data_YBC
# 
_chem_comp.id                                    YBC 
_chem_comp.name                                  "(2~{R},3~{R},4~{S},5~{R},6~{R})-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-4-[4-(2-oxidanyl-1,3-thiazol-4-yl)-1,2,3-triazol-1-yl]oxane-3,5-diol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H16 Cl2 N4 O5 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-30 
_chem_comp.pdbx_modified_date                    2024-05-31 
_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                        491.369 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YBC 
_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        8R74 
_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 
YBC C15 C1  C  0 1 Y N N N N N 29.747 -24.283 -13.239 -3.756 3.682  1.032  C15 YBC 1  
YBC C14 C2  C  0 1 Y N N N N N 31.717 -23.733 -14.238 -3.672 1.739  -0.068 C14 YBC 2  
YBC C13 C3  C  0 1 Y N N N N N 41.772 -22.611 -12.236 3.841  0.185  1.260  C13 YBC 3  
YBC C12 C4  C  0 1 Y N N N N N 41.173 -23.848 -12.430 2.648  -0.356 0.796  C12 YBC 4  
YBC C11 C5  C  0 1 Y N N N N N 41.655 -25.005 -11.867 2.238  -0.110 -0.508 C11 YBC 5  
YBC C10 C6  C  0 1 Y N N N N N 42.833 -25.022 -11.057 3.015  0.671  -1.341 C10 YBC 6  
YBC C8  C7  C  0 1 Y N N N N N 42.883 -22.594 -11.408 4.615  0.966  0.423  C8  YBC 7  
YBC C9  C8  C  0 1 Y N N N N N 43.387 -23.814 -10.819 4.203  1.209  -0.877 C9  YBC 8  
YBC C6  C9  C  0 1 Y N N N N N 34.093 -23.594 -13.330 -2.698 -0.487 0.704  C6  YBC 9  
YBC C5  C10 C  0 1 N N S N N N 36.664 -23.031 -13.295 -1.992 -2.894 0.754  C5  YBC 10 
YBC N1  N1  N  0 1 Y N N N N N 33.747 -22.960 -15.515 -3.554 -0.477 -1.287 N1  YBC 11 
YBC C2  C11 C  0 1 N N R N N N 38.073 -21.997 -11.690 -0.347 -3.108 -1.111 C2  YBC 12 
YBC C3  C12 C  0 1 N N N N N N 38.230 -21.113 -10.490 -0.927 -1.872 -1.801 C3  YBC 13 
YBC O3  O1  O  0 1 N N N N N N 39.652 -20.972 -10.042 0.064  -1.293 -2.652 O3  YBC 14 
YBC C4  C13 C  0 1 N N R N N N 37.146 -24.392 -12.791 -0.833 -2.465 1.660  C4  YBC 15 
YBC O4  O2  O  0 1 N N N N N N 28.838 -24.779 -12.199 -3.557 4.540  2.062  O4  YBC 16 
YBC CL1 CL1 CL 0 0 N N N N N N 44.870 -23.744 -9.802  5.178  2.190  -1.926 CL1 YBC 17 
YBC CL  CL2 CL 0 0 N N N N N N 43.706 -21.060 -11.056 6.102  1.649  1.002  CL  YBC 18 
YBC S   S1  S  0 1 N N N N N N 39.792 -23.956 -13.445 1.659  -1.352 1.860  S   YBC 19 
YBC C   C14 C  0 1 N N R N N N 38.547 -24.269 -12.174 0.251  -1.800 0.807  C   YBC 20 
YBC O2  O3  O  0 1 N N N N N N 37.149 -25.310 -13.866 -0.288 -3.613 2.314  O2  YBC 21 
YBC C1  C15 C  0 1 N N R N N N 36.642 -22.043 -12.182 -1.455 -3.827 -0.336 C1  YBC 22 
YBC O1  O4  O  0 1 N N N N N N 35.763 -22.390 -11.110 -2.514 -4.175 -1.230 O1  YBC 23 
YBC O   O5  O  0 1 N N N N N N 38.471 -23.289 -11.154 0.684  -2.710 -0.206 O   YBC 24 
YBC N   N2  N  0 1 Y N N N N N 35.259 -23.123 -13.825 -2.593 -1.711 0.135  N   YBC 25 
YBC N2  N3  N  0 1 Y N N N N N 35.114 -22.747 -15.135 -3.112 -1.659 -1.041 N2  YBC 26 
YBC C7  C16 C  0 1 Y N N N N N 33.200 -23.494 -14.401 -3.324 0.303  -0.216 C7  YBC 27 
YBC C16 C17 C  0 1 Y N N N N N 30.830 -23.011 -15.095 -4.284 2.446  -1.035 C16 YBC 28 
YBC S1  S2  S  0 1 Y N N N N N 29.129 -23.289 -14.569 -4.507 4.092  -0.447 S1  YBC 29 
YBC N3  N4  N  0 1 Y N N N N N 31.182 -24.315 -13.086 -3.399 2.438  1.027  N3  YBC 30 
YBC H13 H1  H  0 1 N N N N N N 41.394 -21.714 -12.703 4.161  -0.001 2.274  H13 YBC 31 
YBC H11 H2  H  0 1 N N N N N N 41.127 -25.931 -12.042 1.311  -0.529 -0.871 H11 YBC 32 
YBC H10 H3  H  0 1 N N N N N N 43.250 -25.937 -10.663 2.696  0.862  -2.355 H10 YBC 33 
YBC H6  H4  H  0 1 N N N N N N 33.896 -23.963 -12.334 -2.360 -0.196 1.687  H6  YBC 34 
YBC H5  H5  H  0 1 N N N N N N 37.336 -22.680 -14.092 -2.743 -3.418 1.345  H5  YBC 35 
YBC H2  H6  H  0 1 N N N N N N 38.746 -21.676 -12.498 0.067  -3.782 -1.861 H2  YBC 36 
