data_A1JMZ # _chem_comp.id A1JMZ _chem_comp.name "(2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-(naphthalen-2-ylsulfanylmethyl)oxolane-3,4-diol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H19 N5 O3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-08-08 _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 409.462 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1JMZ _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 9SAK _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 A1JMZ C4 C1 C 0 1 Y N N N N N 14.120 23.556 21.579 6.699 -0.078 1.003 C4 A1JMZ 1 A1JMZ C6 C2 C 0 1 Y N N N N N 16.182 22.838 21.281 4.556 -0.409 0.240 C6 A1JMZ 2 A1JMZ N1 N1 N 0 1 N N N N N N 14.244 20.418 23.186 6.786 -3.144 -0.833 N1 A1JMZ 3 A1JMZ C8 C3 C 0 1 Y N N N N N 17.954 21.553 21.334 2.852 -1.372 -0.776 C8 A1JMZ 4 A1JMZ C10 C4 C 0 1 Y N N N N N 15.939 21.668 21.986 4.970 -1.605 -0.371 C10 A1JMZ 5 A1JMZ C11 C5 C 0 1 N N R N N N 18.218 23.731 20.062 2.339 0.802 0.397 C11 A1JMZ 6 A1JMZ N3 N2 N 0 1 Y N N N N N 13.738 22.483 22.279 7.135 -1.191 0.442 N3 A1JMZ 7 A1JMZ C13 C6 C 0 1 N N S N N N 19.575 23.625 18.157 0.175 1.569 0.364 C13 A1JMZ 8 A1JMZ C14 C7 C 0 1 N N N N N N 20.278 22.342 17.759 -1.242 1.257 -0.122 C14 A1JMZ 9 A1JMZ C2 C8 C 0 1 Y N N N N N 14.638 21.500 22.505 6.319 -1.980 -0.249 C2 A1JMZ 10 A1JMZ O12 O1 O 0 1 N N N N N N 18.308 23.238 18.738 0.964 0.361 0.424 O12 A1JMZ 11 A1JMZ C16 C9 C 0 1 Y N N N N N 22.363 21.005 16.450 -3.711 0.062 0.431 C16 A1JMZ 12 A1JMZ C17 C10 C 0 1 Y N N N N N 22.265 20.081 17.486 -3.976 0.558 -0.853 C17 A1JMZ 13 A1JMZ C18 C11 C 0 1 Y N N N N N 22.684 18.795 17.311 -5.187 0.364 -1.439 C18 A1JMZ 14 A1JMZ C19 C12 C 0 1 Y N N N N N 23.230 18.366 16.078 -6.192 -0.343 -0.757 C19 A1JMZ 15 A1JMZ C20 C13 C 0 1 Y N N N N N 23.684 17.043 15.858 -7.453 -0.558 -1.340 C20 A1JMZ 16 A1JMZ C21 C14 C 0 1 Y N N N N N 24.212 16.677 14.652 -8.405 -1.246 -0.652 C21 A1JMZ 17 A1JMZ C22 C15 C 0 1 Y N N N N N 24.312 17.592 13.621 -8.150 -1.743 0.625 C22 A1JMZ 18 A1JMZ C23 C16 C 0 1 Y N N N N N 23.885 18.880 13.789 -6.942 -1.554 1.221 C23 A1JMZ 19 A1JMZ C24 C17 C 0 1 Y N N N N N 23.332 19.303 15.020 -5.933 -0.848 0.542 C24 A1JMZ 20 A1JMZ C25 C18 C 0 1 Y N N N N N 22.888 20.628 15.237 -4.675 -0.635 1.128 C25 A1JMZ 21 A1JMZ C26 C19 C 0 1 N N S N N N 20.293 24.463 19.215 