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 
# 
