data_J0X # _chem_comp.id J0X _chem_comp.name "2-[[2-oxidanylidene-1-[(2R,4S,5R)-4-oxidanyl-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidin-4-yl]amino]ethanoic acid" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-17 _chem_comp.pdbx_modified_date 2022-03-04 _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 365.233 _chem_comp.one_letter_code C _chem_comp.three_letter_code J0X _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 7EAY _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 J0X "C1'" C1 C 0 1 N N R 21.388 -33.565 -24.466 0.305 1.951 -0.808 "C1'" J0X 1 J0X C2 C2 C 0 1 N N N 20.816 -34.829 -26.455 -1.398 0.575 0.253 C2 J0X 2 J0X "C2'" C3 C 0 1 N N N 22.890 -33.237 -24.329 0.536 2.885 0.395 "C2'" J0X 3 J0X "C3'" C4 C 0 1 N N S 22.918 -32.549 -22.965 1.754 2.268 1.126 "C3'" J0X 4 J0X C4 C5 C 0 1 N N N 20.268 -33.750 -28.410 -3.531 0.331 -0.601 C4 J0X 5 J0X "C4'" C6 C 0 1 N N R 21.814 -31.821 -22.967 2.404 1.413 0.008 "C4'" J0X 6 J0X C5 C7 C 0 1 N N N 20.448 -32.522 -27.837 -3.199 1.189 -1.669 C5 J0X 7 J0X "C5'" C8 C 0 1 N N N 21.991 -30.374 -23.494 3.232 0.276 0.611 "C5'" J0X 8 J0X C6 C9 C 0 1 N N N 20.821 -32.503 -26.498 -1.952 1.716 -1.725 C6 J0X 9 J0X C7 C10 C 0 1 N N N 19.163 -32.932 -31.918 -6.558 -1.569 0.447 C7 J0X 10 J0X C8 C11 C 0 1 N N N 19.753 -32.559 -30.541 -5.131 -1.108 0.592 C8 J0X 11 J0X N1 N1 N 0 1 N N N 21.002 -33.644 -25.854 -1.051 1.396 -0.754 N1 J0X 12 J0X N3 N2 N 0 1 N N N 20.466 -34.876 -27.710 -2.621 0.053 0.324 N3 J0X 13 J0X N4 N3 N 0 1 N N N 19.856 -33.812 -29.835 -4.790 -0.217 -0.520 N4 J0X 14 J0X O2 O1 O 0 1 N N N 20.975 -35.887 -25.842 -0.577 0.299 1.112 O2 J0X 15 J0X "O3'" O2 O 0 1 N N N 22.777 -33.684 -22.019 2.650 3.286 1.574 "O3'" J0X 16 J0X "O4'" O3 O 0 1 N N N 20.749 -32.559 -23.924 1.271 0.891 -0.719 "O4'" J0X 17 J0X "O5'" O4 O 0 1 N N N 22.943 -30.318 -24.563 3.912 -0.424 -0.433 "O5'" J0X 18 J0X O8 O5 O 0 1 N N N 18.880 -32.050 -32.743 -7.223 -1.192 -0.489 O8 J0X 19 J0X O9 O6 O 0 1 N N N 18.969 -34.129 -32.179 -7.091 -2.398 1.358 O9 J0X 20 J0X OP1 O7 O 0 1 N N N 21.451 -29.261 -26.310 5.922 -1.301 0.817 OP1 J0X 21 J0X OP2 O8 O 0 1 N N N 22.833 -27.755 -24.857 4.011 -2.905 0.431 OP2 J0X 22 J0X P P1 P 0 1 N N N 22.737 -29.046 -25.585 4.877 -1.683 -0.160 P J0X 23 J0X H1 H1 H 0 1 N N N 21.182 -34.518 -23.957 0.445 2.503 -1.738 H1 J0X 24 J0X H2 H2 H 0 1 N N N 23.504 -34.149 -24.333 0.767 3.895 0.056 H2 J0X 25 