data_F6X # _chem_comp.id F6X _chem_comp.name "[(2R,3R)-3-[2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 N4 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-04-03 _chem_comp.pdbx_modified_date 2020-11-20 _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 336.238 _chem_comp.one_letter_code ? _chem_comp.three_letter_code F6X _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 7BPF _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 F6X "C1'" C1 C 0 1 N N N -25.542 -29.541 16.976 -1.249 2.899 -0.353 "C1'" F6X 1 F6X N1 N1 N 0 1 N N N -22.849 -24.581 15.626 2.877 -0.544 0.438 N1 F6X 2 F6X C6 C2 C 0 1 N N N -23.354 -23.868 14.535 3.229 -1.557 -0.402 C6 F6X 3 F6X C5 C3 C 0 1 N N N -23.394 -22.484 14.521 4.503 -1.630 -0.854 C5 F6X 4 F6X C4 C4 C 0 1 N N N -22.921 -21.814 15.639 5.431 -0.652 -0.441 C4 F6X 5 F6X N3 N2 N 0 1 N N N -22.437 -22.561 16.733 5.043 0.316 0.379 N3 F6X 6 F6X C2 C5 C 0 1 N N N -22.401 -23.941 16.714 3.786 0.374 0.815 C2 F6X 7 F6X O2 O1 O 0 1 N N N -21.969 -24.558 17.689 3.453 1.274 1.568 O2 F6X 8 F6X N4 N3 N 0 1 N N N -22.936 -20.495 15.658 6.732 -0.702 -0.885 N4 F6X 9 F6X "C2'" C6 C 0 1 N N R -25.718 -28.439 15.948 -1.418 1.418 -0.697 "C2'" F6X 10 F6X "C3'" C7 C 0 1 N N R -26.338 -28.992 14.677 -2.894 1.032 -0.576 "C3'" F6X 11 F6X "O3'" O2 O 0 1 N N N -25.343 -29.766 14.048 -3.041 -0.368 -0.825 "O3'" F6X 12 F6X OP1 O3 O 0 1 N N N -27.249 -30.837 12.395 -5.143 -0.856 0.485 OP1 F6X 13 F6X P P1 P 0 1 N N N -25.687 -30.738 12.860 -3.784 -1.366 0.197 P F6X 14 F6X OP2 O4 O 0 1 N N N -24.616 -31.881 12.370 -3.889 -2.830 -0.465 OP2 F6X 15 F6X C3A C8 C 0 1 N N N -26.766 -27.829 13.765 -3.713 1.821 -1.599 C3A F6X 16 F6X "O1'" O5 O 0 1 N N N -26.730 -29.532 17.789 -1.815 3.157 0.934 "O1'" F6X 17 F6X "N2'" N4 N 0 1 N N N -24.432 -27.810 15.599 -0.623 0.608 0.228 "N2'" F6X 18 F6X C2A C9 C 0 1 N N N -24.143 -26.584 16.041 0.682 0.384 -0.022 C2A F6X 19 F6X O2A O6 O 0 1 N N N -24.866 -25.912 16.771 1.199 0.854 -1.014 O2A F6X 20 F6X C2B C10 C 0 1 N N N -22.819 -26.050 15.564 1.500 -0.450 0.930 C2B F6X 21 F6X H1 H1 H 0 1 N N N -25.431 -30.514 16.475 -0.188 3.151 -0.340 H1 F6X 22 F6X H2 H2 H 0 1 N N N -24.655 -29.345 17.596 -1.757 3.507 -1.101 H2 F6X 23 F6X H3 H3 H 0 1 N N N -23.724 -24.412 13.678 2.499 -2.294 -0.704 H3 F6X 24 F6X H4 H4 H 0 1 N N N -23.780 -21.945 13.669 4.804 -2.424 -1.521 H4 F6X 25 F6X H5 H5 H 0 1 N N N -22.599 -20.003 16.461 7.014 -1.412 -1.484 H5 F6X 26 F6X H6 H6 H 0 1 N N N -23.284 -19.988 14.870 7.369 -0.029 -0.599 H6 F6X 27 F6X H7 H7 H 0 1 N N N -26.392 -27.676 16.364 -1.079 1.242 -1.718 H7 F6X 28 F6X H8 H8 H 0 1 N N N -27.218 -29.602 14.929 -3.248 1.262 0.429 H8 F6X 29 F6X HOP2 H10 H 0 0 N N N -25.062 -32.522 11.828 -4.327 -3.485 0.096 H10 F6X 30 F6X H11 H11 H 0 1 N N N -27.542 -27.234 14.268 -4.764 1.546 -1.513 H11 F6X 31 F6X H12 H12 H 0 1 N N N -25.896 -27.191 13.552 -3.601 2.888 -1.409 H12 F6X 32 F6X H13 H13 H 0 1 N N N -27.166 -28.231 12.822 -3.359 1.591 -2.604 H13 F6X 33 F6X H14 H14 H 0 1 N Y N -26.666 -30.210 18.452 -1.677 4.060 1.251 H14 F6X 34 F6X H15 H15 H 0 1 N N N -23.774 -28.303 15.030 -1.036 0.232 1.021 H15 F6X 35 F6X H16 H16 H 0 1 N N N -22.642 -26.373 14.527 1.070 -1.449 0.999 H16 F6X 36 F6X H17 H17 H 0 1 N N N -22.013 -26.431 16.209 1.497 0.015 1.916 H17 F6X 37 F6X OP3 OP4 O 0 1 N Y N -25.485 -29.782 11.743 -2.943 -1.456 1.566 OP4 F6X 38 F6X HOP3 H9 H 0 0 N Y N -26.305 -29.658 11.279 -2.027 -1.742 1.447 H9 F6X 39 # # 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 F6X OP2 P SING N N 1 F6X OP1 P DOUB N N 2 F6X P "O3'" SING N N 3 F6X C3A "C3'" SING N N 4 F6X "O3'" "C3'" SING N N 5 F6X C5 C6 DOUB N N 6 F6X C5 C4 SING N N 7 F6X C6 N1 SING N N 8 F6X "C3'" "C2'" SING N N 9 F6X C2B N1 SING N N 10 F6X C2B C2A SING N N 11 F6X "N2'" "C2'" SING N N 12 F6X "N2'" C2A SING N N 13 F6X N1 C2 SING N N 14 F6X C4 N4 SING N N 15 F6X C4 N3 DOUB N N 16 F6X "C2'" "C1'" SING N N 17 F6X C2A O2A DOUB N N 18 F6X C2 N3 SING N N 19 F6X C2 O2 DOUB N N 20 F6X "C1'" "O1'" SING N N 21 F6X "C1'" H1 SING N N 22 F6X "C1'" H2 SING N N 23 F6X C6 H3 SING N N 24 F6X C5 H4 SING N N 25 F6X N4 H5 SING N N 26 F6X N4 H6 SING N N 27 F6X "C2'" H7 SING N N 28 F6X "C3'" H8 SING N N 29 F6X OP2 HOP2 SING N N 30 F6X C3A H11 SING N N 31 F6X C3A H12 SING N N 32 F6X C3A H13 SING N N 33 F6X "O1'" H14 SING N N 34 F6X "N2'" H15 SING N N 35 F6X C2B H16 SING N N 36 F6X C2B H17 SING N N 37 F6X P OP3 SING N N 38 F6X OP3 HOP3 SING N N 39 # # 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 F6X InChI InChI 1.03 "InChI=1S/C10H17N4O7P/c1-6(21-22(18,19)20)7(5-15)12-9(16)4-14-3-2-8(11)13-10(14)17/h2-3,6-7,15H,4-5H2,1H3,(H,12,16)(H2,11,13,17)(H2,18,19,20)/t6-,7-/m1/s1" F6X InChIKey InChI 1.03 BNPHLZWYYOHAKE-RNFRBKRXSA-N F6X SMILES_CANONICAL CACTVS 3.385 "C[C@@H](O[P](O)(O)=O)[C@@H](CO)NC(=O)CN1C=CC(=NC1=O)N" F6X SMILES CACTVS 3.385 "C[CH](O[P](O)(O)=O)[CH](CO)NC(=O)CN1C=CC(=NC1=O)N" F6X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]([C@@H](CO)NC(=O)CN1C=CC(=NC1=O)N)OP(=O)(O)O" F6X SMILES "OpenEye OEToolkits" 2.0.7 "CC(C(CO)NC(=O)CN1C=CC(=NC1=O)N)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id F6X _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~{R},3~{R})-3-[2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] 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 F6X "Create component" 2020-04-03 PDBJ F6X "Modify internal type" 2020-11-04 PDBJ F6X "Modify linking type" 2020-11-04 PDBJ F6X "Modify leaving atom flag" 2020-11-04 PDBJ F6X "Modify linking type" 2020-11-18 PDBJ F6X "Initial release" 2020-11-25 RCSB ##