data_YJO # _chem_comp.id YJO _chem_comp.name "(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,5-bis(oxidanyl)-4-[4-[oxidanyl(phenyl)-$l^{3}-sulfanyl]-1,2,3-triazol-1-yl]oxan-2-yl]sulfanyl-oxane-3,4,5-triol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H28 N3 O10 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2023-06-19 _chem_comp.pdbx_modified_date 2023-11-03 _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 534.580 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YJO _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 8PF9 _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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 YJO C02 C1 C 0 1 N N R N N N -17.456 7.340 -1.622 0.898 -1.621 -0.973 C02 YJO 1 YJO C03 C2 C 0 1 N N S N N N -16.824 8.398 -2.529 0.915 -0.138 -1.355 C03 YJO 2 YJO C07 C3 C 0 1 Y N N N N N -13.441 8.743 -1.433 4.205 1.160 -0.687 C07 YJO 3 YJO C10 C4 C 0 1 Y N N N N N -11.062 10.197 -1.236 6.389 0.369 0.800 C10 YJO 4 YJO C11 C5 C 0 1 Y N N N N N -10.270 9.670 -2.240 6.036 -0.264 1.986 C11 YJO 5 YJO C12 C6 C 0 1 Y N N N N N -9.416 10.515 -2.930 6.712 -1.399 2.388 C12 YJO 6 YJO C13 C7 C 0 1 Y N N N N N -9.359 11.860 -2.618 7.738 -1.906 1.612 C13 YJO 7 YJO C14 C8 C 0 1 Y N N N N N -10.158 12.369 -1.613 8.092 -1.279 0.432 C14 YJO 8 YJO C15 C9 C 0 1 Y N N N N N -11.017 11.540 -0.912 7.421 -0.144 0.023 C15 YJO 9 YJO C17 C10 C 0 1 Y N N N N N -14.760 8.976 -1.198 2.970 0.804 -0.244 C17 YJO 10 YJO C18 C11 C 0 1 N N R N N N -17.505 9.750 -2.312 0.078 0.649 -0.342 C18 YJO 11 YJO C20 C12 C 0 1 N N S N N N -19.025 9.620 -2.397 -1.341 0.074 -0.308 C20 YJO 12 YJO C22 C13 C 0 1 N N S N N N -21.555 10.772 -2.116 -3.979 0.249 0.727 C22 YJO 13 YJO C23 C14 C 0 1 N N R N N N -22.368 11.301 -0.933 -4.912 0.806 1.805 C23 YJO 14 YJO C25 C15 C 0 1 N N S N N N -23.857 11.093 -1.174 -6.324 0.254 1.582 C25 YJO 15 YJO C27 C16 C 0 1 N N S N N N -24.247 11.689 -2.519 -6.785 0.621 0.168 C27 YJO 16 YJO C29 C17 C 0 1 N N R N N N -23.388 11.043 -3.602 -5.780 0.072 -0.847 C29 YJO 17 YJO C30 C18 C 0 1 N N N N N N -23.698 11.530 -4.997 -6.202 0.485 -2.258 C30 YJO 18 YJO C34 C19 C 0 1 N N R N N N -18.965 7.312 -1.833 -0.552 -2.110 -0.915 C34 YJO 19 YJO C35 C20 C 0 1 N N N N N N -19.673 6.319 -0.946 -0.579 -3.576 -0.476 C35 YJO 20 YJO N04 N1 N 0 1 Y N N N N N -15.387 8.488 -2.281 2.295 0.356 -1.339 N04 YJO 21 YJO N05 N2 N 0 1 Y N N N N N -14.502 7.974 -3.160 3.077 0.441 -2.357 N05 YJO 22 YJO N06 N3 N 0 1 Y N N N N N -13.306 8.130 -2.640 4.218 0.919 -2.006 N06 YJO 23 YJO O01 O1 O 0 1 N N N N N N -17.175 7.660 -0.261 1.511 -1.792 0.307 O01 YJO 24 YJO O09 O2 O 0 1 N N N N N N -12.785 9.997 0.745 6.455 2.409 -0.769 O09 YJO 25 YJO O19 O3 O 0 1 N N N N N N -17.047 10.667 -3.303 0.028 2.023 -0.728 O19 YJO 26 YJO O24 O4 O 0 1 N N N N N N -21.980 10.642 0.268 -4.442 0.408 3.095 O24 YJO 27 YJO O26 O5 O 0 1 N N N N N N -24.620 11.669 -0.122 -7.217 0.826 2.540 O26 