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 ? #