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 #