data_8DT # _chem_comp.id 8DT _chem_comp.name ; 5-(3-(acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H20 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-09-12 _chem_comp.pdbx_modified_date 2016-09-16 _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 405.297 _chem_comp.one_letter_code U _chem_comp.three_letter_code 8DT _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 5LUY _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 8DT OP1 O1 O 0 1 N N N 63.943 -41.715 24.822 -6.906 1.375 0.041 OP1 8DT 1 8DT P P1 P 0 1 N N N 64.098 -41.211 26.238 -5.571 2.011 -0.016 P 8DT 2 8DT OP2 O2 O 0 1 N N N 65.407 -41.748 26.809 -5.123 2.450 1.467 OP2 8DT 3 8DT "O5'" O3 O 0 1 N N N 64.582 -39.689 25.895 -4.503 0.965 -0.612 "O5'" 8DT 4 8DT "C5'" C1 C 0 1 N N N 63.650 -38.895 25.149 -4.292 -0.334 -0.055 "C5'" 8DT 5 8DT "C4'" C2 C 0 1 N N R 64.211 -37.632 24.578 -3.213 -1.064 -0.858 "C4'" 8DT 6 8DT "C3'" C3 C 0 1 N N S 65.563 -37.707 23.956 -2.972 -2.483 -0.284 "C3'" 8DT 7 8DT "O3'" O4 O 0 1 N N N 65.696 -36.741 22.898 -3.889 -3.424 -0.847 "O3'" 8DT 8 8DT "C2'" C4 C 0 1 N N N 66.485 -37.223 25.058 -1.524 -2.778 -0.746 "C2'" 8DT 9 8DT "O4'" O5 O 0 1 N N N 64.302 -36.663 25.643 -1.934 -0.414 -0.700 "O4'" 8DT 10 8DT "C1'" C5 C 0 1 N N R 65.619 -36.170 25.758 -0.926 -1.386 -1.027 "C1'" 8DT 11 8DT N1 N1 N 0 1 N N N 65.922 -35.968 27.158 0.259 -1.175 -0.193 N1 8DT 12 8DT C6 C6 C 0 1 N N N 65.694 -36.960 28.024 1.480 -1.039 -0.788 C6 8DT 13 8DT C2 C7 C 0 1 N N N 66.348 -34.745 27.596 0.121 -1.114 1.141 C2 8DT 14 8DT O2 O6 O 0 1 N N N 66.473 -33.851 26.738 -0.987 -1.237 1.627 O2 8DT 15 8DT N3 N2 N 0 1 N N N 66.593 -34.525 28.929 1.173 -0.922 1.957 N3 8DT 16 8DT C4 C8 C 0 1 N N N 66.407 -35.558 29.808 2.414 -0.783 1.446 C4 8DT 17 8DT O4 O7 O 0 1 N N N 66.617 -35.374 31.035 3.371 -0.610 2.178 O4 8DT 18 8DT C5 C9 C 0 1 N N N 65.968 -36.790 29.373 2.587 -0.842 -0.013 C5 8DT 19 8DT C7 C10 C 0 1 N N N 65.719 -37.973 30.242 3.923 -0.692 -0.625 C7 8DT 20 8DT C1 C11 C 0 1 N N N 65.838 -37.962 31.568 4.969 -0.390 0.133 C1 8DT 21 8DT C3 C12 C 0 1 N N N 65.515 -39.153 32.442 6.309 -0.125 -0.504 C3 8DT 22 8DT N9 N3 N 0 1 N N N 65.863 -38.634 33.761 6.801 1.187 -0.077 N9 8DT 23 8DT C32 C13 C 0 1 N N N 65.022 -38.224 34.734 7.990 1.639 -0.523 C32 8DT 24 8DT O34 O8 O 0 1 N N N 63.772 -38.432 34.695 8.652 0.960 -1.279 O34 8DT 25 8DT C33 C14 C 0 1 N N N 65.778 -37.467 35.847 8.496 2.989 -0.084 C33 8DT 26 8DT H2 H2 H 0 1 N N N 65.843 -42.282 26.155 -4.255 2.875 1.506 H2 8DT 27 8DT H3 H3 H 0 1 N N N 62.818 -38.627 25.817 -3.969 -0.236 0.982 H3 8DT 28 8DT H4 H4 H 0 1 N N N 63.270 -39.506 24.317 -5.221 -0.902 -0.094 H4 8DT 29 8DT H5 H5 H 0 1 N N N 63.507 -37.258 23.820 -3.490 -1.116 -1.911 H5 8DT 30 8DT H6 H6 H 0 1 N N N 65.814 -38.729 23.636 -3.040 -2.479 0.804 H6 8DT 31 8DT H7 H7 H 0 1 N N N 66.564 -36.806 22.516 -3.777 -4.327 -0.518 H7 8DT 32 8DT H8 H8 H 0 1 N N N 66.752 -38.041 25.744 -0.966 -3.280 0.044 H8 8DT 33 8DT H9 H9 H 0 1 N N N 67.402 -36.776 24.645 -1.529 -3.382 -1.654 H9 8DT 34 8DT H10 H10 H 0 1 N N N 65.718 -35.218 25.216 -0.660 -1.303 -2.081 H10 8DT 35 8DT H11 H11 H 0 1 N N N 65.294 -37.899 27.671 1.569 -1.087 -1.863 H11 8DT 36 8DT