data_2DT # _chem_comp.id 2DT _chem_comp.name "3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms "2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-07 _chem_comp.pdbx_modified_date 2021-03-13 _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 306.209 _chem_comp.one_letter_code T _chem_comp.three_letter_code 2DT _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 3BDP _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.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 2DT P P P 0 1 N N N 17.858 46.724 34.563 0.760 -0.138 -4.202 P 2DT 1 2DT OP1 O1P O 0 1 N N N 18.351 46.697 35.969 1.665 0.929 -3.722 OP1 2DT 2 2DT OP2 O2P O 0 1 N N N 17.623 48.032 33.871 1.622 -1.286 -4.930 OP2 2DT 3 2DT OP3 O3P O 0 1 N Y N 18.962 45.940 33.719 -0.296 0.483 -5.246 OP3 2DT 4 2DT "O5'" O5* O 0 1 N N N 16.532 45.853 34.412 -0.031 -0.772 -2.952 "O5'" 2DT 5 2DT N1 N1 N 0 1 N N N 15.120 42.269 35.391 -0.529 -0.306 2.235 N1 2DT 6 2DT C6 C6 C 0 1 N N N 16.065 43.061 36.008 -0.372 -1.162 3.291 C6 2DT 7 2DT C2 C2 C 0 1 N N N 14.891 40.973 35.808 0.107 0.878 2.213 C2 2DT 8 2DT O2 O2 O 0 1 N N N 14.031 40.268 35.320 -0.047 1.624 1.266 O2 2DT 9 2DT N3 N3 N 0 1 N N N 15.694 40.545 36.847 0.913 1.249 3.225 N3 2DT 10 2DT C4 C4 C 0 1 N N N 16.648 41.276 37.517 1.091 0.435 4.286 C4 2DT 11 2DT O4 O4 O 0 1 N N N 17.267 40.769 38.444 1.820 0.770 5.202 O4 2DT 12 2DT C5 C5 C 0 1 N N N 16.826 42.644 37.039 0.430 -0.815 4.320 C5 2DT 13 2DT C5M C5M C 0 1 N N N 17.838 43.518 37.714 0.616 -1.745 5.491 C5M 2DT 14 2DT "C2'" C2* C 0 1 N N N 13.122 43.666 34.603 -2.533 0.350 0.967 "C2'" 2DT 15 2DT "C5'" C5* C 0 1 N N N 15.781 45.861 33.177 -0.773 0.289 -2.351 "C5'" 2DT 16 2DT "C4'" C4* C 0 1 N N S 14.637 44.873 33.227 -1.553 -0.248 -1.149 "C4'" 2DT 17 2DT "O4'" O4* O 0 1 N N N 15.184 43.555 33.429 -0.651 -0.683 -0.106 "O4'" 2DT 18 2DT "C1'" C1* C 0 1 N N R 14.322 42.783 34.256 -1.401 -0.682 1.119 "C1'" 2DT 19 2DT "C3'" C3* C 0 1 N N N 13.626 45.074 34.352 -2.369 0.883 -0.476 "C3'" 2DT 20 2DT HOP2 2HOP H 0 0 N N N 17.308 48.049 32.974 2.079 -0.865 -5.671 HOP2 2DT 21 2DT HOP3 3HOP H 0 0 N N N 18.647 45.957 32.822 -0.865 -0.243 -5.534 HOP3 2DT 22 2DT H6 H6 H 0 1 N N N 16.222 44.093 35.654 -0.887 -2.112 3.301 H6 2DT 23 2DT HN3 HN3 H 0 1 N N N 15.568 39.580 37.154 1.365 2.107 3.193 HN3 2DT 24 2DT H71 1H5M H 0 1 N N N 18.467 43.173 38.567 1.295 -1.290 6.212 H71 2DT 25 2DT H72 2H5M H 0 1 N N N 18.526 43.900 36.925 -0.347 -1.929 5.965 H72 2DT 26 2DT H73 3H5M H 0 1 N N N 17.311 44.444 38.041 1.035 -2.689 5.142 H73 2DT 27 2DT "H2'" 1H2* H 0 1 N N N 12.186 43.407 34.054 -3.505 -0.127 1.089 "H2'" 2DT 28 2DT "H2''" 2H2* H 0 0 N N N 12.709 43.500 35.625 -2.412 1.159 1.688 "H2''" 2DT 29 