YJO 28 YJO O28 O6 O 0 1 N N N N N N -25.628 11.475 -2.779 -8.073 0.051 -0.076 O28 YJO 29 YJO O31 O7 O 0 1 N N N N N N -23.104 10.686 -5.976 -5.330 -0.122 -3.214 O31 YJO 30 YJO O32 O8 O 0 1 N N N N N N -22.007 11.339 -3.338 -4.483 0.600 -0.564 O32 YJO 31 YJO O33 O9 O 0 1 N N N N N N -19.502 8.607 -1.525 -1.283 -1.315 0.023 O33 YJO 32 YJO O36 O10 O 0 1 N N N N N N -21.070 6.313 -1.205 -1.920 -4.065 -0.535 O36 YJO 33 YJO S08 S1 S 1 1 N N R N N N -12.143 9.126 -0.284 5.525 1.814 0.279 S08 YJO 34 YJO S21 S2 S 0 1 N N N N N N -19.815 11.155 -1.917 -2.320 0.953 0.940 S21 YJO 35 YJO H021 H1 H 0 0 N N N N N N -17.039 6.355 -1.878 1.447 -2.196 -1.719 H021 YJO 36 YJO H031 H2 H 0 0 N N N N N N -16.989 8.096 -3.574 0.493 -0.013 -2.352 H031 YJO 37 YJO H111 H3 H 0 0 N N N N N N -10.316 8.618 -2.482 5.235 0.132 2.592 H111 YJO 38 YJO H121 H4 H 0 0 N N N N N N -8.791 10.120 -3.717 6.438 -1.892 3.309 H121 YJO 39 YJO H131 H5 H 0 0 N N N N N N -8.690 12.513 -3.160 8.265 -2.794 1.930 H131 YJO 40 YJO H141 H6 H 0 0 N N N N N N -10.112 13.421 -1.372 8.895 -1.677 -0.171 H141 YJO 41 YJO H151 H7 H 0 0 N N N N N N -11.642 11.936 -0.125 7.695 0.343 -0.901 H151 YJO 42 YJO H171 H8 H 0 0 N N N N N N -15.204 9.448 -0.334 2.600 0.865 0.768 H171 YJO 43 YJO H181 H9 H 0 0 N N N N N N -17.241 10.118 -1.310 0.528 0.564 0.647 H181 YJO 44 YJO H201 H10 H 0 0 N N N N N N -19.323 9.423 -3.438 -1.805 0.195 -1.287 H201 YJO 45 YJO H221 H11 H 0 0 N N N N N N -21.629 9.675 -2.144 -3.928 -0.836 0.815 H221 YJO 46 YJO H231 H12 H 0 0 N N N N N N -22.180 12.381 -0.841 -4.931 1.894 1.744 H231 YJO 47 YJO H251 H13 H 0 0 N N N N N N -24.048 10.010 -1.213 -6.313 -0.830 1.694 H251 YJO 48 YJO H271 H14 H 0 0 N N N N N N -24.032 12.768 -2.500 -6.843 1.705 0.074 H271 YJO 49 YJO H291 H15 H 0 0 N N N N N N -23.545 9.955 -3.567 -5.752 -1.016 -0.780 H291 YJO 50 YJO H301 H16 H 0 0 N N N N N N -23.306 12.551 -5.117 -7.226 0.159 -2.441 H301 YJO 51 YJO H302 H17 H 0 0 N N N N N N -24.788 11.536 -5.142 -6.145 1.569 -2.352 H302 YJO 52 YJO H341 H18 H 0 0 N N N N N N -19.170 7.061 -2.884 -1.006 -2.017 -1.902 H341 YJO 53 YJO H352 H19 H 0 0 N N N N N N -19.267 5.314 -1.135 0.053 -4.166 -1.140 H352 YJO 54 YJO H351 H20 H 0 0 N N N N N N -19.503 6.591 0.106 -0.207 -3.656 0.545 H351 YJO 55 YJO H011 H21 H 0 0 N N N N N N -17.566 7.005 0.306 1.533 -2.709 0.614 H011 YJO 56 YJO H1 H22 H 0 1 N N N N N N -12.141 10.243 1.399 7.249 2.820 -0.402 H1 YJO 57 YJO H191 H23 H 0 0 N N N N N N -17.467 11.509 -3.174 -0.487 2.582 -0.130 H191 YJO 58 YJO H241 H24 H 0 0 N N N N N N -22.492 10.979 0.994 -3.550 0.719 3.302 H241 YJO 59 YJO H261 H25 H 0 0 N N N N N N -24.360 11.283 0.706 -6.980 0.639 3.459 H261 YJO 60 YJO H281 H26 H 0 0 N N N N N N -26.146 11.883 -2.096 -8.759 0.352 0.535 H281 YJO 61 YJO H311 H27 H 0 0 N N N N N N -23.312 11.012 -6.844 -5.540 0.096 -4.132 H311 YJO 62 YJO H361 H28 H 0 0 N N N N N N -21.495 5.682 -0.636 -2.013 -4.990 -0.269 H361 YJO 63 # 