data_A1J1N # _chem_comp.id A1J1N _chem_comp.name "benzyl 3,3-seleno-digalactoside" _chem_comp.type saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C26 H34 O10 Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(2~{R},3~{R},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,5-bis(oxidanyl)-4-phenylmethoxy-oxan-2-yl]-$l^{3}-selanyl]-4-phenylmethoxy-oxane-3,5-diol; SeDG-BN" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2026-03-03 _chem_comp.pdbx_modified_date 2026-09-11 _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 585.502 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1J1N _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 9U2P _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? _chem_comp.pdbx_comp_type ? # 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 A1J1N C12 C1 C 0 1 Y N N N N N -10.263 -10.657 -5.546 -8.487 2.452 -0.659 C10 A1J1N 1 A1J1N C6 C2 C 0 1 N N N N N N -7.908 -10.852 3.527 -1.645 -3.480 1.166 C15 A1J1N 2 A1J1N "C1'" C3 C 0 1 N N S N N N -2.414 -9.299 1.732 1.358 -0.527 -0.964 C20 A1J1N 3 A1J1N "C5'" C4 C 0 1 N N R N N N -1.962 -7.039 1.217 2.527 -2.566 -0.485 C22 A1J1N 4 A1J1N O2 O1 O 0 1 N N N N N N -5.213 -9.870 -1.248 -3.103 0.938 -2.014 O01 A1J1N 5 A1J1N C2 C5 C 0 1 N N R N N N -5.896 -10.686 -0.287 -3.025 -0.349 -1.397 C02 A1J1N 6 A1J1N C3 C6 C 0 1 N N S N N N -7.311 -10.311 -0.136 -3.401 -0.230 0.083 C03 A1J1N 7 A1J1N O3 O2 O 0 1 N N N N N N -7.964 -10.958 -1.287 -4.759 0.199 0.199 O04 A1J1N 8 A1J1N C7 C7 C 0 1 N N N N N N -9.125 -10.317 -1.854 -4.917 1.619 0.246 C05 A1J1N 9 A1J1N C8 C8 C 0 1 Y N N N N N -9.346 -10.890 -3.283 -6.381 1.957 0.367 C06 A1J1N 10 A1J1N C9 C9 C 0 1 Y N N N N N -8.846 -12.187 -3.657 -6.960 2.082 1.616 C07 A1J1N 11 A1J1N C10 C10 C 0 1 Y N N N N N -9.047 -12.700 -4.990 -8.303 2.391 1.728 C08 A1J1N 12 A1J1N C11 C11 C 0 1 Y N N N N N -9.744 -11.933 -5.914 -9.066 2.576 0.590 C09 A1J1N 13 A1J1N C13 C12 C 0 1 Y N N N N N -10.060 -10.140 -4.233 -7.144 2.142 -0.770 C11 A1J1N 14 A1J1N C4 C13 C 0 1 N N R N N N -7.826 -10.969 1.072 -3.238 -1.599 0.751 C12 A1J1N 15 A1J1N O4 O3 O 0 1 N N N N N N -9.248 -10.851 1.085 -3.516 -1.485 2.148 O13 A1J1N 16 A1J1N C5 C14 C 0 1 N N R N N N -7.206 -10.303 2.296 -1.800 -2.086 0.553 C14 A1J1N 17 A1J1N O6 O4 O 0 1 N N N N N N -7.253 -10.353 4.652 -0.277 -3.886 1.086 O16 A1J1N 18 A1J1N O5 O5 O 0 1 N N N N N N -5.741 -10.579 2.364 -1.505 -2.144 -0.844 O17 A1J1N 19 A1J1N C1 C15 C 0 1 N N R N N N -5.208 -11.044 1.084 -1.595 -0.884 -1.512 C18 A1J1N 20 A1J1N SE19 SE1 SE 0 0 N N N N N N -3.292 -10.881 1.072 -0.353 0.385 -0.682 SE19 A1J1N 21 A1J1N "O5'" O6 O 0 1 N N N N N N -2.667 -8.241 