data_Y58
# 
_chem_comp.id                                    Y58 
_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-phenylsulfanyl-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 H27 N3 O9 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-12 
_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                        517.573 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y58 
_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        8PBF 
_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 
Y58 C13  C1  C 0 1 Y N N N N N -10.929 11.702 -0.712 -8.925  0.602  -0.090 C13  Y58 1  
Y58 C12  C2  C 0 1 Y N N N N N -9.636  11.367 -0.327 -9.400  -0.217 -1.098 C12  Y58 2  
Y58 C10  C3  C 0 1 Y N N N N N -10.540 9.687  1.140  -7.555  -1.707 -0.771 C10  Y58 3  
Y58 C02  C4  C 0 1 N N R N N N -18.248 7.363  -0.779 -0.822  2.069  0.333  C02  Y58 4  
Y58 C03  C5  C 0 1 N N S N N N -17.568 8.629  -1.440 -1.062  0.825  -0.528 C03  Y58 5  
Y58 C07  C6  C 0 1 Y N N N N N -14.385 8.953  0.215  -4.353  -0.433 0.203  C07  Y58 6  
Y58 C09  C7  C 0 1 Y N N N N N -11.838 10.025 0.770  -7.074  -0.887 0.242  C09  Y58 7  
Y58 C11  C8  C 0 1 Y N N N N N -9.451  10.358 0.607  -8.715  -1.370 -1.438 C11  Y58 8  
Y58 C14  C9  C 0 1 Y N N N N N -12.021 11.031 -0.181 -7.764  0.271  0.581  C14  Y58 9  
Y58 C15  C10 C 0 1 Y N N N N N -15.747 8.998  0.278  -3.036  -0.332 0.523  C15  Y58 10 
Y58 C16  C11 C 0 1 N N R N N N -18.353 9.925  -1.087 -0.187  -0.319 -0.007 C16  Y58 11 
Y58 C18  C12 C 0 1 N N S N N N -19.797 9.712  -1.510 1.279   0.122  -0.021 C18  Y58 12 
Y58 C20  C13 C 0 1 N N S N N N -22.456 10.738 -1.371 3.998   -0.565 0.423  C20  Y58 13 
Y58 C21  C14 C 0 1 N N R N N N -23.414 11.226 -0.262 5.002   -1.524 1.067  C21  Y58 14 
Y58 C23  C15 C 0 1 N N S N N N -24.887 10.954 -0.740 6.423   -1.012 0.809  C23  Y58 15 
Y58 C25  C16 C 0 1 N N S N N N -25.072 11.663 -2.142 6.638   -0.873 -0.701 C25  Y58 16 
Y58 C27  C17 C 0 1 N N R N N N -23.997 11.092 -3.103 5.570   0.061  -1.276 C27  Y58 17 
Y58 C28  C18 C 0 1 N N N N N N -24.098 11.708 -4.539 5.742   0.158  -2.794 C28  Y58 18 
Y58 C32  C19 C 0 1 N N R N N N -19.715 7.333  -1.240 0.668   2.420  0.307  C32  Y58 19 
Y58 C33  C20 C 0 1 N N N N N N -20.491 6.187  -0.563 0.927   3.625  1.213  C33  Y58 20 
Y58 N04  N1  N 0 1 Y N N N N N -16.212 8.729  -1.015 -2.473  0.439  -0.448 N04  Y58 21 
Y58 N05  N2  N 0 1 Y N N N N N -15.159 8.519  -1.824 -3.394  0.770  -1.283 N05  Y58 22 
Y58 N06  N3  N 0 1 Y N N N N N -14.086 8.663  -1.128 -4.522  0.263  -0.930 N06  Y58 23 
Y58 O01  O1  O 0 1 N N N N N N -18.174 7.505  0.601  -1.226  1.804  1.678  O01  Y58 24 
Y58 O17  O2  O 0 1 N N N N N N -17.800 10.955 -1.869 -0.350  -1.464 -0.847 O17  Y58 25 
Y58 O22  O3  O 0 1 N N N N N N -23.151 10.443 0.893  4.766   -1.589 2.474  O22  Y58 26 
Y58 O24  O4  O 0 1 N N N N N N -25.768 11.599 0.154  7.369   -1.939 1.344  O24  Y58 27 
Y58 O26  O5  O 0 1 N N N N N N -26.333 11.287 -2.633 7.935   -0.328 -0.950 O26  Y58 28 
Y58 O29  O6  O 0 1 N N N N N N -23.761 13.099 -4.465 4.820   1.117  -3.317 O29  Y58 29 
Y58 O30  O7  O 0 1 N N N N N N -22.706 11.399 -2.603 4.273   -0.457 -0.975 O30  Y58 30 
