data_UZL # _chem_comp.id UZL _chem_comp.name "O2'-methylycytidine" _chem_comp.type "RNA OH 3 prime terminus" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N3 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "4-azanyl-1-[(2R,3R,4R,5R)-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-17 _chem_comp.pdbx_modified_date 2023-02-24 _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 257.243 _chem_comp.one_letter_code C _chem_comp.three_letter_code UZL _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 8CLM _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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.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 UZL N1 N1 N 0 1 N N N -0.961 -7.921 9.226 1.128 -0.037 0.501 N1 UZL 1 UZL C2 C1 C 0 1 N N N -2.129 -7.207 8.985 1.529 -0.517 -0.690 C2 UZL 2 UZL N3 N2 N 0 1 N N N -2.071 -5.864 8.941 2.822 -0.673 -0.968 N3 UZL 3 UZL C4 C2 C 0 1 N N N -0.908 -5.217 9.086 3.750 -0.357 -0.073 C4 UZL 4 UZL C5 C3 C 0 1 N N N 0.293 -5.934 9.343 3.362 0.148 1.184 C5 UZL 5 UZL C6 C4 C 0 1 N N N 0.225 -7.270 9.378 2.044 0.305 1.450 C6 UZL 6 UZL O2 O1 O 0 1 N N N -3.161 -7.867 8.832 0.695 -0.814 -1.530 O2 UZL 7 UZL N4 N3 N 0 1 N N N -0.905 -3.891 9.067 5.083 -0.523 -0.371 N4 UZL 8 UZL "C1'" C5 C 0 1 N N R -1.115 -9.398 9.310 -0.302 0.123 0.778 "C1'" UZL 9 UZL "C2'" C6 C 0 1 N N R -1.341 -10.112 7.968 -0.932 1.128 -0.213 "C2'" UZL 10 UZL "O2'" O2 O 0 1 N N N -2.098 -11.292 8.200 -1.041 2.420 0.387 "O2'" UZL 11 UZL CM2 C7 C 0 1 N N N -3.504 -11.122 8.354 -0.951 3.501 -0.543 CM2 UZL 12 UZL "C3'" C8 C 0 1 N N R 0.111 -10.378 7.545 -2.334 0.544 -0.499 "C3'" UZL 13 UZL "C4'" C9 C 0 1 N N R 0.691 -10.818 8.893 -2.385 -0.744 0.352 "C4'" UZL 14 UZL "O4'" O3 O 0 1 N N N 0.064 -9.945 9.875 -1.003 -1.118 0.540 "O4'" UZL 15 UZL "O3'" O4 O 0 1 N N N 0.267 -11.398 6.547 -3.351 1.458 -0.085 "O3'" UZL 16 UZL "C5'" C10 C 0 1 N N N 2.190 -10.741 9.042 -3.137 -1.847 -0.396 "C5'" UZL 17 UZL "O5'" O5 O 0 1 N N N 2.657 -9.431 8.671 -3.275 -2.989 0.452 "O5'" UZL 18 UZL "H1'" H1 H 0 1 N N N 1.228 -5.418 9.504 4.105 0.409 1.923 "H1'" UZL 19 UZL "H2'" H2 H 0 1 N N N 1.128 -7.843 9.530 1.722 0.694 2.405 "H2'" UZL 20 UZL HN41 H3 H 0 0 N N N -1.762 -3.391 8.946 5.347 -0.871 -1.237 HN41 UZL 21 UZL HN42 H4 H 0 0 N N N -0.045 -3.391 9.174 5.759 -0.292 0.285 HN42 UZL 22 UZL H1 H5 H 0 1 N N N -1.972 -9.623 9.961 -0.455 0.454 1.805 H1 UZL 23 UZL H2 H6 H 0 1 N N N -1.833 -9.437 7.252 -0.344 1.181 -1.129 H2 UZL 24 UZL HM21 H7 H 0 0 N N N -3.975 -12.101 8.527 -1.043 4.448 -0.010 HM21 UZL 25 