data_U56
# 
_chem_comp.id                                    U56 
_chem_comp.name                                  N-hydroxycytidine 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H13 N3 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-08-30 
_chem_comp.pdbx_modified_date                    2024-03-08 
_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                        259.216 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     U56 
_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        8TZ5 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
U56 C10  C1  C 0 1 N N R N N N 143.188 158.728 140.432 0.763  0.528  -0.696 C10  U56 1  
U56 C02  C2  C 0 1 N N N N N N 141.284 158.744 138.760 -1.184 -0.349 0.469  C02  U56 2  
U56 C04  C3  C 0 1 N N N N N N 138.890 158.518 139.574 -3.349 0.006  -0.256 C04  U56 3  
U56 C07  C4  C 0 1 N N N N N N 139.387 158.434 140.970 -2.859 0.751  -1.348 C07  U56 4  
U56 C08  C5  C 0 1 N N N N N N 140.848 158.505 141.247 -1.522 0.915  -1.483 C08  U56 5  
U56 C12  C6  C 0 1 N N R N N N 144.312 159.254 142.297 2.794  -0.471 -0.314 C12  U56 6  
U56 C13  C7  C 0 1 N N N N N N 143.994 159.367 143.666 3.472  -1.725 0.241  C13  U56 7  
U56 C15  C8  C 0 1 N N S N N N 143.995 160.608 141.577 2.699  0.617  0.779  C15  U56 8  
U56 C17  C9  C 0 1 N N R N N N 143.667 160.297 140.412 1.332  1.289  0.521  C17  U56 9  
U56 N03  N1  N 0 1 N N N N N N 139.831 158.672 138.482 -2.497 -0.519 0.615  N03  U56 10 
U56 N05  N2  N 0 1 N N N N N N 137.492 158.448 139.316 -4.703 -0.177 -0.095 N05  U56 11 
U56 N09  N3  N 0 1 N N N N N N 141.784 158.658 140.156 -0.686 0.358  -0.562 N09  U56 12 
U56 O01  O1  O 0 1 N N N N N N 142.045 158.869 137.868 -0.422 -0.836 1.286  O01  U56 13 
U56 O06  O2  O 0 1 N N N N N N 136.604 158.300 140.382 -5.191 -0.926 1.003  O06  U56 14 
U56 O11  O3  O 0 1 N N N N N N 143.421 158.252 141.612 1.424  -0.756 -0.671 O11  U56 15 
U56 O14  O4  O 0 1 N N N N N N 142.621 159.583 143.782 3.623  -2.687 -0.804 O14  U56 16 
U56 O16  O5  O 0 1 N N N N N N 145.222 161.486 141.557 3.760  1.564  0.636  O16  U56 17 
U56 O18  O6  O 0 1 N N N N N N 144.826 160.454 139.503 1.505  2.673  0.210  O18  U56 18 
U56 H101 H1  H 0 0 N N N N N N 143.753 158.201 139.649 0.998  1.058  -1.619 H101 U56 19 
U56 H071 H2  H 0 0 N N N N N N 138.688 158.321 141.786 -3.540 1.185  -2.066 H071 U56 20 
U56 H081 H3  H 0 0 N N N N N N 141.209 158.442 142.263 -1.122 1.482  -2.311 H081 U56 21 
U56 H121 H4  H 0 0 N N N N N N 145.370 158.994 142.143 3.343  -0.094 -1.177 H121 U56 22 
U56 H131 H5  H 0 0 N N N N N N 144.270 158.440 144.189 4.453  -1.463 0.638  H131 U56 23 
U56 H132 H6  H 0 0 N N N N N N 144.542 160.213 144.106 2.859  -2.147 1.038  H132 U56 24 
U56 H151 H7  H 0 0 N N N N N N 143.195 161.119 142.133 2.722  0.166  1.770  H151 U56 25 
U56 H171 H8  H 0 0 N N N N N N 142.824 160.891 140.030 0.679  1.170  1.386  H171 U56 26 
U56 H051 H9  H 0 0 N N N N N N 137.149 158.504 138.378 -5.324 0.208  -0.734 H051 U56 27 
U56 H061 H10 H 0 0 N N N N N N 135.714 158.269 140.051 -6.155 -1.000 1.032  H061 U56 28 
U56 H141 H11 H 0 0 N N N N N N 142.389 159.662 144.700 4.046  -3.510 -0.524 H141 U56 29 
U56 H161 H12 H 0 0 N N N N N N 145.462 161.716 142.447 4.643  1.182  0.730  H161 U56 30 
U56 H181 H13 H 0 0 N N N N N N 145.101 161.363 139.494 1.860  3.199  0.940  H181 U56 31 
# 
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 
U56 O01 C02  DOUB N N 1  
U56 N03 C02  SING N N 2  
U56 N03 C04  DOUB N N 3  
U56 C02 N09  SING N N 4  
U56 N05 C04  SING N N 5  
U56 N05 O06  SING N N 6  
U56 O18 C17  SING N N 7  
U56 C04 C07  SING N N 8  
U56 N09 C10  SING N N 9  
U56 N09 C08  SING N N 10 
U56 C17 C10  SING N N 11 
U56 C17 C15  SING N N 12 
U56 C10 O11  SING N N 13 
U56 C07 C08  DOUB N N 14 
U56 O16 C15  SING N N 15 
U56 C15 C12  SING N N 16 
U56 O11 C12  SING N N 17 
U56 C12 C13  SING N N 18 
U56 C13 O14  SING N N 19 
U56 C10 H101 SING N N 20 
U56 C07 H071 SING N N 21 
U56 C08 H081 SING N N 22 
U56 C12 H121 SING N N 23 
U56 C13 H131 SING N N 24 
U56 C13 H132 SING N N 25 
U56 C15 H151 SING N N 26 
U56 C17 H171 SING N N 27 
U56 N05 H051 SING N N 28 
U56 O06 H061 SING N N 29 
U56 O14 H141 SING N N 30 
U56 O16 H161 SING N N 31 
U56 O18 H181 SING N N 32 
# 
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 
U56 SMILES           ACDLabs              12.01 "ONC1=NC(=O)N(C=C1)C1OC(CO)C(O)C1O"                                                                                              
U56 InChI            InChI                1.06  "InChI=1S/C9H13N3O6/c13-3-4-6(14)7(15)8(18-4)12-2-1-5(11-17)10-9(12)16/h1-2,4,6-8,13-15,17H,3H2,(H,10,11,16)/t4-,6-,7-,8-/m1/s1" 
U56 InChIKey         InChI                1.06  XCUAIINAJCDIPM-XVFCMESISA-N                                                                                                      
U56 SMILES_CANONICAL CACTVS               3.385 "OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)NO"                                                                               
U56 SMILES           CACTVS               3.385 "OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)NO"                                                                                    
U56 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1NO)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O"                                                                          
U56 SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1NO)C2C(C(C(O2)CO)O)O"                                                                                            
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
U56 "SYSTEMATIC NAME" ACDLabs              12.01 N-hydroxycytidine                                                                                               
U56 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-4-(oxidanylamino)pyrimidin-2-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
U56 "Create component"   2023-08-30 RCSB 
U56 "Other modification" 2023-08-30 RCSB 
U56 "Initial release"    2024-03-13 RCSB 
# 
