data_THM # _chem_comp.id THM _chem_comp.name THYMIDINE _chem_comp.type "DNA OH 5 prime terminus" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N2 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE ; _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 242.229 _chem_comp.one_letter_code ? _chem_comp.three_letter_code THM _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 1KIM _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI _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 THM "O5'" O5* O 0 1 N N N N N N 17.080 94.434 44.011 2.274 -0.724 -3.790 "O5'" THM 1 THM "C5'" C5* C 0 1 N N N N N N 16.780 95.210 45.165 1.208 0.202 -3.574 "C5'" THM 2 THM "C4'" C4* C 0 1 N N R N N N 17.626 96.447 45.302 0.116 -0.463 -2.735 "C4'" THM 3 THM "O4'" O4* O 0 1 N N N N N N 18.982 96.128 45.630 0.600 -0.760 -1.406 "O4'" THM 4 THM "C3'" C3* C 0 1 N N S N N N 17.760 97.332 44.178 -1.055 0.519 -2.484 "C3'" THM 5 THM "O3'" O3* O 0 1 N N N N N N 18.323 98.514 44.657 -1.993 0.481 -3.562 "O3'" THM 6 THM "C2'" C2* C 0 1 N N N N N N 18.903 96.738 43.506 -1.681 -0.046 -1.186 "C2'" THM 7 THM "C1'" C1* C 0 1 N N R N N N 19.875 96.449 44.597 -0.554 -0.889 -0.560 "C1'" THM 8 THM N1 N1 N 0 1 N N N N N N 20.731 95.216 44.411 -0.246 -0.391 0.782 N1 THM 9 THM C2 C2 C 0 1 N N N N N N 22.075 95.429 44.582 0.165 0.879 0.943 C2 THM 10 THM O2 O2 O 0 1 N N N N N N 22.533 96.539 44.822 0.278 1.600 -0.029 O2 THM 11 THM N3 N3 N 0 1 N N N N N N 22.877 94.370 44.420 0.454 1.363 2.165 N3 THM 12 THM C4 C4 C 0 1 N N N N N N 22.432 93.082 44.088 0.329 0.578 3.254 C4 THM 13 THM O4 O4 O 0 1 N N N N N N 23.259 92.155 43.945 0.590 1.015 4.360 O4 THM 14 THM C5 C5 C 0 1 N N N N N N 20.989 92.899 43.924 -0.098 -0.762 3.099 C5 THM 15 THM C5M C5M C 0 1 N N N N N N 20.433 91.458 43.577 -0.241 -1.662 4.299 C5M THM 16 THM C6 C6 C 0 1 N N N N N N 20.205 93.954 44.081 -0.382 -1.222 1.861 C6 THM 17 THM "HO5'" *HO5 H 0 0 N N N N N N 16.545 93.653 43.924 2.939 -0.266 -4.322 "HO5'" THM 18 THM "H5'1" 1H5* H 0 0 N N N N N N 15.696 95.470 45.192 0.792 0.508 -4.534 "H5'1" THM 19 THM "H5'2" 2H5* H 0 0 N N N N N N 16.845 94.585 46.086 1.588 1.077 -3.047 "H5'2" THM 20 THM "H4'" H4* H 0 1 N N N N N N 17.039 96.972 46.091 -0.241 -1.370 -3.222 "H4'" THM 21 THM "H3'" H3* H 0 1 N N N N N N 16.814 97.484 43.606 -0.686 1.532 -2.328 "H3'" THM 22 THM "HO3'" *HO3 H 0 0 N N N N N N 18.411 99.099 43.913 -2.738 1.040 -3.303 "HO3'" THM 23 THM "H2'1" 1H2* H 0 0 N N N N N N 18.649 95.852 42.877 -2.542 -0.673 -1.420 "H2'1" THM 24 THM "H2'2" 2H2* H 0 0 N N N N N N 19.319 97.362 42.681 -1.969 0.764 -0.517 "H2'2" THM 25 THM "H1'" H1* H 0 1 N N N N N N 20.593 97.293 44.715 -0.859 -1.934 -0.506 "H1'" THM 26 THM HN3 HN3 H 0 1 N N N N N N 23.871 94.552 44.555 0.750 2.281 2.263 HN3 THM 27 THM HM51 1HM5 H 0 0 N N N N N N 19.333 91.318 43.452 0.031 -1.112 5.200 HM51 THM 28 THM HM52 2HM5 H 0 0 N N N N N N 20.948 91.085 42.661 -1.275 -1.999 4.378 HM52 THM 29 THM HM53 3HM5 H 0 0 N N N N N N 20.801 90.736 44.343 0.414 -2.525 4.186 HM53 THM 30 THM H6 H6 H 0 1 N N N N N N 19.124 93.783 43.938 -0.713 -2.240 1.723 H6 THM 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 THM "O5'" "C5'" SING N N 1 THM "O5'" "HO5'" SING N N 2 THM "C5'" "C4'" SING N N 3 THM "C5'" "H5'1" SING N N 4 THM "C5'" "H5'2" SING N N 5 THM "C4'" "O4'" SING N N 6 THM "C4'" "C3'" SING N N 7 THM "C4'" "H4'" SING N N 8 THM "O4'" "C1'" SING N N 9 THM "C3'" "O3'" SING N N 10 THM "C3'" "C2'" SING N N 11 THM "C3'" "H3'" SING N N 12 THM "O3'" "HO3'" SING N N 13 THM "C2'" "C1'" SING N N 14 THM "C2'" "H2'1" SING N N 15 THM "C2'" "H2'2" SING N N 16 THM "C1'" N1 SING N N 17 THM "C1'" "H1'" SING N N 18 THM N1 C2 SING N N 19 THM N1 C6 SING N N 20 THM C2 O2 DOUB N N 21 THM C2 N3 SING N N 22 THM N3 C4 SING N N 23 THM N3 HN3 SING N N 24 THM C4 O4 DOUB N N 25 THM C4 C5 SING N N 26 THM C5 C5M SING N N 27 THM C5 C6 DOUB N N 28 THM C5M HM51 SING N N 29 THM C5M HM52 SING N N 30 THM C5M HM53 SING N N 31 THM C6 H6 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 THM SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)CO" THM SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O" THM SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O" THM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O" THM SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O" THM InChI InChI 1.03 "InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1" THM InChIKey InChI 1.03 IQFYYKKMVGJFEH-XLPZGREQSA-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 THM "SYSTEMATIC NAME" ACDLabs 10.04 thymidine THM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-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 THM "Create component" 1999-07-08 EBI THM "Modify descriptor" 2011-06-04 RCSB THM "Modify linking type" 2017-08-21 RCSB THM "Modify synonyms" 2020-06-05 PDBE THM "Modify PCM" 2024-12-02 RCSB # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 THM DEOXYTHYMIDINE ? ? 2 THM "2'-DEOXYTHYMIDINE" ? ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id THM _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 C5M _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 ? #