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 #