Y58 O31  O8  O 0 1 N N N N N N -20.346 8.569  -0.861 1.427   1.301  0.774  O31  Y58 31 
Y58 O34  O9  O 0 1 N N N N N N -21.845 6.183  -0.987 2.295   4.022  1.100  O34  Y58 32 
Y58 S08  S1  S 0 1 N N N N N N -13.203 9.181  1.469  -5.592  -1.313 1.095  S08  Y58 33 
Y58 S19  S2  S 0 1 N N N N N N -20.723 11.161 -0.885 2.316   -1.201 0.661  S19  Y58 34 
Y58 H131 H1  H 0 0 N N N N N N -11.085 12.492 -1.431 -9.459  1.503  0.170  H131 Y58 35 
Y58 H121 H2  H 0 0 N N N N N N -8.787  11.885 -0.749 -10.308 0.044  -1.621 H121 Y58 36 
Y58 H101 H3  H 0 0 N N N N N N -10.379 8.891  1.852  -7.020  -2.608 -1.037 H101 Y58 37 
Y58 H021 H4  H 0 0 N N N N N N -17.732 6.455  -1.126 -1.400  2.904  -0.063 H021 Y58 38 
Y58 H031 H5  H 0 0 N N N N N N -17.605 8.496  -2.531 -0.800  1.043  -1.563 H031 Y58 39 
Y58 H111 H6  H 0 0 N N N N N N -8.452  10.094 0.921  -9.090  -2.007 -2.226 H111 Y58 40 
Y58 H141 H7  H 0 0 N N N N N N -13.019 11.288 -0.505 -7.393  0.911  1.368  H141 Y58 41 
Y58 H151 H8  H 0 0 N N N N N N -16.348 9.201  1.152  -2.538  -0.773 1.374  H151 Y58 42 
Y58 H161 H9  H 0 0 N N N N N N -18.287 10.131 -0.008 -0.483  -0.570 1.012  H161 Y58 43 
Y58 H181 H10 H 0 0 N N N N N N -19.904 9.686  -2.605 1.586   0.333  -1.045 H181 Y58 44 
Y58 H201 H11 H 0 0 N N N N N N -22.505 9.643  -1.467 4.084   0.417  0.887  H201 Y58 45 
Y58 H211 H12 H 0 0 N N N N N N -23.271 12.301 -0.078 4.888   -2.517 0.632  H211 Y58 46 
Y58 H231 H13 H 0 0 N N N N N N -25.074 9.873  -0.827 6.553   -0.041 1.288  H231 Y58 47 
Y58 H251 H14 H 0 0 N N N N N N -24.960 12.752 -2.036 6.557   -1.852 -1.172 H251 Y58 48 
Y58 H271 H15 H 0 0 N N N N N N -24.133 10.003 -3.179 5.677   1.052  -0.835 H271 Y58 49 
Y58 H282 H16 H 0 0 N N N N N N -25.124 11.595 -4.919 6.760   0.469  -3.025 H282 Y58 50 
Y58 H281 H17 H 0 0 N N N N N N -23.398 11.193 -5.213 5.548   -0.816 -3.244 H281 Y58 51 
Y58 H321 H18 H 0 0 N N N N N N -19.750 7.199  -2.331 0.967   2.662  -0.713 H321 Y58 52 
Y58 H332 H19 H 0 0 N N N N N N -20.025 5.227  -0.831 0.282   4.451  0.912  H332 Y58 53 
Y58 H331 H20 H 0 0 N N N N N N -20.454 6.320  0.528  0.711   3.355  2.247  H331 Y58 54 
Y58 H011 H21 H 0 0 N N N N N N -18.578 6.754  1.019  -1.100  2.550  2.281  H011 Y58 55 
Y58 H171 H22 H 0 0 N N N N N N -16.896 11.097 -1.613 0.177   -2.229 -0.575 H171 Y58 56 
Y58 H221 H23 H 0 0 N N N N N N -23.725 10.717 1.599  3.881   -1.901 2.711  H221 Y58 57 
Y58 H241 H24 H 0 0 N N N N N N -25.691 11.204 1.015  7.286   -2.081 2.297  H241 Y58 58 
Y58 H261 H25 H 0 0 N N N N N N -27.010 11.626 -2.060 8.661   -0.868 -0.607 H261 Y58 59 
Y58 H291 H26 H 0 0 N N N N N N -23.818 13.486 -5.331 4.873   1.230  -4.276 H291 Y58 60 
Y58 H341 H27 H 0 0 N N N N N N -22.309 5.472  -0.561 2.530   4.783  1.648  H341 Y58 61 
# 
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 
Y58 C28 O29  SING N N 1  
Y58 C28 C27  SING N N 2  
Y58 C27 O30  SING N N 3  
Y58 C27 C25  SING N N 4  
Y58 O26 C25  SING N N 5  
Y58 O30 C20  SING N N 6  
Y58 C25 C23  SING N N 7  
Y58 O17 C16  SING N N 8  
Y58 N05 N06  DOUB Y N 9  
Y58 N05 N04  SING Y N 10 
Y58 C18 C16  SING N N 11 
Y58 C18 S19  SING N N 12 