H12 H12 H 0 1 N N N 66.901 -33.630 29.251 1.039 -0.883 2.916 H12 8DT 37 8DT H13 H13 H 0 1 N N N 65.424 -38.897 29.767 4.048 -0.827 -1.689 H13 8DT 38 8DT H14 H14 H 0 1 N N N 66.183 -37.056 32.044 4.861 -0.335 1.206 H14 8DT 39 8DT H15 H15 H 0 1 N N N 64.450 -39.421 32.382 7.016 -0.896 -0.197 H15 8DT 40 8DT H16 H16 H 0 1 N N N 66.129 -40.027 32.177 6.205 -0.138 -1.589 H16 8DT 41 8DT H17 H17 H 0 1 N N N 66.840 -38.575 33.968 6.272 1.731 0.528 H17 8DT 42 8DT H18 H18 H 0 1 N N N 65.063 -37.130 36.612 8.600 3.002 1.001 H18 8DT 43 8DT H19 H19 H 0 1 N N N 66.519 -38.137 36.308 9.465 3.181 -0.545 H19 8DT 44 8DT H20 H20 H 0 1 N N N 66.291 -36.595 35.414 7.789 3.760 -0.391 H20 8DT 45 8DT OP3 OP3 O 0 1 N Y N 63.019 -41.101 27.334 -5.636 3.311 -0.964 OP3 8DT 46 8DT H1 H1 H 0 1 N N N 62.187 -41.408 26.992 -6.261 3.986 -0.664 H1 8DT 47 # 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 8DT "O3'" "C3'" SING N N 1 8DT "C3'" "C4'" SING N N 2 8DT "C3'" "C2'" SING N N 3 8DT "C4'" "C5'" SING N N 4 8DT "C4'" "O4'" SING N N 5 8DT OP1 P DOUB N N 6 8DT "C2'" "C1'" SING N N 7 8DT "C5'" "O5'" SING N N 8 8DT "O4'" "C1'" SING N N 9 8DT "C1'" N1 SING N N 10 8DT "O5'" P SING N N 11 8DT P OP2 SING N N 12 8DT O2 C2 DOUB N N 13 8DT N1 C2 SING N N 14 8DT N1 C6 SING N N 15 8DT C2 N3 SING N N 16 8DT C6 C5 DOUB N N 17 8DT N3 C4 SING N N 18 8DT C5 C4 SING N N 19 8DT C5 C7 SING N N 20 8DT C4 O4 DOUB N N 21 8DT C7 C1 DOUB N E 22 8DT C1 C3 SING N N 23 8DT C3 N9 SING N N 24 8DT N9 C32 SING N N 25 8DT O34 C32 DOUB N N 26 8DT C32 C33 SING N N 27 8DT OP2 H2 SING N N 28 8DT "C5'" H3 SING N N 29 8DT "C5'" H4 SING N N 30 8DT "C4'" H5 SING N N 31 8DT "C3'" H6 SING N N 32 8DT "O3'" H7 SING N N 33 8DT "C2'" H8 SING N N 34 8DT "C2'" H9 SING N N 35 8DT "C1'" H10 SING N N 36 8DT C6 H11 SING N N 37 8DT N3 H12 SING N N 38 8DT C7 H13 SING N N 39 8DT C1 H14 SING N N 40 8DT C3 H15 SING N N 41 8DT C3 H16 SING N N 42 8DT N9 H17 SING N N 43 8DT C33 H18 SING N N 44 8DT C33 H19 SING N N 45 8DT C33 H20 SING N N 46 8DT P OP3 SING N N 47 8DT OP3 H1 SING N N 48 # 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 8DT InChI InChI 1.03 "InChI=1S/C14H20N3O9P/c1-8(18)15-4-2-3-9-6-17(14(21)16-13(9)20)12-5-10(19)11(26-12)7-25-27(22,23)24/h2-3,6,10-12,19H,4-5,7H2,1H3,(H,15,18)(H,16,20,21)(H2,22,23,24)/b3-2+/t10-,11+,12+/m0/s1" 8DT InChIKey InChI 1.03 JBKMBEZUJCTZND-FBUKTIRESA-N 8DT SMILES_CANONICAL CACTVS 3.385 "CC(=O)NC/C=C/C1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" 8DT SMILES CACTVS 3.385 "CC(=O)NCC=CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" 8DT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "CC(=O)NC/C=C/C1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 8DT SMILES "OpenEye OEToolkits" 2.0.5 "CC(=O)NCC=CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" # 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 8DT "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.5 "[(2~{R},3~{S},5~{R})-5-[5-[(~{E})-3-acetamidoprop-1-enyl]-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-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 8DT "Create component" 2016-09-12 EBI 8DT "Other modification" 2016-09-13 EBI 8DT "Initial release" 2016-09-21 RCSB #