data_TDR # _chem_comp.id TDR _chem_comp.name THYMINE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C5 H6 N2 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2024-12-02 _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 126.113 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TDR _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1TPT _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm Y # 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 TDR N1 N1 N 0 1 N N N N N N 14.122 33.441 14.446 -1.242 0.001 -1.098 N1 TDR 1 TDR C2 C2 C 0 1 N N N N N N 15.442 33.075 14.555 0.032 -0.000 -1.526 C2 TDR 2 TDR O2 O2 O 0 1 N N N N N N 16.201 33.570 15.372 0.264 -0.000 -2.720 O2 TDR 3 TDR N3 N3 N 0 1 N N N N N N 15.863 32.101 13.672 1.056 -0.002 -0.652 N3 TDR 4 TDR C4 C4 C 0 1 N N N N N N 15.092 31.477 12.713 0.816 0.002 0.674 C4 TDR 5 TDR O4 O4 O 0 1 N N N N N N 15.581 30.617 11.977 1.741 0.001 1.466 O4 TDR 6 TDR C5 C5 C 0 1 N N N N N N 13.721 31.927 12.675 -0.521 -0.001 1.138 C5 TDR 7 TDR CM5 CM5 C 0 1 N N N N N N 12.812 31.300 11.660 -0.816 -0.001 2.616 CM5 TDR 8 TDR C6 C6 C 0 1 N N N N N N 13.284 32.873 13.522 -1.528 0.000 0.239 C6 TDR 9 TDR HN1 HN1 H 0 1 N N N N N N 14.089 34.452 14.314 -1.966 0.002 -1.744 HN1 TDR 10 TDR HN3 HN3 H 0 1 N N N N N N 16.839 31.814 13.734 1.969 -0.003 -0.977 HN3 TDR 11 TDR H5M1 1H5M H 0 0 N N N N N N 11.753 31.647 11.630 0.119 -0.003 3.174 H5M1 TDR 12 TDR H5M2 2H5M H 0 0 N N N N N N 13.262 31.407 10.645 -1.390 0.889 2.872 H5M2 TDR 13 TDR H5M3 3H5M H 0 0 N N N N N N 12.832 30.191 11.782 -1.393 -0.890 2.871 H5M3 TDR 14 TDR H6 H6 H 0 1 N N N N N N 12.228 33.186 13.458 -2.555 0.001 0.575 H6 TDR 15 # 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 TDR N1 C2 SING N N 1 TDR N1 C6 SING N N 2 TDR N1 HN1 SING N N 3 TDR C2 O2 DOUB N N 4 TDR C2 N3 SING N N 5 TDR N3 C4 SING N N 6 TDR N3 HN3 SING N N 7 TDR C4 O4 DOUB N N 8 TDR C4 C5 SING N N 9 TDR C5 CM5 SING N N 10 TDR C5 C6 DOUB N N 11 TDR CM5 H5M1 SING N N 12 TDR CM5 H5M2 SING N N 13 TDR CM5 H5M3 SING N N 14 TDR C6 H6 SING N N 15 # 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 TDR SMILES ACDLabs 10.04 "O=C1C(=CNC(=O)N1)C" TDR SMILES_CANONICAL CACTVS 3.341 "CC1=CNC(=O)NC1=O" TDR SMILES CACTVS 3.341 "CC1=CNC(=O)NC1=O" TDR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CNC(=O)NC1=O" TDR SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CNC(=O)NC1=O" TDR InChI InChI 1.03 "InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)" TDR InChIKey InChI 1.03 RWQNBRDOKXIBIV-UHFFFAOYSA-N # 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 TDR "SYSTEMATIC NAME" ACDLabs 10.04 "5-methylpyrimidine-2,4(1H,3H)-dione" TDR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 5-methyl-1H-pyrimidine-2,4-dione # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site TDR "Create component" 1999-07-08 PDBJ TDR "Modify descriptor" 2011-06-04 RCSB TDR "Modify PCM" 2024-12-02 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id TDR _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom CM5 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #