data_DT # _chem_comp.id DT _chem_comp.name "THYMIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-12-05 _chem_comp.pdbx_modified_date 2024-09-27 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces T _chem_comp.formula_weight 322.208 _chem_comp.one_letter_code T _chem_comp.three_letter_code DT _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye OEToolkits" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 214D _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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 DT OP3 O3P O 0 1 N Y N N N N -9.026 1.725 3.724 -3.912 -2.311 1.636 OP3 DT 1 DT P P P 0 1 N N N N N N -9.022 3.199 4.397 -3.968 -1.665 3.118 P DT 2 DT OP1 O1P O 0 1 N N N N N N -10.026 3.204 5.484 -4.406 -2.599 4.208 OP1 DT 3 DT OP2 O2P O 0 1 N N N N N N -9.105 4.208 3.318 -4.901 -0.360 2.920 OP2 DT 4 DT "O5'" O5* O 0 1 N N N N N N -7.560 3.311 5.073 -2.493 -1.028 3.315 "O5'" DT 5 DT "C5'" C5* C 0 1 N N N N N N -7.109 2.360 6.021 -2.005 -0.136 2.327 "C5'" DT 6 DT "C4'" C4* C 0 1 N N R N N N -5.658 2.634 6.432 -0.611 0.328 2.728 "C4'" DT 7 DT "O4'" O4* O 0 1 N N N N N N -4.829 2.409 5.301 0.247 -0.829 2.764 "O4'" DT 8 DT "C3'" C3* C 0 1 N N S N N N -5.462 4.089 6.875 0.008 1.286 1.720 "C3'" DT 9 DT "O3'" O3* O 0 1 N N N N N N -4.884 4.104 8.170 0.965 2.121 2.368 "O3'" DT 10 DT "C2'" C2* C 0 1 N N N N N N -4.523 4.629 5.799 0.710 0.360 0.754 "C2'" DT 11 DT "C1'" C1* C 0 1 N N R N N N -3.800 3.379 5.307 1.157 -0.778 1.657 "C1'" DT 12 DT N1 N1 N 0 1 N N N N N N -3.270 3.542 3.936 1.164 -2.047 0.989 N1 DT 13 DT C2 C2 C 0 1 N N N N N N -1.901 3.405 3.707 2.333 -2.544 0.374 C2 DT 14 DT O2 O2 O 0 1 N N N N N N -1.071 3.251 4.601 3.410 -1.945 0.363 O2 DT 15 DT N3 N3 N 0 1 N N N N N N -1.498 3.450 2.382 2.194 -3.793 -0.240 N3 DT 16 DT C4 C4 C 0 1 N N N N N N -2.323 3.658 1.287 1.047 -4.570 -0.300 C4 DT 17 DT O4 O4 O 0 1 N N N N N N -1.837 3.662 0.158 0.995 -5.663 -0.857 O4 DT 18 DT C5 C5 C 0 1 N N N N N N -3.726 3.853 1.624 -0.143 -3.980 0.369 C5 DT 19 DT C7 C5M C 0 1 N N N N N N -4.751 4.099 0.540 -1.420 -4.757 0.347 C7 DT 20 DT C6 C6 C 0 1 N N N N N N -4.141 3.790 2.913 -0.013 -2.784 0.958 C6 DT 21 DT HOP3 3HOP H 0 0 N N N N N N -9.027 1.808 2.778 -4.684 -2.823 1.313 HOP3 DT 22 DT HOP2 2HOP H 0 0 N N N N N N -9.123 5.078 3.698 -5.874 -0.475 2.871 HOP2 DT 23 DT "H5'" 1H5* H 0 1 N N N N N N -7.749 2.415 6.914 -1.971 -0.654 1.366 "H5'" DT 24 DT "H5''" 2H5* H 0 0 N N N N N N -7.161 1.360 5.565 -2.683 0.718 2.254 "H5''" DT 25 DT "H4'" H4* H 0 1 N N N N N N -5.403 1.971 7.272 -0.644 0.753 3.736 "H4'" DT 26 DT "H3'" H3* H 0 1 N N N N N N -6.380 4.689 6.958 -0.722 1.941 1.236 "H3'" DT 27 DT "HO3'" H3T H 0 0 N Y N N N N -3.937 4.107 8.095 0.743 3.042 2.146 "HO3'" DT 28 DT "H2'" 1H2* H 0 1 N N N N N N -5.078 5.122 4.987 -0.003 -0.001 0.003 "H2'" DT 29 DT "H2''" 2H2* H 0 0 N N N N N N -3.836 5.400 6.177 1.556 0.818 0.232 "H2''" DT 30 DT "H1'" H1* H 0 1 N N N N N N -2.932 3.128 5.934 2.163 -0.604 2.054 "H1'" DT 31 DT H3 H3 H 0 1 N N N N N N -0.523 3.321 2.199 3.023 -4.171 -0.689 H3 DT 32 DT H71 1H5M H 0 1 N N N N N N -5.753 4.159 0.989 -1.735 -4.916 -0.683 H71 DT 33 DT H72 2H5M H 0 1 N N N N N N -4.522 5.045 0.027 -2.195 -4.208 0.881 H72 DT 34 DT H73 3H5M H 0 1 N N N N N N -4.723 3.272 -0.185 -1.272 -5.721 0.833 H73 DT 35 DT H6 H6 H 0 1 N N N N N N -5.187 3.940 3.137 -0.857 -2.318 1.458 H6 DT 36 # 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 DT OP3 P SING N N 1 DT OP3 HOP3 SING N N 2 DT P OP1 DOUB N N 3 DT P OP2 SING N N 4 DT P "O5'" SING N N 5 DT OP2 HOP2 SING N N 6 DT "O5'" "C5'" SING N N 7 DT "C5'" "C4'" SING N N 8 DT "C5'" "H5'" SING N N 9 DT "C5'" "H5''" SING N N 10 DT "C4'" "O4'" SING N N 11 DT "C4'" "C3'" SING N N 12 DT "C4'" "H4'" SING N N 13 DT "O4'" "C1'" SING N N 14 DT "C3'" "O3'" SING N N 15 DT "C3'" "C2'" SING N N 16 DT "C3'" "H3'" SING N N 17 DT "O3'" "HO3'" SING N N 18 DT "C2'" "C1'" SING N N 19 DT "C2'" "H2'" SING N N 20 DT "C2'" "H2''" SING N N 21 DT "C1'" N1 SING N N 22 DT "C1'" "H1'" SING N N 23 DT N1 C2 SING N N 24 DT N1 C6 SING N N 25 DT C2 O2 DOUB N N 26 DT C2 N3 SING N N 27 DT N3 C4 SING N N 28 DT N3 H3 SING N N 29 DT C4 O4 DOUB N N 30 DT C4 C5 SING N N 31 DT C5 C7 SING N N 32 DT C5 C6 DOUB N N 33 DT C7 H71 SING N N 34 DT C7 H72 SING N N 35 DT C7 H73 SING N N 36 DT C6 H6 SING N N 37 # 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 DT SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O" DT SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" DT SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" DT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" DT SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" DT InChI InChI 1.03 "InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" DT InChIKey InChI 1.03 GYOZYWVXFNDGLU-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 DT "SYSTEMATIC NAME" ACDLabs 10.04 ;5'-thymidylic acid ; DT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DT "Create component" 2006-12-05 RCSB DT "Modify descriptor" 2011-06-04 RCSB DT "Modify PCM" 2024-09-27 PDBE # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 DT PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C3'" O3P ? ? 2 DT PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C5'" O3P ? ? 3 DT PTR None "Covalent chemical modification" "Amino-acid side chain" "Any position" "O3'" P ? ? 4 DT SER None "Covalent chemical modification" "Amino-acid side chain" "Any position" P OG ? ? 5 DT TYR None "Covalent chemical modification" "Amino-acid side chain" "Any position" P OH ? ? #