data_T5O # _chem_comp.id T5O _chem_comp.name "2'-deoxy-5-methoxyuridine 5'-(dihydrogen phosphate)" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms "5-methoxy-2'-deoxyuridine-5'-phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-08-05 _chem_comp.pdbx_modified_date 2021-03-01 _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 338.208 _chem_comp.one_letter_code U _chem_comp.three_letter_code T5O _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 3IJK _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 T5O P P P 0 1 N N N 8.625 18.044 7.485 -4.502 1.064 -0.225 P T5O 1 T5O N1 N1 N 0 1 N N N 7.819 14.270 3.369 2.080 -0.315 -0.037 N1 T5O 2 T5O C2 C2 C 0 1 N N N 7.974 13.326 2.376 2.071 0.260 1.179 C2 T5O 3 T5O O2 O2 O 0 1 N N N 7.151 12.477 2.132 1.107 0.110 1.906 O2 T5O 4 T5O N3 N3 N 0 1 N N N 9.133 13.405 1.661 3.113 0.998 1.605 N3 T5O 5 T5O C4 C4 C 0 1 N N N 10.150 14.311 1.865 4.190 1.175 0.815 C4 T5O 6 T5O O4 O4 O 0 1 N N N 11.169 14.309 1.189 5.133 1.842 1.201 O4 T5O 7 T5O C5 C5 C 0 1 N N N 9.949 15.274 2.922 4.216 0.576 -0.472 C5 T5O 8 T5O O5 O5 O 0 1 N N N 11.002 16.217 3.119 5.294 0.740 -1.289 O5 T5O 9 T5O C6 C6 C 0 1 N N N 8.805 15.218 3.620 3.156 -0.161 -0.875 C6 T5O 10 T5O "C1'" C1* C 0 1 N N R 6.549 14.221 4.187 0.933 -1.117 -0.469 C1* T5O 11 T5O OP3 OP3 O 0 1 N N N 8.178 18.049 8.896 -4.765 2.151 -1.383 OP3 T5O 12 T5O "C2'" C2* C 0 1 N N N 6.622 13.185 5.311 0.740 -2.329 0.470 C2* T5O 13 T5O OP2 OP2 O 0 1 N N N 10.059 17.982 7.187 -5.755 0.056 -0.140 OP2 T5O 14 T5O "C3'" C3* C 0 1 N N S 7.060 14.042 6.495 -0.794 -2.477 0.580 C3* T5O 15 T5O "O3'" O3* O 0 1 N N N 6.737 13.494 7.766 -1.211 -3.749 0.078 O3* T5O 16 T5O "C4'" C4* C 0 1 N N R 6.180 15.254 6.228 -1.347 -1.338 -0.305 C4* T5O 17 T5O "O4'" O4* O 0 1 N N N 6.310 15.470 4.802 -0.288 -0.356 -0.345 O4* T5O 18 T5O "C5'" C5* C 0 1 N N N 6.569 16.508 6.980 -2.606 -0.738 0.323 C5* T5O 19 T5O "O5'" O5* O 0 1 N N N 7.940 16.802 6.753 -3.166 0.231 -0.565 O5* T5O 20 T5O C7 C7 C 0 1 N N N 10.727 17.150 4.165 5.241 0.104 -2.568 C7 T5O 21 T5O H6 H6 H 0 1 N N N 8.643 15.938 4.409 3.158 -0.628 -1.848 H6 T5O 22 T5O "H1'" H1* H 0 1 N N N 5.746 13.953 3.485 1.070 -1.450 -1.498 H1* T5O 23 T5O HOP3 HOP3 H 0 0 N N N 8.628 18.739 9.369 -5.556 2.690 -1.243 HOP3 T5O 24 T5O "H2'" H2* H 0 1 N N N 5.652 12.697 5.489 1.180 -3.224 0.032 H2* T5O 25 T5O "H2'A" H2*A H 0 0 N N N 7.343 12.384 5.090 1.175 -2.127 1.448 H2*A T5O 26 T5O HOP2 HOP2 H 0 0 N N N 10.492 18.746 7.551 -5.923 -0.432 -0.958 HOP2 T5O 27 T5O "H3'" H3* H 0 1 N N N 8.148 14.192 6.552 -1.117 -2.351 1.613 H3* T5O 28 T5O "HO3'" HO3* H 0 0 N N N 7.039 14.080 8.450 -0.844 -4.502 0.560 HO3* T5O 29 T5O "H4'" H4* H 0 1 N N N 5.155 15.053 6.574 -1.562 -1.707 -1.308 H4* T5O 30 T5O "H5'" H5* H 0 1 N N N 5.953 17.349 6.629 -3.334 -1.530 0.503 H5* T5O 31 T5O "H5'A" H5*A H 0 0 N N N 6.403 16.353 8.056 -2.349 -0.260 1.268 H5*A T5O 32 T5O HC7 HC7 H 0 1 N N N 11.572 17.847 4.267 5.136 -0.973 -2.434 HC7 T5O 33 T5O HC7A HC7A H 0 0 N N N 9.814 17.714 3.922 4.388 0.486 -3.128 HC7A T5O 34 T5O HC7B HC7B H 0 0 N N N 10.583 16.608 5.111 6.160 0.314 -3.116 HC7B T5O 35 T5O HN3 HN3 H 0 1 N N N 9.255 12.744 0.921 3.088 1.405 2.486 HN3 T5O 36 T5O OP1 OP1 O 0 1 N N N 9.639 19.435 8.106 -4.335 1.755 1.073 OP1 T5O 37 # # 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 T5O P OP3 SING N N 1 T5O N1 C6 SING N N 2 T5O N1 "C1'" SING N N 3 T5O C2 N1 SING N N 4 T5O O2 C2 DOUB N N 5 T5O N3 C2 SING N N 6 T5O N3 C4 SING N N 7 T5O N3 HN3 SING N N 8 T5O C4 C5 SING N N 9 T5O O4 C4 DOUB N N 10 T5O C5 O5 SING N N 11 T5O C5 C6 DOUB N N 12 T5O O5 C7 SING N N 13 T5O C6 H6 SING N N 14 T5O "C1'" "O4'" SING N N 15 T5O "C1'" "C2'" SING N N 16 T5O "C1'" "H1'" SING N N 17 T5O OP3 HOP3 SING N N 18 T5O "C2'" "C3'" SING N N 19 T5O "C2'" "H2'" SING N N 20 T5O "C2'" "H2'A" SING N N 21 T5O OP2 P SING N N 22 T5O OP2 HOP2 SING N N 23 T5O "C3'" "O3'" SING N N 24 T5O "C3'" "H3'" SING N N 25 T5O "O3'" "HO3'" SING N N 26 T5O "C4'" "C3'" SING N N 27 T5O "C4'" "C5'" SING N N 28 T5O "C4'" "H4'" SING N N 29 T5O "O4'" "C4'" SING N N 30 T5O "C5'" "H5'" SING N N 31 T5O "C5'" "H5'A" SING N N 32 T5O "O5'" P SING N N 33 T5O "O5'" "C5'" SING N N 34 T5O C7 HC7 SING N N 35 T5O C7 HC7A SING N N 36 T5O C7 HC7B SING N N 37 T5O P OP1 DOUB N N 38 # # 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 T5O SMILES ACDLabs 11.02 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(OC)=C1)CC2O" T5O SMILES_CANONICAL CACTVS 3.352 "COC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" T5O SMILES CACTVS 3.352 "COC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" T5O SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "COC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" T5O SMILES "OpenEye OEToolkits" 1.7.0 "COC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" T5O InChI InChI 1.03 "InChI=1S/C10H15N2O9P/c1-19-6-3-12(10(15)11-9(6)14)8-2-5(13)7(21-8)4-20-22(16,17)18/h3,5,7-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,7+,8+/m0/s1" T5O InChIKey InChI 1.03 GEADDYZDICTQHP-UIISKDMLSA-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 T5O "SYSTEMATIC NAME" ACDLabs 11.02 "2'-deoxy-5-methoxyuridine 5'-(dihydrogen phosphate)" T5O "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-3-hydroxy-5-(5-methoxy-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 T5O "Create component" 2009-08-05 RCSB T5O "Modify descriptor" 2011-06-04 RCSB T5O "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id T5O _pdbx_chem_comp_synonyms.name "5-methoxy-2'-deoxyuridine-5'-phosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##