    C6  C 0 1 Y N N N N N 90.241 -16.059 36.653 6.649  2.186  -0.979 C19 A1H4D 6  
A1H4D "C3'"  C7  C 0 1 N N R N N N 86.182 -14.525 28.924 -2.526 2.741  1.268  C2  A1H4D 7  
A1H4D C20    C8  C 0 1 Y N N N N N 88.180 -16.252 33.542 4.547  0.712  0.385  C20 A1H4D 8  
A1H4D "C1'"  C9  C 0 1 N N R N N N 83.940 -13.727 28.871 -3.454 0.999  -0.159 C22 A1H4D 9  
A1H4D C4     C10 C 0 1 Y N N N N N 81.860 -12.177 29.070 -5.527 -0.361 -0.669 C24 A1H4D 10 
A1H4D C2     C11 C 0 1 Y N N N N N 80.883 -10.662 27.749 -7.364 -0.159 -2.035 C26 A1H4D 11 
A1H4D C6     C12 C 0 1 Y N N N N N 79.885 -10.974 29.824 -7.239 -2.058 -0.730 C28 A1H4D 12 
A1H4D "C4'"  C13 C 0 1 N N S N N N 85.204 -15.611 28.427 -1.459 1.911  0.520  C3  A1H4D 13 
A1H4D C5     C14 C 0 1 Y N N N N N 80.912 -11.950 30.071 -6.019 -1.594 -0.208 C30 A1H4D 14 
A1H4D C8     C15 C 0 1 Y N N N N N 82.238 -13.428 30.804 -4.143 -1.225 0.814  C32 A1H4D 15 
A1H4D "C2'"  C16 C 0 1 N N S N N N 85.296 -13.444 29.551 -3.868 2.127  0.811  C33 A1H4D 16 
A1H4D "C5'"  C17 C 0 1 N N N N N N 85.411 -17.005 29.048 -0.236 1.688  1.412  C4  A1H4D 17 
A1H4D C3     C18 C 0 1 N N N N N N 87.075 -16.664 31.288 2.401  0.669  1.670  C6  A1H4D 18 
A1H4D C7     C19 C 0 1 Y N N N N N 87.572 -17.143 32.640 3.570  -0.029 1.023  C7  A1H4D 19 
A1H4D C1     C20 C 0 1 Y N N N N N 87.431 -18.492 32.973 3.661  -1.405 1.070  C8  A1H4D 20 
A1H4D C9     C21 C 0 1 Y N N N N N 87.885 -18.978 34.214 4.743  -2.053 0.471  C9  A1H4D 21 
A1H4D N15    N1  N 0 1 Y N N N N N 89.260 -15.797 35.709 6.616  0.833  -0.860 N15 A1H4D 22 
A1H4D N18    N2  N 0 1 Y N N N N N 90.605 -15.010 37.362 7.721  2.519  -1.644 N18 A1H4D 23 
A1H4D N9     N3  N 0 1 Y N N N N N 82.706 -13.146 29.564 -4.341 -0.157 -0.009 N23 A1H4D 24 
A1H4D N3     N4  N 0 1 Y N N N N N 81.895 -11.549 27.863 -6.226 0.316  -1.574 N25 A1H4D 25 
A1H4D N1     N5  N 0 1 Y N N N N N 79.889 -10.334 28.612 -7.866 -1.312 -1.633 N27 A1H4D 26 
A1H4D N6     N6  N 0 1 N N N N N N 78.870 -10.649 30.737 -7.773 -3.265 -0.315 N29 A1H4D 27 
A1H4D N7     N7  N 0 1 Y N N N N N 81.163 -12.740 31.136 -5.127 -2.068 0.695  N31 A1H4D 28 
A1H4D "O3'"  O1  O 0 1 N N N N N N 87.096 -14.035 27.958 -2.449 4.116  0.887  O1  A1H4D 29 
A1H4D O11    O2  O 0 1 N N N N N N 87.806 -20.803 35.744 5.886  -4.150 -0.064 O11 A1H4D 30 
A1H4D O12    O3  O 0 1 N N N N N N 87.454 -21.219 33.583 3.981  -4.176 1.075  O12 A1H4D 31 
A1H4D "O4'"  O4  O 0 1 N N N N N N 83.911 -15.125 28.805 -2.107 0.653  0.231  O21 A1H4D 32 
A1H4D "O2'"  O5  O 0 1 N N N N N N 85.720 -12.105 29.318 -4.661 3.104  0.133  O34 A1H4D 33 
A1H4D S1     S1  S 0 1 N N N N N N 85.348 -17.096 30.867 1.057  0.841  0.464  S5  A1H4D 34 
A1H4D H45    H1  H 0 1 N N N N N N 88.847 -18.425 36.067 6.567  -1.800 -0.641 H45 A1H4D 35 
A1H4D H46    H2  H 0 1 N N N N N N 88.309 -13.841 35.334 8.013  -0.691 -1.594 H46 A1H4D 36 
