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 
# 
