data_84E # _chem_comp.id 84E _chem_comp.name "[(2S,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-2-(trifluoromethylsulfanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H14 F3 N2 O8 P S" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-11-24 _chem_comp.pdbx_modified_date 2022-11-11 _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 422.271 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 84E _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 7W0V _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 84E "O5'" O1 O 0 1 N N N 6.571 -5.033 6.355 1.731 1.499 -0.194 "O5'" 84E 1 84E P P1 P 0 1 N N N 8.024 -4.320 6.266 2.619 2.732 0.339 P 84E 2 84E OP3 O2 O 0 1 N Y N 8.992 -5.139 7.038 3.930 2.888 -0.584 OP1 84E 3 84E OP2 O3 O 0 1 N N N 8.316 -4.020 4.842 1.752 4.087 0.273 OP2 84E 4 84E "O3'" O4 O 0 1 N N N 4.203 -8.547 7.129 1.057 -1.447 -3.086 "O3'" 84E 5 84E "C5'" C1 C 0 1 N N N 6.018 -5.392 7.622 2.182 0.144 -0.163 "C5'" 84E 6 84E "C4'" C2 C 0 1 N N S 4.677 -6.143 7.568 1.099 -0.768 -0.742 "C4'" 84E 7 84E "S4'" S1 S 0 1 N N N 4.225 -6.529 9.302 1.652 -2.495 -0.688 "S4'" 84E 8 84E "C6'" C3 C 0 1 N N N 2.403 -6.496 9.394 1.799 -2.821 1.090 "C6'" 84E 9 84E F1 F1 F 0 1 N N N 1.989 -6.964 10.625 0.555 -2.636 1.703 F1 84E 10 84E F2 F2 F 0 1 N N N 1.812 -7.293 8.436 2.225 -4.139 1.289 F2 84E 11 84E F3 F3 F 0 1 N N N 1.908 -5.214 9.261 2.730 -1.940 1.651 F3 84E 12 84E "O4'" O5 O 0 1 N N N 3.703 -5.249 7.054 -0.117 -0.621 0.011 "O4'" 84E 13 84E "C1'" C4 C 0 1 N N R 3.093 -5.806 5.902 -1.210 -0.777 -0.919 "C1'" 84E 14 84E N1 N1 N 0 1 N N N 2.793 -4.738 4.918 -2.431 -0.164 -0.388 N1 84E 15 84E C6 C5 C 0 1 N N N 3.817 -4.077 4.275 -3.580 -0.901 -0.310 C6 84E 16 84E C5 C6 C 0 1 N N N 3.555 -3.062 3.410 -4.705 -0.336 0.180 C5 84E 17 84E C7 C7 C 0 1 N N N 4.715 -2.390 2.698 -5.981 -1.133 0.274 C7 84E 18 84E C4 C8 C 0 1 N N N 2.174 -2.631 3.166 -4.669 1.014 0.604 C4 84E 19 84E O4 O6 O 0 1 N N N 1.804 -1.705 2.446 -5.671 1.545 1.049 O4 84E 20 84E N3 N2 N 0 1 N N N 1.216 -3.365 3.822 -3.516 1.707 0.510 N3 84E 21 84E C2 C9 C 0 1 N N N 1.452 -4.425 4.663 -2.409 1.117 0.023 C2 84E 22 84E O2 O7 O 0 1 N N N 0.496 -5.037 5.138 -1.376 1.754 -0.056 O2 84E 23 84E "C3'" C10 C 0 1 N N S 4.769 -7.350 6.599 0.793 -0.361 -2.196 "C3'" 84E 24 84E "C2'" C11 C 0 1 N N N 4.044 -6.865 5.353 -0.721 -0.023 -2.181 "C2'" 84E 25 84E HP3 H1 H 0 1 N Y N 9.255 -4.667 7.819 3.736 3.057 -1.516 H1 84E 26 84E HP2 H2 H 0 1 N N N 8.308 -3.080 4.708 2.226 4.872 0.580 H2 84E 27 84E "HO3'" H3 H 0 1 N N N 4.687 -8.811 7.903 0.882 -1.246 -4.015 H4 84E 28 84E "H5'" H4 H 0 1 N N N 6.746 -6.034 8.140 3.092 0.050 -0.757 "H5'" 84E 29 84E "H5''" H5 H 0 0 N N N 5.867 -4.468 8.200 2.389 -0.147 0.867 "H5''" 84E 30 84E "H1'" H6 H 0 1 N N N 2.152 -6.302 