A1H4D H47    H3  H 0 1 N N N N N N 89.907 -13.002 37.265 9.323  1.378  -2.537 H47 A1H4D 37 
A1H4D H48    H4  H 0 1 N N N N N N 90.670 -17.040 36.795 5.910  2.871  -0.589 H48 A1H4D 38 
A1H4D "H3'"  H5  H 0 1 N N N N N N 86.760 -14.975 29.744 -2.405 2.636  2.346  H35 A1H4D 39 
A1H4D H49    H6  H 0 1 N N N N N N 88.289 -15.212 33.273 4.471  1.789  0.352  H49 A1H4D 40 
A1H4D "H1'"  H7  H 0 1 N N N N N N 83.983 -13.311 27.854 -3.470 1.358  -1.188 H37 A1H4D 41 
A1H4D H2     H8  H 0 1 N N N N N N 80.861 -10.123 26.813 -7.907 0.417  -2.771 H50 A1H4D 42 
A1H4D "H4'"  H9  H 0 1 N N N N N N 85.282 -15.690 27.333 -1.169 2.411  -0.403 H36 A1H4D 43 
A1H4D H8     H10 H 0 1 N N N N N N 82.702 -14.150 31.460 -3.293 -1.353 1.469  H53 A1H4D 44 
A1H4D "H2'"  H11 H 0 1 N N N N N N 85.202 -13.638 30.630 -4.411 1.718  1.663  H38 A1H4D 45 
A1H4D "H5'2" H12 H 0 1 N N N N N N 84.628 -17.668 28.652 0.140  2.650  1.760  H41 A1H4D 46 
A1H4D "H5'1" H13 H 0 1 N N N N N N 86.398 -17.371 28.728 -0.518 1.076  2.269  H40 A1H4D 47 
A1H4D H42    H14 H 0 1 N N N N N N 87.728 -17.098 30.517 2.053  0.083  2.520  H42 A1H4D 48 
A1H4D H43    H15 H 0 1 N N N N N N 87.162 -15.568 31.267 2.711  1.656  2.011  H43 A1H4D 49 
A1H4D H44    H16 H 0 1 N N N N N N 86.969 -19.170 32.271 2.895  -1.980 1.569  H44 A1H4D 50 
A1H4D HN61   H17 H 0 1 N N N N N N 78.269 -9.957  30.336 -7.304 -3.802 0.344  H51 A1H4D 51 
A1H4D HN62   H18 H 0 1 N N N N N N 78.338 -11.469 30.950 -8.615 -3.575 -0.682 H52 A1H4D 52 
A1H4D "HO3'" H19 H 0 1 N N N N N N 87.610 -14.756 27.613 -3.134 4.673  1.281  H39 A1H4D 53 
A1H4D H1     H20 H 0 1 N N N N N N 87.654 -21.739 35.806 5.909  -5.115 -0.006 H1  A1H4D 54 
A1H4D "HO2'" H21 H 0 1 N N N N N N 85.117 -11.504 29.740 -4.899 3.866  0.680  H54 A1H4D 55 
# 
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 
A1H4D "O3'" "C3'"  SING N N 1  
A1H4D "C3'" "C2'"  SING N N 2  
A1H4D "C3'" "C4'"  SING N N 3  
A1H4D "C4'" "C5'"  SING N N 4  
A1H4D "O4'" "C4'"  SING N N 5  
A1H4D "C5'" S1     SING N N 6  
A1H4D S1    C3     SING N N 7  
A1H4D C3    C7     SING N N 8  
A1H4D C7    C20    DOUB Y N 9  
A1H4D C7    C1     SING Y N 10 
A1H4D C1    C9     DOUB Y N 11 
A1H4D C9    C10    SING N N 12 
A1H4D C13   C9     SING Y N 13 
A1H4D O11   C10    SING N N 14 
A1H4D C10   O12    DOUB N N 15 
A1H4D C14   C13    DOUB Y N 16 
A1H4D N15   C14    SING N N 17 
A1H4D C20   C14    SING Y N 18 
A1H4D C19   N15    SING Y N 19 
A1H4D N15   C16    SING Y N 20 
A1H4D C16   C17    DOUB Y N 21 
A1H4D C17   N18    SING Y N 22 
A1H4D N18   C19    DOUB Y N 23 
A1H4D "C1'" "O4'"  SING N N 24 
A1H4D N9    "C1'"  SING N N 25 
A1H4D "C2'" "C1'"  SING N N 26 
A1H4D C8    N9     SING Y N 27 
A1H4D N9    C4     SING Y N 28 
A1H4D C4    N3     SING Y N 29 
A1H4D C4    C5     DOUB Y N 30 
A1H4D N3    C2     DOUB Y N 31 