0.908 2.469 -0.656 C26 A1JMZ 22 A1JMZ C28 C20 C 0 1 N N R N N N 19.653 23.983 20.518 2.364 1.953 -0.634 C28 A1JMZ 23 A1JMZ N5 N3 N 0 1 Y N N N N N 15.314 23.824 21.042 5.444 0.313 0.915 N5 A1JMZ 24 A1JMZ N7 N4 N 0 1 Y N N N N N 17.489 22.751 20.863 3.217 -0.289 -0.033 N7 A1JMZ 25 A1JMZ N9 N5 N 0 1 Y N N N N N 17.067 20.865 22.013 3.884 -2.141 -0.977 N9 A1JMZ 26 A1JMZ O27 O2 O 0 1 N N N N N N 20.083 25.856 19.004 0.855 3.837 -0.245 O27 A1JMZ 27 A1JMZ O29 O3 O 0 1 N N N N N N 19.685 24.990 21.525 3.255 2.986 -0.209 O29 A1JMZ 28 A1JMZ S15 S1 S 0 1 N N N N N N 21.756 22.637 16.757 -2.128 0.325 1.158 S15 A1JMZ 29 A1JMZ H4 H1 H 0 1 N N N N N N 13.360 24.309 21.427 7.395 0.531 1.559 H4 A1JMZ 30 A1JMZ H1A H2 H 0 1 N N N N N N 13.281 20.514 23.437 6.180 -3.712 -1.334 H1A A1JMZ 31 A1JMZ H1B H3 H 0 1 N N N N N N 14.360 19.605 22.616 7.719 -3.393 -0.741 H1B A1JMZ 32 A1JMZ H8 H4 H 0 1 N N N N N N 18.962 21.205 21.162 1.857 -1.562 -1.149 H8 A1JMZ 33 A1JMZ H11 H5 H 0 1 N N N N N N 17.675 24.688 20.072 2.640 1.166 1.379 H11 A1JMZ 34 A1JMZ H13 H6 H 0 1 N N N N N N 19.410 24.241 17.261 0.143 2.051 1.341 H13 A1JMZ 35 A1JMZ H14A H7 H 0 0 N N N N N N 20.574 21.805 18.672 -1.770 2.188 -0.324 H14A A1JMZ 36 A1JMZ H14B H8 H 0 0 N N N N N N 19.578 21.722 17.179 -1.190 0.663 -1.034 H14B A1JMZ 37 A1JMZ H17 H9 H 0 1 N N N N N N 21.853 20.385 18.437 -3.208 1.102 -1.382 H17 A1JMZ 38 A1JMZ H18 H10 H 0 1 N N N N N N 22.598 18.093 18.127 -5.376 0.753 -2.429 H18 A1JMZ 39 A1JMZ H20 H11 H 0 1 N N N N N N 23.612 16.315 16.652 -7.665 -0.178 -2.328 H20 A1JMZ 40 A1JMZ H21 H12 H 0 1 N N N N N N 24.554 15.664 14.503 -9.372 -1.410 -1.104 H21 A1JMZ 41 A1JMZ H22 H13 H 0 1 N N N N N N 24.731 17.287 12.674 -8.924 -2.285 1.149 H22 A1JMZ 42 A1JMZ H23 H14 H 0 1 N N N N N N 23.971 19.582 12.973 -6.759 -1.944 2.212 H23 A1JMZ 43 A1JMZ H25 H15 H 0 1 N N N N N N 22.962 21.353 14.440 -4.464 -1.014 2.117 H25 A1JMZ 44 A1JMZ H26 H16 H 0 1 N N N N N N 21.365 24.218 19.217 0.474 2.352 -1.649 H26 A1JMZ 45 A1JMZ H28 H17 H 0 1 N N N N N N 20.121 23.046 20.855 2.652 1.581 -1.617 H28 A1JMZ 46 A1JMZ H27 H18 H 0 1 N N N N N N 20.540 26.351 19.674 1.300 4.446 -0.850 H27 A1JMZ 47 A1JMZ H29 H19 H 0 1 N N N N N N 19.280 24.658 22.318 3.265 3.760 -0.789 H29 A1JMZ 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 A1JMZ N1 C2 SING N N 1 A1JMZ C2 N3 SING Y N 2 A1JMZ N3 C4 DOUB Y N 3 A1JMZ C4 N5 SING Y N 4 A1JMZ N5 C6 DOUB Y N 5 A1JMZ C6 N7 SING Y N 6 A1JMZ N7 C8 SING Y N 7 A1JMZ C8 N9 DOUB Y N 8 A1JMZ N9 C10 SING Y N 9 A1JMZ N7 C11 SING N N 10 A1JMZ C11 O12 SING N N 11 A1JMZ O12 C13 SING N N 12 A1JMZ C13 C14 SING N N 13 A1JMZ C14 S15 SING N N 14 A1JMZ S15 C16 SING N N 15 A1JMZ C16 C17 SING Y N 16 A1JMZ C17 C18 DOUB Y N 17 A1JMZ C18 C19 SING Y N 18 A1JMZ C19 C20 SING Y N 19 A1JMZ C20 C21 DOUB Y N 20 A1JMZ C21 C22 SING Y N 21 A1JMZ C22 C23 DOUB Y N 22 A1JMZ C23 C24 SING Y N 23 A1JMZ C24 C25 SING Y N 24 A1JMZ C13 C26 SING N N 25 A1JMZ C26 O27 SING N N 26 A1JMZ C26 C28 SING N N 27 A1JMZ C28 O29 SING N N 28 A1JMZ C10 C2 DOUB Y N 29 A1JMZ C28 C11 SING N N 30 A1JMZ C10 C6 SING Y N 31 A1JMZ C25 C16 DOUB Y N 32 A1JMZ C24 C19 DOUB Y N 33 A1JMZ C4 H4 SING N N 34 A1JMZ N1 H1A SING N N 35 A1JMZ N1 H1B SING N N 36 A1JMZ C8 H8 SING N N 37 A1JMZ C11 H11 SING N N 38 A1JMZ C13 H13 SING N N 39 A1JMZ C14 H14A SING N N 40 A1JMZ C14 H14B SING N N 41 A1JMZ C17 H17 SING N N 42 A1JMZ C18 H18 SING N N 43 A1JMZ C20 H20 SING N N 44 A1JMZ C21 H21 SING N N 45 A1JMZ C22 H22 SING N N 46 A1JMZ C23 H23 SING N N 47 A1JMZ C25 H25 SING N N 48 A1JMZ C26 H26 SING N N 49 A1JMZ C28 H28 SING N N 50 A1JMZ O27 H27 SING N N 51 A1JMZ O29 H29 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 A1JMZ InChI InChI 1.06 "InChI=1S/C20H19N5O3S/c21-18-15-19(23-9-22-18)25(10-24-15)20-17(27)16(26)14(28-20)8-29-13-6-5-11-3-1-2-4-12(11)7-13/h1-7,9-10,14,16-17,20,26-27H,8H2,(H2,21,22,23)/t14-,16-,17-,20-/m1/s1" A1JMZ InChIKey InChI 1.06 XAHNLKRFYZFWKR-WVSUBDOOSA-N A1JMZ SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSc4ccc5ccccc5c4)[C@@H](O)[C@H]3O" A1JMZ SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSc4ccc5ccccc5c4)[CH](O)[CH]3O" A1JMZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2cc(ccc2c1)SC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O" A1JMZ SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc2cc(ccc2c1)SCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O" # _pdbx_chem_comp_identifier.comp_id A1JMZ _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~{S},5~{S})-2-(6-aminopurin-9-yl)-5-(naphthalen-2-ylsulfanylmethyl)oxolane-3,4-diol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1JMZ "Create component" 2025-08-08 PDBE A1JMZ "Initial release" 2026-01-21 RCSB #