data_Y45 # _chem_comp.id Y45 _chem_comp.name "Agrocinopine D-like (C2-C2 linked; with two alpha-D-glucopyranoses)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H23 O14 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Agrocinopine D-like; bis[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate; D-glucose-2-phosphate-2-glucose" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-09 _chem_comp.pdbx_modified_date 2024-01-19 _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 422.276 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y45 _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 8CHC _chem_comp.pdbx_subcomponent_list "GLC ALX" _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 Y45 C1 C1 C 0 1 N N S N N N 16.659 -1.317 -16.918 -3.434 1.287 -0.306 C1 GLC 1 Y45 C2 C2 C 0 1 N N R N N N 15.567 -0.865 -15.956 -2.645 0.081 0.211 C2 GLC 2 Y45 C3 C3 C 0 1 N N S N N N 14.843 0.373 -16.467 -3.345 -1.207 -0.234 C3 GLC 3 Y45 C4 C4 C 0 1 N N S N N N 15.826 1.484 -16.819 -4.789 -1.193 0.278 C4 GLC 4 Y45 C5 C5 C 0 1 N N R N N N 16.888 0.944 -17.777 -5.495 0.061 -0.242 C5 GLC 5 Y45 C6 C8 C 0 1 N N N N N N 17.982 1.937 -18.094 -6.919 0.113 0.315 C6 GLC 6 Y45 O1 O2 O 0 1 N N N N N N 16.198 -1.859 -18.131 -3.446 1.271 -1.735 O1 GLC 7 Y45 O2 O3 O 0 1 N N N N N N 14.564 -1.897 -15.880 -1.320 0.113 -0.323 O2 GLC 8 Y45 O3 O7 O 0 1 N N N N N N 13.885 0.788 -15.493 -2.656 -2.336 0.306 O3 GLC 9 Y45 O4 O8 O 0 1 N N N N N N 15.136 2.566 -17.443 -5.472 -2.357 -0.191 O4 GLC 10 Y45 O5 O9 O 0 1 N N N N N N 17.529 -0.220 -17.219 -4.776 1.221 0.182 O5 GLC 11 Y45 O6 O1 O 0 1 N N N N N N 18.544 2.483 -16.901 -7.616 1.220 -0.260 O6 GLC 12 Y45 C11 C6 C 0 1 N N S N N N 11.303 -3.084 -12.611 3.295 -1.298 -0.228 C1 ALX 13 Y45 O11 O10 O 0 1 N N N N N N 11.918 -2.645 -11.429 3.302 -1.374 -1.655 O1 ALX 14 Y45 OA2 O6 O 0 1 N N N N N N 13.206 -1.982 -13.699 1.309 0.078 -0.323 O2 ALX 15 Y45 C21 C7 C 0 1 N N R N N N 11.800 -2.328 -13.849 2.633 0.011 0.210 C2 ALX 16 Y45 C31 C9 C 0 1 N N S N N N 11.159 -0.950 -13.971 3.457 1.191 -0.314 C3 ALX 17 Y45 C51 C11 C 0 1 N N R N N N 9.291 -1.744 -12.548 5.468 -0.285 -0.237 C5 ALX 18 Y45 C61 C12 C 0 1 N N N N N N 7.802 -1.924 -12.339 6.883 -0.443 0.325 C6 ALX 19 Y45 OAN O4 O 0 1 N N N N N N 15.576 -2.848 -13.866 0.015 1.595 1.391 OAN ALX 20 Y45 PAM P1 P 0 1 N N N N N N 14.223 -2.737 -14.535 -0.004 0.191 0.602 PAM ALX 21 Y45 OAO O5 O 0 1 N N N N N N 13.693 -4.063 -15.042 -0.019 -0.923 1.576 OAO ALX 22 Y45 O31 O11 O 0 1 N N N N N N 11.533 -0.328 -15.202 2.887 2.416 0.152 O3 ALX 23 Y45 C41 C10 C 0 1 N N S N N N 9.644 -1.054 -13.863 4.894 1.065 0.201 C4 ALX 24 Y45 O41 O12 O 0 1 N N N N N N 9.068 0.254 -13.877 5.689 2.121 -0.340 O4 ALX 25 Y45 O61 O14 O 0 1 N N N N N N 7.230 -2.709 -13.371 7.462 -1.649 -0.177 O6 ALX 26 Y45 O51 O13 O 0 1 N N N N N N 9.872 -3.057 -12.535 4.638 -1.337 0.258 O5 ALX 27 Y45 H1 H1 H 0 1 N N N N N N 17.248 -2.086 -16.396 -2.965 2.206 0.043 H1 GLC 28 Y45 H2 H2 H 0 1 N N N N N N 16.001 -0.662 -14.966 -2.601 0.115 1.299 H2 GLC 29 Y45 H3 H3 H 0 1 N N N N N N 14.313 0.093 -17.389 -3.344 -1.265 -1.322 H3 GLC 30 Y45 H4 H4 H 0 1 N N N N N N 16.320 1.828 -15.898 -4.788 -1.186 1.368 H4 GLC 31 Y45 H5 H5 H 0 1 N N N N N N 16.390 0.667 -18.718 -5.531 0.033 -1.331 H5 GLC 32 Y45 H61 H10 H 0 1 N N N N N N 18.774 1.429 -18.664 -7.440 -0.812 0.067 H61 GLC 33 Y45 H62 H11 H 0 1 N N N N N N 17.561 2.754 -18.699 -6.882 0.230 1.398 H62 GLC 34 Y45 HO1 H9 H 0 1 N N N N N N 15.618 -2.590 -17.952 -3.930 2.008 -2.133 HO1 GLC 35 Y45 HO3 H13 H 0 1 N N N N N N 13.294 0.069 -15.303 -3.046 -3.187 0.064 HO3 GLC 36 Y45 HO4 H14 H 0 1 N N N N N N 14.475 2.904 -16.851 -6.394 -2.414 0.097 HO4 GLC 37 Y45 HO6 H6 H 0 1 N N N N N N 19.228 3.103 -17.127 -8.528 1.314 0.048 HO6 GLC 38 Y45 H6 H7 H 0 1 N N N N N N 11.596 -4.133 -12.763 2.737 -2.142 0.178 H1 ALX 39 Y45 H7 H20 H 0 1 N N N N N N 11.579 -3.140 -10.692 3.708 -2.179 -2.004 HO1 ALX 40 Y45 H8 H8 H 0 1 N N N N N N 11.622 -2.920 -14.759 2.590 0.050 1.299 H2 ALX 41 Y45 H9 H15 H 0 1 N N N N N N 11.517 -0.335 -13.132 3.458 1.179 -1.404 H3 ALX 42 Y45 H10 H17 H 0 1 N N N N N N 9.696 -1.147 -11.718 5.502 -0.329 -1.325 H5 ALX 43 Y45 H11 H19 H 0 1 N N N N N N 7.633 -2.423 -11.373 7.492 0.407 0.020 H61 ALX 44 Y45 H12 H18 H 0 1 N N N N N N 7.319 -0.936 -12.330 6.839 -0.487 1.413 H62 ALX 45 Y45 H15 H12 H 0 1 N N N N N N 15.864 -3.753 -13.881 0.025 2.370 0.814 H8 ALX 46 Y45 H13 H21 H 0 1 N N N N N N 12.480 -0.271 -15.254 3.364 3.206 -0.137 HO3 ALX 47 Y45 H14 H16 H 0 1 N N N N N N 9.261 -1.654 -14.701 4.897 1.127 1.290 H4 ALX 48 Y45 H16 H22 H 0 1 N N N N N N 8.123 0.185 -13.809 6.613 2.104 -0.055 HO4 ALX 49 Y45 H17 H23 H 0 1 N N N N N N 6.298 -2.806 -13.216 8.361 -1.815 0.138 HO6 ALX 50 # 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 Y45 O1 C1 SING N N 1 Y45 C6 C5 SING N N 2 Y45 C6 O6 SING N N 3 Y45 C5 O5 SING N N 4 Y45 C5 