6.184 -1.377 -1.831 -1.142 "H1'" 84E 31 84E H6 H7 H 0 1 N N N 4.840 -4.369 4.461 -3.589 -1.930 -0.638 H6 84E 32 84E H72 H8 H 0 1 N N N 5.660 -2.855 3.016 -6.029 -1.629 1.244 H72 84E 33 84E H73 H9 H 0 1 N N N 4.596 -2.508 1.611 -6.835 -0.465 0.165 H73 84E 34 84E H71 H10 H 0 1 N N N 4.730 -1.320 2.951 -6.001 -1.882 -0.518 H71 84E 35 84E H3 H11 H 0 1 N N N 0.262 -3.104 3.674 -3.484 2.632 0.798 H3 84E 36 84E "H3'" H12 H 0 1 N N N 5.828 -7.513 6.350 1.379 0.514 -2.478 "H3'" 84E 37 84E "H2'" H13 H 0 1 N N N 3.489 -7.685 4.874 -1.212 -0.404 -3.077 "H2'" 84E 38 84E "H2''" H14 H 0 0 N N N 4.749 -6.428 4.630 -0.880 1.051 -2.079 "H2''" 84E 39 84E OP1 O8 O 0 1 N N N 7.799 -2.935 7.071 3.029 2.476 1.738 O1 84E 40 # 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 84E O4 C4 DOUB N N 1 84E C7 C5 SING N N 2 84E C4 C5 SING N N 3 84E C4 N3 SING N N 4 84E C5 C6 DOUB N N 5 84E N3 C2 SING N N 6 84E C6 N1 SING N N 7 84E C2 N1 SING N N 8 84E C2 O2 DOUB N N 9 84E OP2 P SING N N 10 84E N1 "C1'" SING N N 11 84E "C2'" "C1'" SING N N 12 84E "C2'" "C3'" SING N N 13 84E "C1'" "O4'" SING N N 14 84E P "O5'" SING N N 15 84E P OP3 SING N N 16 84E "O5'" "C5'" SING N N 17 84E "C3'" "O3'" SING N N 18 84E "C3'" "C4'" SING N N 19 84E "O4'" "C4'" SING N N 20 84E "C4'" "C5'" SING N N 21 84E "C4'" "S4'" SING N N 22 84E F2 "C6'" SING N N 23 84E F3 "C6'" SING N N 24 84E "S4'" "C6'" SING N N 25 84E "C6'" F1 SING N N 26 84E OP3 HP3 SING N N 27 84E OP2 HP2 SING N N 28 84E "O3'" "HO3'" SING N N 29 84E "C5'" "H5'" SING N N 30 84E "C5'" "H5''" SING N N 31 84E "C1'" "H1'" SING N N 32 84E C6 H6 SING N N 33 84E C7 H72 SING N N 34 84E C7 H73 SING N N 35 84E C7 H71 SING N N 36 84E N3 H3 SING N N 37 84E "C3'" "H3'" SING N N 38 84E "C2'" "H2'" SING N N 39 84E "C2'" "H2''" SING N N 40 84E P OP1 DOUB N N 41 # 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 84E InChI InChI 1.03 "InChI=1S/C11H14F3N2O8PS/c1-5-3-16(9(19)15-8(5)18)7-2-6(17)10(24-7,26-11(12,13)14)4-23-25(20,21)22/h3,6-7,17H,2,4H2,1H3,(H,15,18,19)(H2,20,21,22)/t6-,7+,10-/m0/s1" 84E InChIKey InChI 1.03 JESWWYATFFIOBE-PJKMHFRUSA-N 84E SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@](CO[P](O)(O)=O)(O2)SC(F)(F)F)C(=O)NC1=O" 84E SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[C](CO[P](O)(O)=O)(O2)SC(F)(F)F)C(=O)NC1=O" 84E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@](O2)(COP(=O)(O)O)SC(F)(F)F)O" 84E SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)(COP(=O)(O)O)SC(F)(F)F)O" # _pdbx_chem_comp_identifier.comp_id 84E _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{S},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-2-(trifluoromethylsulfanyl)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 84E "Create component" 2021-11-24 PDBJ 84E "Initial release" 2022-11-16 RCSB #