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 YJO O31 C30 SING N N 1 YJO C30 C29 SING N N 2 YJO C29 O32 SING N N 3 YJO C29 C27 SING N N 4 YJO O32 C22 SING N N 5 YJO O19 C18 SING N N 6 YJO N05 N06 DOUB Y N 7 YJO N05 N04 SING Y N 8 YJO C12 C13 DOUB Y N 9 YJO C12 C11 SING Y N 10 YJO O28 C27 SING N N 11 YJO N06 C07 SING Y N 12 YJO C13 C14 SING Y N 13 YJO C03 C18 SING N N 14 YJO C03 N04 SING N N 15 YJO C03 C02 SING N N 16 YJO C27 C25 SING N N 17 YJO C20 C18 SING N N 18 YJO C20 S21 SING N N 19 YJO C20 O33 SING N N 20 YJO N04 C17 SING Y N 21 YJO C11 C10 DOUB Y N 22 YJO C22 S21 SING N N 23 YJO C22 C23 SING N N 24 YJO C34 C02 SING N N 25 YJO C34 O33 SING N N 26 YJO C34 C35 SING N N 27 YJO C02 O01 SING N N 28 YJO C14 C15 DOUB Y N 29 YJO C07 C17 DOUB Y N 30 YJO C07 S08 SING N N 31 YJO C10 C15 SING Y N 32 YJO C10 S08 SING N N 33 YJO O36 C35 SING N N 34 YJO C25 C23 SING N N 35 YJO C25 O26 SING N N 36 YJO C23 O24 SING N N 37 YJO S08 O09 SING N N 38 YJO C02 H021 SING N N 39 YJO C03 H031 SING N N 40 YJO C11 H111 SING N N 41 YJO C12 H121 SING N N 42 YJO C13 H131 SING N N 43 YJO C14 H141 SING N N 44 YJO C15 H151 SING N N 45 YJO C17 H171 SING N N 46 YJO C18 H181 SING N N 47 YJO C20 H201 SING N N 48 YJO C22 H221 SING N N 49 YJO C23 H231 SING N N 50 YJO C25 H251 SING N N 51 YJO C27 H271 SING N N 52 YJO C29 H291 SING N N 53 YJO C30 H301 SING N N 54 YJO C30 H302 SING N N 55 YJO C34 H341 SING N N 56 YJO C35 H352 SING N N 57 YJO C35 H351 SING N N 58 YJO O01 H011 SING N N 59 YJO O09 H1 SING N N 60 YJO O19 H191 SING N N 61 YJO O24 H241 SING N N 62 YJO O26 H261 SING N N 63 YJO O28 H281 SING N N 64 YJO O31 H311 SING N N 65 YJO O36 H361 SING N N 66 # 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 YJO InChI InChI 1.06 "InChI=1S/C20H28N3O10S2/c24-7-10-14(26)13(23-6-12(21-22-23)35(31)9-4-2-1-3-5-9)16(28)19(32-10)34-20-18(30)17(29)15(27)11(8-25)33-20/h1-6,10-11,13-20,24-31H,7-8H2/q+1/t10-,11-,13+,14+,15-,16-,17+,18-,19+,20+,35-/m1/s1" YJO InChIKey InChI 1.06 CNUXDWRJKZUXTP-HFTUCEKPSA-N YJO SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@@H](S[C@@H]2O[C@H](CO)[C@H](O)[C@@H]([C@H]2O)n3cc(nn3)[S@+](O)c4ccccc4)[C@H](O)[C@@H](O)[C@@H]1O" YJO SMILES CACTVS 3.385 "OC[CH]1O[CH](S[CH]2O[CH](CO)[CH](O)[CH]([CH]2O)n3cc(nn3)[S+](O)c4ccccc4)[CH](O)[CH](O)[CH]1O" YJO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)[S@+](c2cn(nn2)[C@H]3[C@H]([C@H](O[C@H]([C@@H]3O)S[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)CO)O)O" YJO SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)[S+](c2cn(nn2)C3C(C(OC(C3O)SC4C(C(C(C(O4)CO)O)O)O)CO)O)O" # _pdbx_chem_comp_identifier.comp_id YJO _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~{R},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-3,5-bis(oxidanyl)oxan-4-yl]-1,2,3-triazol-4-yl]-oxidanyl-phenyl-sulfanium" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YJO "Create component" 2023-06-19 PDBE YJO "Initial release" 2023-11-08 RCSB #