0.784 1.331 -1.802 -0.319 O21 A1J1N 22 A1J1N "C6'" C16 C 0 1 N N N N N N -2.494 -5.937 0.322 2.372 -3.915 0.220 C23 A1J1N 23 A1J1N "O6'" O7 O 0 1 N N N N N N -3.843 -5.803 0.492 1.347 -4.674 -0.424 O24 A1J1N 24 A1J1N "C4'" C17 C 0 1 N N S N N N -0.492 -7.255 1.065 3.706 -1.803 0.125 C25 A1J1N 25 A1J1N "O4'" O8 O 0 1 N N N N N N -0.041 -7.469 -0.312 3.492 -1.635 1.528 O26 A1J1N 26 A1J1N "C3'" C18 C 0 1 N N S N N N -0.127 -8.385 2.009 3.817 -0.430 -0.545 C27 A1J1N 27 A1J1N "O3'" O9 O 0 1 N N N N N N 1.255 -8.768 1.856 4.869 0.317 0.069 O28 A1J1N 28 A1J1N "C7'" C19 C 0 1 N N N N N N 2.196 -8.035 2.548 5.513 1.243 -0.809 C29 A1J1N 29 A1J1N "C8'" C20 C 0 1 Y N N N N N 3.529 -8.842 2.488 6.599 1.972 -0.062 C30 A1J1N 30 A1J1N "C9'" C21 C 0 1 Y N N N N N 3.589 -10.124 1.918 7.883 1.460 -0.035 C31 A1J1N 31 A1J1N "C10'" C22 C 0 1 Y N N N N N 4.811 -10.811 1.865 8.880 2.128 0.651 C32 A1J1N 32 A1J1N "C11'" C23 C 0 1 Y N N N N N 5.945 -10.230 2.365 8.593 3.309 1.310 C33 A1J1N 33 A1J1N "C12'" C24 C 0 1 Y N N N N N 5.887 -8.934 2.954 7.309 3.822 1.282 C34 A1J1N 34 A1J1N "C13'" C25 C 0 1 Y N N N N N 4.703 -8.247 3.001 6.313 3.155 0.592 C35 A1J1N 35 A1J1N "C2'" C26 C 0 1 N N R N N N -0.969 -9.557 1.700 2.490 0.317 -0.374 C36 A1J1N 36 A1J1N "O2'" O10 O 0 1 N N N N N N -0.654 -10.599 2.691 2.557 1.571 -1.057 O37 A1J1N 37 A1J1N H12 H1 H 0 0 N N N N N N -10.816 -10.076 -6.269 -9.084 2.592 -1.548 H101 A1J1N 38 A1J1N H62 H2 H 0 0 N N N N N N -8.960 -10.529 3.533 -1.956 -3.455 2.210 H151 A1J1N 39 A1J1N H61 H3 H 0 0 N N N N N N -7.862 -11.951 3.525 -2.267 -4.188 0.619 H152 A1J1N 40 A1J1N "H1'" H4 H 0 0 N N N N N N -2.802 -9.097 2.741 1.526 -0.664 -2.033 H201 A1J1N 41 A1J1N "H5'" H5 H 0 0 N N N N N N -2.201 -6.811 2.266 2.710 -2.730 -1.547 H221 A1J1N 42 A1J1N HO1 H6 H 0 1 N N N N N N -4.307 -10.147 -1.312 -2.878 0.938 -2.955 H1 A1J1N 43 A1J1N H04 H7 H 0 0 N N N N N N -5.952 -11.667 -0.781 -3.712 -1.033 -1.894 H021 A1J1N 44 A1J1N H3 H8 H 0 0 N N N N N N -7.461 -9.221 -0.122 -2.747 0.494 0.568 H031 A1J1N 45 A1J1N H72 H9 H 0 0 N N N N N N -10.007 -10.523 -1.229 -4.380 2.016 1.107 H051 A1J1N 46 A1J1N H71 H10 H 0 0 N N N N N N -8.961 -9.231 -1.909 -4.517 2.060 -0.667 H052 A1J1N 47 A1J1N H9 H11 H 0 0 N N N N N N -8.314 -12.783 -2.931 -6.364 1.938 2.505 H071 A1J1N 48 A1J1N H10 H12 H 0 0 N N N N N N -8.660 -13.670 -5.266 -8.755 2.490 2.704 H081 A1J1N 49 A1J1N H11 H13 H 0 0 N N N N N N -9.894 -12.305 -6.917 -10.115 2.819 0.677 H091 A1J1N 50 A1J1N H13 H14 H 0 0 N N N N N N -10.456 -9.171 -3.968 -6.692 2.044 -1.746 H111 A1J1N 51 A1J1N H4 H15 H 0 0 N N N N N N -7.536 -12.030 1.063 -3.929 -2.310 0.298 H121 A1J1N 52 A1J1N HO4 