data_RY3 # _chem_comp.id RY3 _chem_comp.name "(2S,3R,4R,5R,6S)-2-methyl-6-[4-[oxidanyl(oxidanylidene)-$l^4-azanyl]phenoxy]oxane-3,4,5-triol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H15 N O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-04-04 _chem_comp.pdbx_modified_date 2024-03-29 _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 285.250 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RY3 _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 8IWF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 RY3 C02 C1 C 0 1 N N S N N N -34.038 31.296 -33.387 -1.253 -0.864 -0.748 C02 RY3 1 RY3 C03 C2 C 0 1 N N R N N N -35.173 30.261 -33.462 -2.670 -1.378 -0.477 C03 RY3 2 RY3 C05 C3 C 0 1 N N R N N N -36.389 30.636 -32.686 -3.295 -0.557 0.654 C05 RY3 3 RY3 C07 C4 C 0 1 N N R N N N -36.775 32.049 -32.887 -3.279 0.924 0.265 C07 RY3 4 RY3 C09 C5 C 0 1 N N S N N N -35.590 32.943 -32.539 -1.839 1.350 -0.034 C09 RY3 5 RY3 C11 C6 C 0 1 N N N N N N -35.956 34.393 -32.569 -1.822 2.813 -0.482 C11 RY3 6 RY3 C12 C7 C 0 1 Y N N N N N -31.985 31.093 -32.329 0.871 -0.739 0.313 C12 RY3 7 RY3 C13 C8 C 0 1 Y N N N N N -31.166 31.889 -31.555 1.710 -0.895 1.406 C13 RY3 8 RY3 C14 C9 C 0 1 Y N N N N N -29.776 31.814 -31.697 3.051 -0.579 1.297 C14 RY3 9 RY3 C15 C10 C 0 1 Y N N N N N -29.231 30.953 -32.600 3.556 -0.107 0.099 C15 RY3 10 RY3 C16 C11 C 0 1 Y N N N N N -30.046 30.150 -33.372 2.721 0.049 -0.992 C16 RY3 11 RY3 C17 C12 C 0 1 Y N N N N N -31.435 30.227 -33.233 1.381 -0.271 -0.889 C17 RY3 12 RY3 N18 N1 N 1 1 N N N N N N -27.791 30.872 -32.739 4.992 0.231 -0.015 N18 RY3 13 RY3 O01 O1 O 0 1 N N N N N N -33.406 31.170 -32.163 -0.448 -1.049 0.418 O01 RY3 14 RY3 O04 O2 O 0 1 N N N N N N -35.540 30.098 -34.837 -3.461 -1.242 -1.660 O04 RY3 15 RY3 O06 O3 O 0 1 N N N N N N -37.478 29.752 -33.121 -4.643 -0.983 0.865 O06 RY3 16 RY3 O08 O4 O 0 1 N N N N N N -37.898 32.397 -32.048 -3.794 1.707 1.344 O08 RY3 17 RY3 O10 O5 O 0 1 N N N N N N -34.495 32.681 -33.507 -1.307 0.527 -1.074 O10 RY3 18 RY3 O19 O6 O -1 1 N N N N N N -27.291 29.825 -32.854 5.438 0.646 -1.070 O19 RY3 19 RY3 O20 O7 O 0 1 N N N N N N -27.001 32.032 -32.720 5.728 0.094 0.945 O20 RY3 20 RY3 H1 H1 H 0 1 N N N N N N -33.330 31.082 -34.201 -0.819 -1.416 -1.581 H1 RY3 21 RY3 H2 H2 H 0 1 N N N N N N -34.789 29.307 -33.072 -2.627 -2.427 -0.186 H2 RY3 22 RY3 H3 H3 H 0 1 N N N N N N -36.194 30.467 -31.617 -2.720 -0.700 1.569 H3 RY3 23 RY3 H4 H4 H 0 1 N N N N N N -37.037 32.207 -33.944 -3.895 1.074 -0.622 H4 RY3 24 RY3 H5 H5 H 0 1 N N N N N N -35.243 32.685 -31.528 -1.233 1.237 0.865 H5 RY3 25 RY3 H6 