data_A1JMY # _chem_comp.id A1JMY _chem_comp.name "1-[2-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]ethyl]-3-ethyl-urea" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H23 N7 O4 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-08-07 _chem_comp.pdbx_modified_date 2026-01-16 _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 397.453 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1JMY _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 9SAJ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _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 A1JMY C1 C1 C 0 1 N N N N N N 24.255 37.020 14.162 10.353 -1.489 0.989 C1 A1JMY 1 A1JMY C2 C2 C 0 1 N N N N N N 24.597 38.421 13.745 9.225 -1.499 -0.045 C2 A1JMY 2 A1JMY N3 N1 N 0 1 N N N N N N 23.766 39.408 14.429 8.045 -0.834 0.513 N3 A1JMY 3 A1JMY C4 C3 C 0 1 N N N N N N 23.261 40.480 13.783 6.923 -0.723 -0.224 C4 A1JMY 4 A1JMY C7 C4 C 0 1 N N N N N N 21.886 42.504 14.005 4.616 0.009 -0.511 C7 A1JMY 5 A1JMY C8 C5 C 0 1 N N N N N N 21.387 43.426 15.103 3.544 0.739 0.299 C8 A1JMY 6 A1JMY C10 C6 C 0 1 N N N N N N 20.491 42.685 17.678 0.899 1.765 0.420 C10 A1JMY 7 A1JMY C11 C7 C 0 1 N N S N N N 19.679 43.940 17.937 -0.445 1.972 -0.281 C11 A1JMY 8 A1JMY C13 C8 C 0 1 N N R N N N 18.194 44.178 19.736 -2.506 0.919 -0.368 C13 A1JMY 9 A1JMY C14 C9 C 0 1 N N R N N N 19.588 44.549 20.243 -2.615 1.901 0.826 C14 A1JMY 10 A1JMY C16 C10 C 0 1 N N S N N N 20.286 44.925 18.936 -1.379 2.809 0.614 C16 A1JMY 11 A1JMY C19 C11 C 0 1 Y N N N N N 17.964 42.058 21.105 -2.623 -1.471 0.433 C19 A1JMY 12 A1JMY C21 C12 C 0 1 Y N N N N N 15.945 42.163 21.744 -4.732 -1.916 0.191 C21 A1JMY 13 A1JMY C22 C13 C 0 1 Y N N N N N 14.649 41.997 22.274 -6.032 -2.445 0.127 C22 A1JMY 14 A1JMY C24 C14 C 0 1 Y N N N N N 14.096 44.005 21.263 -6.773 -0.429 -0.719 C24 A1JMY 15 A1JMY C26 C15 C 0 1 Y N N N N N 16.168 43.305 20.990 -4.532 -0.592 -0.234 C26 A1JMY 16 A1JMY N18 N2 N 0 1 Y N N N N N 17.479 43.226 20.579 -3.194 -0.338 -0.066 N18 A1JMY 17 A1JMY N20 N3 N 0 1 Y N N N N N 17.088 41.383 21.810 -3.526 -2.397 0.580 N20 A1JMY 18 A1JMY N23 N4 N 0 1 Y N N N N N 13.733 42.956 22.009 -7.009 -1.669 -0.331 N23 A1JMY 19 A1JMY N25 N5 N 0 1 Y N N N N N 15.285 44.267 20.712 -5.573 0.109 -0.673 N25 A1JMY 20 A1JMY N27 N6 N 0 1 N N N N N N 14.275 40.938 23.001 -6.290 -3.743 0.531 N27 A1JMY 21 A1JMY N6 N7 N 0 1 N N N N N N 22.509 41.303 14.543 5.837 -0.111 0.290 N6 A1JMY 22 A1JMY O12 O1 O 0 1 N N N N N N 18.380 43.586 18.463 -1.084 0.702 -0.497 O12 A1JMY 23 A1JMY O15 O2 O 0 1 N N N N N N 19.526 45.653 21.139 -3.824 2.660 0.754 O15 A1JMY 24 A1JMY O17 O3 O 0 1 N N N N N N 20.016 46.271 18.562 -1.755 4.018 -0.049 O17 A1JMY 25 A1JMY O5 O4 O 0 1 N N N N N N 23.470 40.690 12.590 6.889 -1.176 -1.352 O5 A1JMY 26 A1JMY S9 S1 S 0 1 N N N N N N 22.014 42.977 16.745 2.032 0.888 -0.692 S9 A1JMY 27 A1JMY H1A H1 H 0 1 N N N N N N 24.901 36.309 13.626 10.603 -0.459 1.244 H1A A1JMY 28 A1JMY H1B H2 H 0 1 N N N N N N 24.411 36.912 15.246 10.029 -2.016 1.886 H1B A1JMY 29 A1JMY H1C H3 H 0 1 N N N N N N 23.202 36.812 13.920 11.231 -1.984 0.574 H1C A1JMY 30 A1JMY H2A H4 H 0 1 N N N N N N 25.653 38.616 13.985 9.550 -0.971 -0.942 H2A A1JMY 31 A1JMY H2B H5 H 0 1 N N N N N N 24.444 38.517 12.660 8.975 -2.529 -0.299 H2B A1JMY 32 A1JMY H3 H6 H 0 1 N N N N N N 23.566 39.286 15.401 8.073 -0.472 1.413 H3 A1JMY 33 A1JMY H7A H7 H 0 1 N N N N N N 22.625 43.045 13.395 4.257 -0.985 -0.777 H7A A1JMY 34 A1JMY H7B H8 H 0 1 N N N N N N 21.034 42.210 13.374 4.832 0.572 -1.419 H7B A1JMY 35 A1JMY H8A H9 H 0 1 N N N N N N 21.710 44.452 14.873 3.329 0.176 1.207 H8A A1JMY 36 A1JMY H8B