Y58 C18 O31  SING N N 13 
Y58 C03 C16  SING N N 14 
Y58 C03 N04  SING N N 15 
Y58 C03 C02  SING N N 16 
Y58 C20 S19  SING N N 17 
Y58 C20 C21  SING N N 18 
Y58 C32 O31  SING N N 19 
Y58 C32 C02  SING N N 20 
Y58 C32 C33  SING N N 21 
Y58 N06 C07  SING Y N 22 
Y58 N04 C15  SING Y N 23 
Y58 O34 C33  SING N N 24 
Y58 C02 O01  SING N N 25 
Y58 C23 C21  SING N N 26 
Y58 C23 O24  SING N N 27 
Y58 C13 C12  DOUB Y N 28 
Y58 C13 C14  SING Y N 29 
Y58 C12 C11  SING Y N 30 
Y58 C21 O22  SING N N 31 
Y58 C14 C09  DOUB Y N 32 
Y58 C07 C15  DOUB Y N 33 
Y58 C07 S08  SING N N 34 
Y58 C11 C10  DOUB Y N 35 
Y58 C09 C10  SING Y N 36 
Y58 C09 S08  SING N N 37 
Y58 C13 H131 SING N N 38 
Y58 C12 H121 SING N N 39 
Y58 C10 H101 SING N N 40 
Y58 C02 H021 SING N N 41 
Y58 C03 H031 SING N N 42 
Y58 C11 H111 SING N N 43 
Y58 C14 H141 SING N N 44 
Y58 C15 H151 SING N N 45 
Y58 C16 H161 SING N N 46 
Y58 C18 H181 SING N N 47 
Y58 C20 H201 SING N N 48 
Y58 C21 H211 SING N N 49 
Y58 C23 H231 SING N N 50 
Y58 C25 H251 SING N N 51 
Y58 C27 H271 SING N N 52 
Y58 C28 H282 SING N N 53 
Y58 C28 H281 SING N N 54 
Y58 C32 H321 SING N N 55 
Y58 C33 H332 SING N N 56 
Y58 C33 H331 SING N N 57 
Y58 O01 H011 SING N N 58 
Y58 O17 H171 SING N N 59 
Y58 O22 H221 SING N N 60 
Y58 O24 H241 SING N N 61 
Y58 O26 H261 SING N N 62 
Y58 O29 H291 SING N N 63 
Y58 O34 H341 SING N N 64 
# 
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 
Y58 InChI            InChI                1.06  "InChI=1S/C20H27N3O9S2/c24-7-10-14(26)13(23-6-12(21-22-23)33-9-4-2-1-3-5-9)16(28)19(31-10)34-20-18(30)17(29)15(27)11(8-25)32-20/h1-6,10-11,13-20,24-30H,7-8H2/t10-,11-,13+,14+,15-,16-,17+,18-,19+,20+/m1/s1" 
Y58 InChIKey         InChI                1.06  ROQDROPGJRNKKP-VTOAZQAJSA-N                                                                                                                                                                                   
Y58 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(Sc4ccccc4)nn3)[C@H](O)[C@@H](O)[C@@H]1O"                                                                                                       
Y58 SMILES           CACTVS               3.385 "OC[CH]1O[CH](S[CH]2O[CH](CO)[CH](O)[CH]([CH]2O)n3cc(Sc4ccccc4)nn3)[CH](O)[CH](O)[CH]1O"                                                                                                                      
Y58 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)Sc2cn(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"                                                                                                     
Y58 SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)Sc2cn(nn2)C3C(C(OC(C3O)SC4C(C(C(C(O4)CO)O)O)O)CO)O"                                                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           Y58 
_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~{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-phenylsulfanyl-1,2,3-triazol-1-yl)oxan-2-yl]sulfanyl-oxane-3,4,5-triol" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y58 "Create component" 2023-06-12 PDBE 
Y58 "Initial release"  2023-11-08 RCSB 
# 
