data_Y4H # _chem_comp.id Y4H _chem_comp.name "Agrocinopine D-like (C2-C2 linked; with an alpha and beta-D-glucopyranose)" _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; [(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-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 Y4H _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 8CAY _chem_comp.pdbx_subcomponent_list "GLC BNX" _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 Y4H C1 C5 C 0 1 N N S N N N 10.335 -24.391 16.234 -3.415 -1.334 0.240 C1 GLC 1 Y4H C2 C6 C 0 1 N N R N N N 10.909 -23.701 17.487 -2.615 -0.098 -0.178 C2 GLC 2 Y4H C3 C7 C 0 1 N N S N N N 12.016 -24.542 18.110 -3.317 1.157 0.350 C3 GLC 3 Y4H C4 C1 C 0 1 N N S N N N 11.522 -25.962 18.353 -4.753 1.187 -0.181 C4 GLC 4 Y4H C5 C2 C 0 1 N N R N N N 11.047 -26.552 17.029 -5.471 -0.099 0.237 C5 GLC 5 Y4H C6 C3 C 0 1 N N N N N N 10.534 -27.973 17.131 -6.887 -0.104 -0.340 C6 GLC 6 Y4H O1 O1 O 0 1 N N N N N N 11.261 -24.314 15.193 -3.446 -1.422 1.666 O1 GLC 7 Y4H O2 O8 O 0 1 N N N N N N 11.405 -22.301 17.229 -1.297 -0.174 0.369 O2 GLC 8 Y4H O3 O2 O 0 1 N N N N N N 12.453 -23.985 19.351 -2.617 2.320 -0.098 O3 GLC 9 Y4H O4 O3 O 0 1 N N N N N N 12.551 -26.754 18.946 -5.440 2.316 0.363 O4 GLC 10 Y4H O5 O4 O 0 1 N N N N N N 9.966 -25.750 16.516 -4.750 -1.228 -0.260 O5 GLC 11 Y4H O6 O5 O 0 1 N N N N N N 9.637 -28.140 18.216 -7.596 -1.246 0.145 O6 GLC 12 Y4H OAN O6 O 0 1 N N N N N N 9.381 -21.417 18.451 0.056 -1.533 -1.430 OAN BNX 13 Y4H PAM P1 P 0 1 N N N N N N 10.758 -21.109 17.919 0.031 -0.191 -0.541 PAM BNX 14 Y4H OAO O7 O 0 1 N N N N N N 10.853 -19.834 17.104 0.033 0.991 -1.432 OAO BNX 15 Y4H OA2 O9 O 0 1 N N N N N N 11.605 -20.909 19.299 1.332 -0.150 0.407 O2 BNX 16 Y4H C21 C4 C 0 1 N N R N N N 12.753 -20.040 19.390 2.663 -0.050 -0.103 C2 BNX 17 Y4H C31 C8 C 0 1 N N S N N N 13.933 -20.910 19.807 3.474 -1.272 0.338 C3 BNX 18 Y4H O31 O10 O 0 1 N N N N N N 14.274 -21.811 18.758 2.904 -2.454 -0.229 O3 BNX 19 Y4H C41 C9 C 0 1 N N S N N N 15.138 -20.073 20.218 4.918 -1.116 -0.147 C4 BNX 20 Y4H O41 O11 O 0 1 N N N N N N 16.135 -20.923 20.760 5.701 -2.216 0.321 O4 BNX 21 Y4H C51 C10 C 0 1 N N R N N N 14.706 -19.052 21.271 5.494 0.192 0.402 C5 BNX 22 Y4H C61 C11 C 0 1 N N N N N N 15.801 -18.106 21.695 6.916 0.385 -0.128 C6 BNX 23 Y4H O61 O12 O 0 1 N N N N N N 16.371 -17.480 20.570 7.496 1.544 0.475 O6 BNX 24 Y4H O51 O13 O 0 1 N N N N N N 13.654 -18.244 20.722 4.676 1.285 -0.020 O5 BNX 25 Y4H C11 C12 C 0 1 N N R N N N 12.446 -18.973 20.437 3.326 1.217 0.444 C1 BNX 26 Y4H O11 O14 O 0 1 N N N N N N 11.675 -17.859 20.144 2.607 2.365 -0.010 O1 BNX 27 Y4H H1 H6 H 0 1 N N N N N N 9.429 -23.838 15.947 -2.944 -2.228 -0.169 H1 GLC 28 Y4H H2 H7 H 0 1 N N N N N N 10.094 -23.634 18.223 -2.557 -0.052 -1.266 H2 GLC 29 Y4H H3 H8 H 0 1 N N N N N N 12.859 -24.583 17.405 -3.331 1.136 1.440 H3 GLC 30 Y4H H4 H1 H 0 1 N N N N N N 10.660 -25.913 19.035 -4.738 1.260 -1.268 H4 GLC 31 Y4H H5 H2 H 0 1 N N N N N N 11.887 -26.534 16.319 -5.521 -0.149 1.325 H5 GLC 32 Y4H H61 H3 H 0 1 N N N N N N 10.013 -28.230 16.197 -7.408 0.804 -0.033 H61 GLC 33 Y4H H62 H4 H 0 1 N N N N N N 11.390 -28.650 17.271 -6.836 -0.143 -1.428 H62 GLC 34 Y4H HO1 H9 H 0 1 N N N N N N 11.483 -23.404 15.033 -3.938 -2.183 2.003 HO1 GLC 35 Y4H HO3 H10 H 0 1 N