H10 H 0 1 N N N N N N 20.288 43.384 15.124 3.903 1.733 0.565 H8B A1JMY 37 A1JMY H10A H11 H 0 0 N N N N N N 19.867 41.980 17.110 1.324 2.733 0.683 H10A A1JMY 38 A1JMY H10B H12 H 0 0 N N N N N N 20.759 42.239 18.647 0.750 1.176 1.325 H10B A1JMY 39 A1JMY H11 H13 H 0 1 N N N N N N 19.547 44.466 16.980 -0.292 2.476 -1.235 H11 A1JMY 40 A1JMY H13 H14 H 0 1 N N N N N N 17.601 45.099 19.640 -2.912 1.370 -1.274 H13 A1JMY 41 A1JMY H14 H15 H 0 1 N N N N N N 20.075 43.675 20.700 -2.549 1.369 1.775 H14 A1JMY 42 A1JMY H16 H16 H 0 1 N N N N N N 21.367 44.744 19.026 -0.899 3.029 1.567 H16 A1JMY 43 A1JMY H19 H17 H 0 1 N N N N N N 18.979 41.722 20.953 -1.575 -1.585 0.668 H19 A1JMY 44 A1JMY H24 H18 H 0 1 N N N N N N 13.325 44.739 21.082 -7.597 0.168 -1.082 H24 A1JMY 45 A1JMY H27A H19 H 0 0 N N N N N N 13.311 41.028 23.251 -5.568 -4.300 0.864 H27A A1JMY 46 A1JMY H27B H20 H 0 0 N N N N N N 14.403 40.104 22.465 -7.192 -4.097 0.483 H27B A1JMY 47 A1JMY H6 H21 H 0 1 N N N N N N 22.375 41.081 15.509 5.864 0.250 1.189 H6 A1JMY 48 A1JMY H15 H22 H 0 1 N N N N N N 20.401 45.866 21.441 -3.938 3.289 1.479 H15 A1JMY 49 A1JMY H17 H23 H 0 1 N N N N N N 20.464 46.470 17.748 -2.389 4.557 0.445 H17 A1JMY 50 # 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 A1JMY C1 C2 SING N N 1 A1JMY C2 N3 SING N N 2 A1JMY N3 C4 SING N N 3 A1JMY C4 O5 DOUB N N 4 A1JMY C4 N6 SING N N 5 A1JMY N6 C7 SING N N 6 A1JMY C7 C8 SING N N 7 A1JMY C8 S9 SING N N 8 A1JMY S9 C10 SING N N 9 A1JMY C10 C11 SING N N 10 A1JMY C11 O12 SING N N 11 A1JMY O12 C13 SING N N 12 A1JMY C13 C14 SING N N 13 A1JMY C14 O15 SING N N 14 A1JMY C14 C16 SING N N 15 A1JMY C16 O17 SING N N 16 A1JMY C13 N18 SING N N 17 A1JMY N18 C19 SING Y N 18 A1JMY C19 N20 DOUB Y N 19 A1JMY N20 C21 SING Y N 20 A1JMY C21 C22 SING Y N 21 A1JMY C22 N23 DOUB Y N 22 A1JMY N23 C24 SING Y N 23 A1JMY C24 N25 DOUB Y N 24 A1JMY N25 C26 SING Y N 25 A1JMY C22 N27 SING N N 26 A1JMY C16 C11 SING N N 27 A1JMY C26 N18 SING Y N 28 A1JMY C26 C21 DOUB Y N 29 A1JMY C1 H1A SING N N 30 A1JMY C1 H1B SING N N 31 A1JMY C1 H1C SING N N 32 A1JMY C2 H2A SING N N 33 A1JMY C2 H2B SING N N 34 A1JMY N3 H3 SING N N 35 A1JMY C7 H7A SING N N 36 A1JMY C7 H7B SING N N 37 A1JMY C8 H8A SING N N 38 A1JMY C8 H8B SING N N 39 A1JMY C10 H10A SING N N 40 A1JMY C10 H10B SING N N 41 A1JMY C11 H11 SING N N 42 A1JMY C13 H13 SING N N 43 A1JMY C14 H14 SING N N 44 A1JMY C16 H16 SING N N 45 A1JMY C19 H19 SING N N 46 A1JMY C24 H24 SING N N 47 A1JMY N27 H27A SING N N 48 A1JMY N27 H27B SING N N 49 A1JMY N6 H6 SING N N 50 A1JMY O15 H15 SING N N 51 A1JMY O17 H17 SING N N 52 # 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 A1JMY InChI InChI 1.06 "InChI=1S/C15H23N7O4S/c1-2-17-15(25)18-3-4-27-5-8-10(23)11(24)14(26-8)22-7-21-9-12(16)19-6-20-13(9)22/h6-8,10-11,14,23-24H,2-5H2,1H3,(H2,16,19,20)(H2,17,18,25)/t8-,10-,11-,14-/m1/s1" A1JMY InChIKey InChI 1.06 CACMCLIHCDTJHL-IDTAVKCVSA-N A1JMY SMILES_CANONICAL CACTVS 3.385 "CCNC(=O)NCCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" A1JMY SMILES CACTVS 3.385 "CCNC(=O)NCCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" A1JMY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCNC(=O)NCCSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" A1JMY SMILES "OpenEye OEToolkits" 2.0.7 "CCNC(=O)NCCSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O" # _pdbx_chem_comp_identifier.comp_id A1JMY _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 "1-[2-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]ethyl]-3-ethyl-urea" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1JMY "Create component" 2025-08-07 PDBE A1JMY "Initial release" 2026-01-21 RCSB #