2DT "H5'" 1H5* H 0 1 N N N 15.426 46.886 32.919 -1.470 0.704 -3.080 "H5'" 2DT 30 2DT "H5''" 2H5* H 0 0 N N N 16.439 45.681 32.295 -0.088 1.069 -2.019 "H5''" 2DT 31 2DT "H4'" H4* H 0 1 N N N 14.096 45.020 32.263 -2.208 -1.065 -1.453 "H4'" 2DT 32 2DT "H1'" H1* H 0 1 N N N 13.897 41.873 33.770 -1.823 -1.672 1.296 "H1'" 2DT 33 2DT "H3'1" 1H3* H 0 0 N N N 12.829 45.823 34.136 -3.339 1.004 -0.959 "H3'1" 2DT 34 2DT "H3'2" 2H3* H 0 0 N N N 14.026 45.594 35.253 -1.813 1.821 -0.484 "H3'2" 2DT 35 # # 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 2DT P OP1 DOUB N N 1 2DT P OP2 SING N N 2 2DT P OP3 SING N N 3 2DT P "O5'" SING N N 4 2DT OP2 HOP2 SING N N 5 2DT OP3 HOP3 SING N N 6 2DT "O5'" "C5'" SING N N 7 2DT N1 C6 SING N N 8 2DT N1 C2 SING N N 9 2DT N1 "C1'" SING N N 10 2DT C6 C5 DOUB N N 11 2DT C6 H6 SING N N 12 2DT C2 O2 DOUB N N 13 2DT C2 N3 SING N N 14 2DT N3 C4 SING N N 15 2DT N3 HN3 SING N N 16 2DT C4 O4 DOUB N N 17 2DT C4 C5 SING N N 18 2DT C5 C5M SING N N 19 2DT C5M H71 SING N N 20 2DT C5M H72 SING N N 21 2DT C5M H73 SING N N 22 2DT "C2'" "C1'" SING N N 23 2DT "C2'" "C3'" SING N N 24 2DT "C2'" "H2'" SING N N 25 2DT "C2'" "H2''" SING N N 26 2DT "C5'" "C4'" SING N N 27 2DT "C5'" "H5'" SING N N 28 2DT "C5'" "H5''" SING N N 29 2DT "C4'" "O4'" SING N N 30 2DT "C4'" "C3'" SING N N 31 2DT "C4'" "H4'" SING N N 32 2DT "O4'" "C1'" SING N N 33 2DT "C1'" "H1'" SING N N 34 2DT "C3'" "H3'1" SING N N 35 2DT "C3'" "H3'2" SING N N 36 # # 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 2DT SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(CC2)COP(=O)(O)O" 2DT SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2CC[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" 2DT SMILES CACTVS 3.341 "CC1=CN([CH]2CC[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" 2DT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2CC[C@H](O2)COP(=O)(O)O" 2DT SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CCC(O2)COP(=O)(O)O" 2DT InChI InChI 1.03 "InChI=1S/C10H15N2O7P/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(19-8)5-18-20(15,16)17/h4,7-8H,2-3,5H2,1H3,(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1" 2DT InChIKey InChI 1.03 WVNRRNJFRREKAR-JGVFFNPUSA-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 2DT "SYSTEMATIC NAME" ACDLabs 10.04 "[(2S,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate" 2DT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,5R)-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 2DT "Create component" 1999-07-07 RCSB 2DT "Modify descriptor" 2011-06-04 RCSB 2DT "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 2DT _pdbx_chem_comp_synonyms.name "2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##