C4 SING N N 5 Y45 O4 C4 SING N N 6 Y45 O5 C1 SING N N 7 Y45 C1 C2 SING N N 8 Y45 C4 C3 SING N N 9 Y45 C3 C2 SING N N 10 Y45 C3 O3 SING N N 11 Y45 C2 O2 SING N N 12 Y45 O2 PAM SING N N 13 Y45 O31 C31 SING N N 14 Y45 OAO PAM DOUB N N 15 Y45 PAM OAN SING N N 16 Y45 PAM OA2 SING N N 17 Y45 C31 C41 SING N N 18 Y45 C31 C21 SING N N 19 Y45 O41 C41 SING N N 20 Y45 C41 C51 SING N N 21 Y45 C21 OA2 SING N N 22 Y45 C21 C11 SING N N 23 Y45 O61 C61 SING N N 24 Y45 C11 O51 SING N N 25 Y45 C11 O11 SING N N 26 Y45 C51 O51 SING N N 27 Y45 C51 C61 SING N N 28 Y45 C1 H1 SING N N 29 Y45 C2 H2 SING N N 30 Y45 C3 H3 SING N N 31 Y45 C4 H4 SING N N 32 Y45 C5 H5 SING N N 33 Y45 O6 HO6 SING N N 34 Y45 C11 H6 SING N N 35 Y45 C21 H8 SING N N 36 Y45 O1 HO1 SING N N 37 Y45 C6 H61 SING N N 38 Y45 C6 H62 SING N N 39 Y45 OAN H15 SING N N 40 Y45 O3 HO3 SING N N 41 Y45 O4 HO4 SING N N 42 Y45 C31 H9 SING N N 43 Y45 C41 H14 SING N N 44 Y45 C51 H10 SING N N 45 Y45 C61 H12 SING N N 46 Y45 C61 H11 SING N N 47 Y45 O11 H7 SING N N 48 Y45 O31 H13 SING N N 49 Y45 O41 H16 SING N N 50 Y45 O61 H17 SING N N 51 # 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 Y45 InChI InChI 1.06 "InChI=1S/C12H23O14P/c13-1-3-5(15)7(17)9(11(19)23-3)25-27(21,22)26-10-8(18)6(16)4(2-14)24-12(10)20/h3-20H,1-2H2,(H,21,22)/t3-,4-,5-,6-,7+,8+,9-,10-,11+,12+/m1/s1" Y45 InChIKey InChI 1.06 DCDHSOINTWUWCZ-NCFXGAEVSA-N Y45 SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@H](O)[C@H](O[P](O)(=O)O[C@H]2[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@@H](O)[C@@H]1O" Y45 SMILES CACTVS 3.385 "OC[CH]1O[CH](O)[CH](O[P](O)(=O)O[CH]2[CH](O)O[CH](CO)[CH](O)[CH]2O)[CH](O)[CH]1O" Y45 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)OP(=O)(O)O[C@@H]2[C@H]([C@@H]([C@H](O[C@@H]2O)CO)O)O)O)O)O" Y45 SMILES "OpenEye OEToolkits" 2.0.7 "C(C1C(C(C(C(O1)O)OP(=O)(O)OC2C(C(C(OC2O)CO)O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id Y45 _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 "bis[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate" # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 Y45 "Agrocinopine D-like" AUTHOR ? 2 Y45 "bis[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate" PDB ? 3 Y45 D-glucose-2-phosphate-2-glucose AUTHOR ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y45 "Create component" 2023-06-09 PDBE Y45 "Other modification" 2023-12-03 PDBE Y45 "Modify name" 2023-12-05 PDBE Y45 "Initial release" 2024-01-24 RCSB #