A1H4D C2    N1     SING Y N 32 
A1H4D N1    C6     DOUB Y N 33 
A1H4D C6    C5     SING Y N 34 
A1H4D N6    C6     SING N N 35 
A1H4D C5    N7     SING Y N 36 
A1H4D N7    C8     DOUB Y N 37 
A1H4D "O2'" "C2'"  SING N N 38 
A1H4D C13   H45    SING N N 39 
A1H4D C16   H46    SING N N 40 
A1H4D C17   H47    SING N N 41 
A1H4D C19   H48    SING N N 42 
A1H4D "C3'" "H3'"  SING N N 43 
A1H4D C20   H49    SING N N 44 
A1H4D "C1'" "H1'"  SING N N 45 
A1H4D C2    H2     SING N N 46 
A1H4D "C4'" "H4'"  SING N N 47 
A1H4D C8    H8     SING N N 48 
A1H4D "C2'" "H2'"  SING N N 49 
A1H4D "C5'" "H5'2" SING N N 50 
A1H4D "C5'" "H5'1" SING N N 51 
A1H4D C3    H42    SING N N 52 
A1H4D C3    H43    SING N N 53 
A1H4D C1    H44    SING N N 54 
A1H4D N6    HN61   SING N N 55 
A1H4D N6    HN62   SING N N 56 
A1H4D "O3'" "HO3'" SING N N 57 
A1H4D O11   H1     SING N N 58 
A1H4D "O2'" "HO2'" SING N N 59 
# 
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 
A1H4D InChI            InChI                1.06  "InChI=1S/C21H21N7O5S/c22-18-15-19(25-8-24-18)28(10-26-15)20-17(30)16(29)14(33-20)7-34-6-11-3-12(21(31)32)5-13(4-11)27-2-1-23-9-27/h1-5,8-10,14,16-17,20,29-30H,6-7H2,(H,31,32)(H2,22,24,25)" 
A1H4D InChIKey         InChI                1.06  YCJODFCZOYGSRH-UHFFFAOYSA-N                                                                                                                                                                   
A1H4D SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCc4cc(cc(c4)C(O)=O)n5ccnc5)[C@H](O)[C@@H]3O"                                                                                                                 
A1H4D SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSCc4cc(cc(c4)C(O)=O)n5ccnc5)[CH](O)[CH]3O"                                                                                                                       
A1H4D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cn(cn1)c2cc(cc(c2)C(=O)O)CSC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O"                                                                                                               
A1H4D SMILES           "OpenEye OEToolkits" 2.0.7 "c1cn(cn1)c2cc(cc(c2)C(=O)O)CSCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O"                                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           A1H4D 
_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]-5-imidazol-1-yl-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 
A1H4D "Create component" 2024-02-13 PDBE 
A1H4D "Initial release"  2024-02-21 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1H4D 
_pdbx_chem_comp_synonyms.name         "3-(((((2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)thio)methyl)-5-(1H-imidazol-1-yl)benzoic acid" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