N N N N N 13.142 -24.527 19.717 -3.007 3.153 0.200 HO3 GLC 36 Y4H HO4 H11 H 0 1 N N N N N N 12.822 -26.359 19.766 -6.357 2.398 0.069 HO4 GLC 37 Y4H HO6 H12 H 0 1 N N N N N N 9.339 -29.042 18.245 -8.503 -1.314 -0.181 HO6 GLC 38 Y4H H7 H13 H 0 1 N N N N N N 8.776 -20.737 18.178 0.056 -2.349 -0.910 H1A BNX 39 Y4H H6 H5 H 0 1 N N N N N N 12.964 -19.563 18.422 2.634 -0.006 -1.192 H2 BNX 40 Y4H H8 H14 H 0 1 N N N N N N 13.620 -21.493 20.686 3.460 -1.345 1.426 H3 BNX 41 Y4H H9 H15 H 0 1 N N N N N N 15.010 -22.348 19.028 3.368 -3.268 0.010 HO3 BNX 42 Y4H H10 H16 H 0 1 N N N N N N 15.523 -19.539 19.337 4.935 -1.094 -1.237 H4 BNX 43 Y4H H11 H17 H 0 1 N N N N N N 16.888 -20.404 21.017 6.628 -2.182 0.050 HO4 BNX 44 Y4H H12 H18 H 0 1 N N N N N N 14.340 -19.593 22.156 5.514 0.152 1.491 H5 BNX 45 Y4H H13 H19 H 0 1 N N N N N N 16.580 -18.669 22.230 7.517 -0.491 0.117 H61 BNX 46 Y4H H14 H20 H 0 1 N N N N N N 15.380 -17.339 22.362 6.887 0.515 -1.210 H62 BNX 47 Y4H H15 H21 H 0 1 N N N N N N 17.058 -16.888 20.851 8.399 1.728 0.185 HO6 BNX 48 Y4H H16 H22 H 0 1 N N N N N N 12.083 -19.468 21.350 3.317 1.190 1.534 H1 BNX 49 Y4H H17 H23 H 0 1 N N N N N N 11.597 -17.315 20.919 2.972 3.206 0.299 HO1 BNX 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 Y4H O1 C1 SING N N 1 Y4H C1 O5 SING N N 2 Y4H C1 C2 SING N N 3 Y4H O5 C5 SING N N 4 Y4H C5 C6 SING N N 5 Y4H C5 C4 SING N N 6 Y4H OAO PAM DOUB N N 7 Y4H C6 O6 SING N N 8 Y4H O2 C2 SING N N 9 Y4H O2 PAM SING N N 10 Y4H C2 C3 SING N N 11 Y4H PAM OAN SING N N 12 Y4H PAM OA2 SING N N 13 Y4H C3 C4 SING N N 14 Y4H C3 O3 SING N N 15 Y4H C4 O4 SING N N 16 Y4H O31 C31 SING N N 17 Y4H OA2 C21 SING N N 18 Y4H C21 C31 SING N N 19 Y4H C21 C11 SING N N 20 Y4H C31 C41 SING N N 21 Y4H O11 C11 SING N N 22 Y4H C41 O41 SING N N 23 Y4H C41 C51 SING N N 24 Y4H C11 O51 SING N N 25 Y4H O61 C61 SING N N 26 Y4H O51 C51 SING N N 27 Y4H C51 C61 SING N N 28 Y4H C4 H4 SING N N 29 Y4H C5 H5 SING N N 30 Y4H C6 H61 SING N N 31 Y4H C6 H62 SING N N 32 Y4H C21 H6 SING N N 33 Y4H C1 H1 SING N N 34 Y4H C2 H2 SING N N 35 Y4H C3 H3 SING N N 36 Y4H O1 HO1 SING N N 37 Y4H O3 HO3 SING N N 38 Y4H O4 HO4 SING N N 39 Y4H O6 HO6 SING N N 40 Y4H OAN H7 SING N N 41 Y4H C31 H8 SING N N 42 Y4H O31 H9 SING N N 43 Y4H C41 H10 SING N N 44 Y4H O41 H11 SING N N 45 Y4H C51 H12 SING N N 46 Y4H C61 H13 SING N N 47 Y4H C61 H14 SING N N 48 Y4H O61 H15 SING N N 49 Y4H C11 H16 SING N N 50 Y4H O11 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 Y4H 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" Y4H InChIKey InChI 1.06 DCDHSOINTWUWCZ-BTLHAWITSA-N Y4H 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" Y4H 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" Y4H 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" Y4H 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 Y4H _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~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y4H "Create component" 2023-06-09 PDBE Y4H "Other modification" 2023-12-03 PDBE Y4H "Modify name" 2023-12-05 PDBE Y4H "Initial release" 2024-01-24 RCSB # 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 Y4H "Agrocinopine D-like" AUTHOR ? 2 Y4H "[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate" PDB ? 3 Y4H D-glucose-2-phosphate-2-glucose AUTHOR ? #