UZL HM22 H8 H 0 0 N N N -3.702 -10.463 9.212 0.012 3.463 -1.053 HM22 UZL 26 UZL HM23 H9 H 0 0 N N N -3.921 -10.671 7.442 -1.753 3.418 -1.276 HM23 UZL 27 UZL "H3'" H10 H 0 1 N N N 0.583 -9.437 7.227 -2.440 0.307 -1.558 "H3'" UZL 28 UZL "H4'" H11 H 0 1 N N N 0.376 -11.855 9.079 -2.860 -0.546 1.313 "H4'" UZL 29 UZL "HO3'" H12 H 0 0 N Y N 1.189 -11.502 6.341 -4.251 1.142 -0.242 "HO3'" UZL 30 UZL "H5'" H13 H 0 1 N N N 2.660 -11.493 8.390 -4.125 -1.484 -0.679 "H5'" UZL 31 UZL "H5''" H14 H 0 0 N N N 2.462 -10.941 10.089 -2.581 -2.124 -1.291 "H5''" UZL 32 UZL "HO5'" H15 H 0 0 N N N 3.601 -9.392 8.768 -3.743 -3.729 0.043 "HO5'" UZL 33 # 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 UZL "O3'" "C3'" SING N N 1 UZL "C3'" "C2'" SING N N 2 UZL "C3'" "C4'" SING N N 3 UZL "C2'" "O2'" SING N N 4 UZL "C2'" "C1'" SING N N 5 UZL "O2'" CM2 SING N N 6 UZL "O5'" "C5'" SING N N 7 UZL O2 C2 DOUB N N 8 UZL "C4'" "C5'" SING N N 9 UZL "C4'" "O4'" SING N N 10 UZL N3 C2 SING N N 11 UZL N3 C4 DOUB N N 12 UZL C2 N1 SING N N 13 UZL N4 C4 SING N N 14 UZL C4 C5 SING N N 15 UZL N1 "C1'" SING N N 16 UZL N1 C6 SING N N 17 UZL "C1'" "O4'" SING N N 18 UZL C5 C6 DOUB N N 19 UZL C5 "H1'" SING N N 20 UZL C6 "H2'" SING N N 21 UZL N4 HN41 SING N N 22 UZL N4 HN42 SING N N 23 UZL "C1'" H1 SING N N 24 UZL "C2'" H2 SING N N 25 UZL CM2 HM21 SING N N 26 UZL CM2 HM22 SING N N 27 UZL CM2 HM23 SING N N 28 UZL "C3'" "H3'" SING N N 29 UZL "C4'" "H4'" SING N N 30 UZL "O3'" "HO3'" SING N N 31 UZL "C5'" "H5'" SING N N 32 UZL "C5'" "H5''" SING N N 33 UZL "O5'" "HO5'" SING N N 34 # 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 UZL InChI InChI 1.06 "InChI=1S/C10H15N3O5/c1-17-8-7(15)5(4-14)18-9(8)13-3-2-6(11)12-10(13)16/h2-3,5,7-9,14-15H,4H2,1H3,(H2,11,12,16)/t5-,7-,8-,9-/m1/s1" UZL InChIKey InChI 1.06 RFCQJGFZUQFYRF-ZOQUXTDFSA-N UZL SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N2C=CC(=NC2=O)N" UZL SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO)O[CH]1N2C=CC(=NC2=O)N" UZL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO)O" UZL SMILES "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1N2C=CC(=NC2=O)N)CO)O" # _pdbx_chem_comp_identifier.comp_id UZL _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 "4-azanyl-1-[(2~{R},3~{R},4~{R},5~{R})-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UZL _pdbx_chem_comp_synonyms.name "4-azanyl-1-[(2R,3R,4R,5R)-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UZL "Create component" 2023-02-17 PDBE UZL "Modify leaving atom flag" 2023-02-21 PDBE UZL "Initial release" 2023-03-01 RCSB #