H6 H 0 1 N N N N N N -36.767 34.582 -31.851 -2.229 3.440 0.311 H6 RY3 26 RY3 H7 H7 H 0 1 N N N N N N -35.078 34.998 -32.298 -0.797 3.115 -0.695 H7 RY3 27 RY3 H8 H8 H 0 1 N N N N N N -36.291 34.666 -33.581 -2.428 2.925 -1.381 H8 RY3 28 RY3 H9 H9 H 0 1 N N N N N N -31.599 32.571 -30.838 1.316 -1.262 2.342 H9 RY3 29 RY3 H10 H10 H 0 1 N N N N N N -29.136 32.438 -31.091 3.705 -0.700 2.148 H10 RY3 30 RY3 H11 H11 H 0 1 N N N N N N -29.611 29.463 -34.083 3.118 0.413 -1.928 H11 RY3 31 RY3 H12 H12 H 0 1 N N N N N N -32.074 29.602 -33.840 0.729 -0.149 -1.742 H12 RY3 32 RY3 H13 H13 H 0 1 N N N N N N -36.242 29.461 -34.905 -3.120 -1.733 -2.420 H13 RY3 33 RY3 H14 H14 H 0 1 N N N N N N -38.271 29.966 -32.643 -4.727 -1.915 1.110 H14 RY3 34 RY3 H15 H15 H 0 1 N N N N N N -38.131 33.307 -32.191 -3.813 2.658 1.166 H15 RY3 35 # 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 RY3 O04 C03 SING N N 1 RY3 O10 C02 SING N N 2 RY3 O10 C09 SING N N 3 RY3 C03 C02 SING N N 4 RY3 C03 C05 SING N N 5 RY3 C02 O01 SING N N 6 RY3 C16 C17 DOUB Y N 7 RY3 C16 C15 SING Y N 8 RY3 C17 C12 SING Y N 9 RY3 O06 C05 SING N N 10 RY3 C07 C05 SING N N 11 RY3 C07 C09 SING N N 12 RY3 C07 O08 SING N N 13 RY3 O19 N18 SING N N 14 RY3 N18 O20 DOUB N N 15 RY3 N18 C15 SING N N 16 RY3 C15 C14 DOUB Y N 17 RY3 C11 C09 SING N N 18 RY3 C12 O01 SING N N 19 RY3 C12 C13 DOUB Y N 20 RY3 C14 C13 SING Y N 21 RY3 C02 H1 SING N N 22 RY3 C03 H2 SING N N 23 RY3 C05 H3 SING N N 24 RY3 C07 H4 SING N N 25 RY3 C09 H5 SING N N 26 RY3 C11 H6 SING N N 27 RY3 C11 H7 SING N N 28 RY3 C11 H8 SING N N 29 RY3 C13 H9 SING N N 30 RY3 C14 H10 SING N N 31 RY3 C16 H11 SING N N 32 RY3 C17 H12 SING N N 33 RY3 O04 H13 SING N N 34 RY3 O06 H14 SING N N 35 RY3 O08 H15 SING N N 36 # 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 RY3 InChI InChI 1.06 "InChI=1S/C12H15NO7/c1-6-9(14)10(15)11(16)12(19-6)20-8-4-2-7(3-5-8)13(17)18/h2-6,9-12,14-16H,1H3/t6-,9-,10+,11+,12-/m0/s1" RY3 InChIKey InChI 1.06 YILIDCGSXCGACV-UOAXWKJLSA-N RY3 SMILES_CANONICAL CACTVS 3.385 "C[C@@H]1O[C@@H](Oc2ccc(cc2)[N+]([O-])=O)[C@H](O)[C@H](O)[C@H]1O" RY3 SMILES CACTVS 3.385 "C[CH]1O[CH](Oc2ccc(cc2)[N+]([O-])=O)[CH](O)[CH](O)[CH]1O" RY3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc2ccc(cc2)[N+](=O)[O-])O)O)O" RY3 SMILES "OpenEye OEToolkits" 2.0.7 "CC1C(C(C(C(O1)Oc2ccc(cc2)[N+](=O)[O-])O)O)O" # _pdbx_chem_comp_identifier.comp_id RY3 _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~{R},5~{R},6~{S})-2-methyl-6-(4-nitrophenoxy)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 RY3 "Create component" 2023-04-04 PDBJ RY3 "Initial release" 2024-04-03 RCSB #