H16 H 0 1 N N N N N N -9.594 -11.273 1.862 -3.432 -2.316 2.635 H2 A1J1N 53 A1J1N H5 H17 H 0 0 N N N N N N -7.374 -9.217 2.239 -1.112 -1.396 1.042 H141 A1J1N 54 A1J1N HO6 H18 H 0 0 N N N N N N -7.675 -10.683 5.437 -0.105 -4.763 1.456 H161 A1J1N 55 A1J1N H1 H19 H 0 0 N N N N N N -5.316 -12.137 1.134 -1.337 -1.011 -2.563 H181 A1J1N 56 A1J1N "H62'" H20 H 0 0 N N N N N N -1.999 -4.989 0.579 3.315 -4.461 0.170 H231 A1J1N 57 A1J1N "H61'" H21 H 0 0 N N N N N N -2.283 -6.188 -0.728 2.103 -3.751 1.263 H232 A1J1N 58 A1J1N "HO6'" H22 H 0 0 N N N N N N -4.167 -5.111 -0.072 1.194 -5.544 -0.028 H241 A1J1N 59 A1J1N "H4'" H23 H 0 0 N N N N N N 0.009 -6.351 1.440 4.626 -2.364 -0.039 H251 A1J1N 60 A1J1N "HO4'" H24 H 0 0 N N N N N N 0.900 -7.598 -0.321 3.408 -2.466 2.015 H261 A1J1N 61 A1J1N "H3'" H25 H 0 0 N N N N N N -0.315 -8.061 3.043 4.031 -0.558 -1.606 H271 A1J1N 62 A1J1N "H71'" H26 H 0 0 N N N N N N 2.329 -7.049 2.078 5.949 0.703 -1.650 H291 A1J1N 63 A1J1N "H72'" H27 H 0 0 N N N N N N 1.880 -7.903 3.593 4.782 1.961 -1.180 H292 A1J1N 64 A1J1N "H9'" H28 H 0 0 N N N N N N 2.695 -10.581 1.521 8.107 0.537 -0.549 H311 A1J1N 65 A1J1N "H10'" H29 H 0 0 N N N N N N 4.857 -11.798 1.430 9.882 1.728 0.673 H321 A1J1N 66 A1J1N "H11'" H30 H 0 0 N N N N N N 6.887 -10.756 2.313 9.371 3.832 1.846 H331 A1J1N 67 A1J1N "H12'" H31 H 0 0 N N N N N N 6.782 -8.491 3.366 7.085 4.745 1.797 H341 A1J1N 68 A1J1N "H13'" H32 H 0 0 N N N N N N 4.667 -7.256 3.428 5.312 3.558 0.568 H351 A1J1N 69 A1J1N "H2'" H33 H 0 0 N N N N N N -0.699 -9.929 0.701 2.303 0.488 0.686 H361 A1J1N 70 A1J1N "HO2'" H34 H 0 0 N N N N N N 0.279 -10.775 2.680 1.748 2.096 -0.995 H371 A1J1N 71 # 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 A1J1N C12 C11 DOUB Y N 1 A1J1N C12 C13 SING Y N 2 A1J1N C6 C5 SING N N 3 A1J1N C6 O6 SING N N 4 A1J1N "C1'" SE19 SING N N 5 A1J1N "C1'" "O5'" SING N N 6 A1J1N "C1'" "C2'" SING N N 7 A1J1N "C5'" "O5'" SING N N 8 A1J1N "C5'" "C6'" SING N N 9 A1J1N "C5'" "C4'" SING N N 10 A1J1N O2 C2 SING N N 11 A1J1N C2 C3 SING N N 12 A1J1N C2 C1 SING N N 13 A1J1N C3 O3 SING N N 14 A1J1N C3 C4 SING N N 15 A1J1N O3 C7 SING N N 16 A1J1N C7 C8 SING N N 17 A1J1N C8 C9 SING Y N 18 A1J1N C8 C13 DOUB Y N 19 A1J1N C9 C10 DOUB Y N 20 A1J1N C10 C11 SING Y N 21 A1J1N C4 O4 SING N N 22 A1J1N C4 C5 SING N N 23 A1J1N C5 O5 SING N N 24 A1J1N O5 C1 SING N N 25 A1J1N C1 SE19 SING N N 26 A1J1N "C6'" "O6'" SING N N 27 A1J1N "C4'" "O4'" SING N N 28 A1J1N "C4'" "C3'" SING N N 29 A1J1N "C3'" "O3'" SING N N 30 A1J1N "C3'" "C2'" SING N N 31 A1J1N "O3'" "C7'" SING N N 32 A1J1N "C7'" "C8'" SING N N 33 A1J1N "C8'" "C9'" DOUB Y N 34 A1J1N "C8'" "C13'" SING Y N 35 A1J1N "C9'" "C10'" SING Y N 36 A1J1N "C10'" "C11'" DOUB Y N 37 A1J1N "C11'" "C12'" SING Y N 38 A1J1N "C12'" "C13'" DOUB Y N 39 A1J1N "C2'" "O2'" SING N N 40 A1J1N C12 H12 SING N N 41 A1J1N C6 H62 SING N N 42 A1J1N C6 H61 SING N N 43 A1J1N "C1'" "H1'" SING N N 44 A1J1N "C5'" "H5'" SING N N 45 A1J1N O2 HO1 SING N N 46 A1J1N C2 H04 SING N N 47 A1J1N C3 H3 SING N N 48 A1J1N C7 H72 SING N N 49 A1J1N C7 H71 SING N N 50 A1J1N C9 H9 SING N N 51 A1J1N C10 H10 SING N N 52 A1J1N C11 H11 SING N N 53 A1J1N C13 H13 SING N N 54 A1J1N C4 H4 SING N N 55 A1J1N O4 HO4 SING N N 56 A1J1N C5 H5 SING N N 57 A1J1N O6 HO6 SING N N 58 A1J1N C1 H1 SING N N 59 A1J1N "C6'" "H62'" SING N N 60 A1J1N "C6'" "H61'" SING N N 61 A1J1N "O6'" "HO6'" SING N N 62 A1J1N "C4'" "H4'" SING N N 63 A1J1N "O4'" "HO4'" SING N N 64 A1J1N "C3'" "H3'" SING N N 65 A1J1N "C7'" "H71'" SING N N 66 A1J1N "C7'" "H72'" SING N N 67 A1J1N "C9'" "H9'" SING N N 68 A1J1N "C10'" "H10'" SING N N 69 A1J1N "C11'" "H11'" SING N N 70 A1J1N "C12'" "H12'" SING N N 71 A1J1N "C13'" "H13'" SING N N 72 A1J1N "C2'" "H2'" SING N N 73 A1J1N "O2'" "HO2'" SING N N 74 # 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 A1J1N InChI InChI 1.06 "InChI=1S/C26H34O10Se/c27-11-17-19(29)23(33-13-15-7-3-1-4-8-15)21(31)25(35-17)37-26-22(32)24(20(30)18(12-28)36-26)34-14-16-9-5-2-6-10-16/h1-10,17-32H,11-14H2/t17-,18-,19-,20+,21-,22-,23+,24+,25-,26+/m1/s1" A1J1N InChIKey InChI 1.06 SEYZNJQMWNTLIS-BXSGEKIVSA-N A1J1N SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@H]([Se][C@@H]2O[C@H](CO)[C@H](O)[C@H](OCc3ccccc3)[C@H]2O)[C@H](O)[C@@H](OCc4ccccc4)[C@@H]1O" A1J1N SMILES CACTVS 3.385 "OC[CH]1O[CH]([Se][CH]2O[CH](CO)[CH](O)[CH](OCc3ccccc3)[CH]2O)[CH](O)[CH](OCc4ccccc4)[CH]1O" A1J1N SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CO[C@H]2[C@@H]([C@H](O[C@@H]([C@@H]2O)[Se][C@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)OCc4ccccc4)O)CO)O" A1J1N SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)COC2C(C(OC(C2O)[Se]C3C(C(C(C(O3)CO)O)OCc4ccccc4)O)CO)O" # _pdbx_chem_comp_identifier.comp_id A1J1N _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-(hydroxymethyl)-6-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,5-bis(oxidanyl)-4-phenylmethoxy-oxan-2-yl]selanyl-4-phenylmethoxy-oxane-3,5-diol" # 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 A1J1N "(2~{R},3~{R},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,5-bis(oxidanyl)-4-phenylmethoxy-oxan-2-yl]-$l^{3}-selanyl]-4-phenylmethoxy-oxane-3,5-diol" PDB ? 2 A1J1N SeDG-BN 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 A1J1N "Create component" 2026-03-04 PDBE A1J1N "Initial release" 2026-09-16 RCSB #