YBC H31 H7  H  0 1 N N N N N N 37.841 -20.114 -10.738 -1.793 -2.161 -2.397 H31 YBC 37 
YBC H32 H8  H  0 1 N N N N N N 37.644 -21.539 -9.663  -1.230 -1.144 -1.049 H32 YBC 38 
YBC HO3 H9  H  0 1 N N N N N N 39.690 -20.404 -9.282  -0.234 -0.503 -3.123 HO3 YBC 39 
YBC H4  H10 H  0 1 N N N N N N 36.454 -24.735 -12.008 -1.196 -1.759 2.406  H4  YBC 40 
YBC HO4 H11 H  0 1 N N N N N N 27.955 -24.481 -12.382 -2.715 5.014  2.021  HO4 YBC 41 
YBC H   H12 H  0 1 N N N N N N 38.816 -25.242 -11.736 -0.154 -0.902 0.341  H   YBC 42 
YBC HO2 H13 H  0 1 N N N N N N 36.275 -25.371 -14.233 0.452  -3.415 2.905  HO2 YBC 43 
YBC H1  H14 H  0 1 N N N N N N 36.373 -21.055 -12.583 -1.053 -4.730 0.123  H1  YBC 44 
YBC HO1 H15 H  0 1 N N N N N N 35.800 -21.718 -10.439 -2.246 -4.766 -1.947 HO1 YBC 45 
YBC H16 H16 H  0 1 N N N N N N 31.132 -22.394 -15.929 -4.591 2.069  -1.999 H16 YBC 46 
# 
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 
YBC CL1 C9  SING N N 1  
YBC C9  C10 SING Y N 2  
YBC C9  C8  DOUB Y N 3  
YBC C10 C11 DOUB Y N 4  
YBC C11 C12 SING Y N 5  
YBC C12 C13 DOUB Y N 6  
YBC C12 S   SING N N 7  
YBC C13 C8  SING Y N 8  
YBC C8  CL  SING N N 9  
YBC S   C   SING N N 10 
YBC C   C4  SING N N 11 
YBC C   O   SING N N 12 
YBC C4  O2  SING N N 13 
YBC C4  C5  SING N N 14 
YBC C5  C1  SING N N 15 
YBC C5  N   SING N N 16 
YBC C1  O1  SING N N 17 
YBC C1  C2  SING N N 18 
YBC C2  C3  SING N N 19 
YBC C2  O   SING N N 20 
YBC C3  O3  SING N N 21 
YBC N   N2  SING Y N 22 
YBC N   C6  SING Y N 23 
YBC N2  N1  DOUB Y N 24 
YBC N1  C7  SING Y N 25 
YBC C7  C6  DOUB Y N 26 
YBC C7  C14 SING N N 27 
YBC C14 C16 DOUB Y N 28 
YBC C14 N3  SING Y N 29 
YBC C16 S1  SING Y N 30 
YBC S1  C15 SING Y N 31 
YBC C15 N3  DOUB Y N 32 
YBC C15 O4  SING N N 33 
YBC C13 H13 SING N N 34 
YBC C11 H11 SING N N 35 
YBC C10 H10 SING N N 36 
YBC C6  H6  SING N N 37 
YBC C5  H5  SING N N 38 
YBC C2  H2  SING N N 39 
YBC C3  H31 SING N N 40 
YBC C3  H32 SING N N 41 
YBC O3  HO3 SING N N 42 
YBC C4  H4  SING N N 43 
YBC O4  HO4 SING N N 44 
YBC C   H   SING N N 45 
YBC O2  HO2 SING N N 46 
YBC C1  H1  SING N N 47 
YBC O1  HO1 SING N N 48 
YBC C16 H16 SING N N 49 
# 
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 
YBC InChI            InChI                1.06  "InChI=1S/C17H16Cl2N4O5S2/c18-8-2-1-7(3-9(8)19)30-16-15(26)13(14(25)12(5-24)28-16)23-4-10(21-22-23)11-6-29-17(27)20-11/h1-4,6,12-16,24-26H,5H2,(H,20,27)/t12-,13+,14+,15-,16-/m1/s1" 
YBC InChIKey         InChI                1.06  BWEZCWXAMQJAHD-LYYZXLFJSA-N                                                                                                                                                          
YBC SMILES_CANONICAL CACTVS               3.385 "OC[C@H]1O[C@H](Sc2ccc(Cl)c(Cl)c2)[C@H](O)[C@H]([C@H]1O)n3cc(nn3)c4csc(O)n4"                                                                                                         
YBC SMILES           CACTVS               3.385 "OC[CH]1O[CH](Sc2ccc(Cl)c(Cl)c2)[CH](O)[CH]([CH]1O)n3cc(nn3)c4csc(O)n4"                                                                                                              
YBC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1S[C@@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)n3cc(nn3)c4csc(n4)O)O)Cl)Cl"                                                                                                     
YBC SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1SC2C(C(C(C(O2)CO)O)n3cc(nn3)c4csc(n4)O)O)Cl)Cl"                                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           YBC 
_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~{R},6~{R})-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-4-[4-(2-oxidanyl-1,3-thiazol-4-yl)-1,2,3-triazol-1-yl]oxane-3,5-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 
YBC "Create component" 2023-11-30 PDBE 
YBC "Initial release"  2024-06-05 RCSB 
# 