J0X H3 H3 H 0 1 N N N 23.230 -32.562 -25.128 -0.337 2.891 1.048 H3 J0X 26 J0X H4 H4 H 0 1 N N N 23.852 -31.988 -22.811 1.432 1.641 1.957 H4 J0X 27 J0X H5 H5 H 0 1 N N N 21.370 -31.766 -21.962 3.022 2.034 -0.640 H5 J0X 28 J0X H6 H6 H 0 1 N N N 20.307 -31.610 -28.398 -3.928 1.426 -2.430 H6 J0X 29 J0X H7 H7 H 0 1 N N N 22.340 -29.734 -22.670 3.961 0.689 1.308 H7 J0X 30 J0X H8 H8 H 0 1 N N N 21.021 -30.005 -23.859 2.573 -0.412 1.141 H8 J0X 31 J0X H9 H9 H 0 1 N N N 20.962 -31.562 -25.987 -1.674 2.375 -2.533 H9 J0X 32 J0X H10 H10 H 0 1 N N N 20.744 -32.096 -30.656 -5.016 -0.573 1.535 H10 J0X 33 J0X H11 H11 H 0 1 N N N 19.085 -31.867 -30.007 -4.467 -1.972 0.582 H11 J0X 34 J0X H12 H12 H 0 1 N N N 19.659 -34.683 -30.285 -5.452 -0.014 -1.199 H12 J0X 35 J0X H13 H13 H 0 1 N N N 22.783 -33.356 -21.127 2.259 3.902 2.209 H13 J0X 36 J0X H14 H14 H 0 1 N N N 18.599 -34.208 -33.050 -8.011 -2.666 1.223 H14 J0X 37 J0X H16 H16 H 0 1 N N N 22.030 -27.262 -24.978 3.306 -3.208 -0.157 H16 J0X 38 J0X OP3 O9 O 0 1 N Y N 23.908 -29.161 -26.663 5.571 -2.136 -1.540 O1 J0X 39 J0X H15 H15 H 0 1 N Y N 23.535 -29.339 -27.519 6.168 -2.892 -1.450 H15 J0X 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 J0X O8 C7 DOUB N N 1 J0X O9 C7 SING N N 2 J0X C7 C8 SING N N 3 J0X C8 N4 SING N N 4 J0X N4 C4 SING N N 5 J0X C4 C5 SING N N 6 J0X C4 N3 DOUB N N 7 J0X C5 C6 DOUB N N 8 J0X N3 C2 SING N N 9 J0X C6 N1 SING N N 10 J0X C2 N1 SING N N 11 J0X C2 O2 DOUB N N 12 J0X OP1 P DOUB N N 13 J0X N1 "C1'" SING N N 14 J0X P OP2 SING N N 15 J0X P "O5'" SING N N 16 J0X "O5'" "C5'" SING N N 17 J0X "C1'" "C2'" SING N N 18 J0X "C1'" "O4'" SING N N 19 J0X "C2'" "C3'" SING N N 20 J0X "O4'" "C4'" SING N N 21 J0X "C5'" "C4'" SING N N 22 J0X "C4'" "C3'" SING N N 23 J0X "C3'" "O3'" SING N N 24 J0X "C1'" H1 SING N N 25 J0X "C2'" H2 SING N N 26 J0X "C2'" H3 SING N N 27 J0X "C3'" H4 SING N N 28 J0X "C4'" H5 SING N N 29 J0X C5 H6 SING N N 30 J0X "C5'" H7 SING N N 31 J0X "C5'" H8 SING N N 32 J0X C6 H9 SING N N 33 J0X C8 H10 SING N N 34 J0X C8 H11 SING N N 35 J0X N4 H12 SING N N 36 J0X "O3'" H13 SING N N 37 J0X O9 H14 SING N N 38 J0X OP2 H16 SING N N 39 J0X P OP3 SING N N 40 J0X OP3 H15 SING 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 J0X InChI InChI 1.03 "InChI=1S/C11H16N3O9P/c15-6-3-9(23-7(6)5-22-24(19,20)21)14-2-1-8(13-11(14)18)12-4-10(16)17/h1-2,6-7,9,15H,3-5H2,(H,16,17)(H,12,13,18)(H2,19,20,21)/t6-,7+,9+/m0/s1" J0X InChIKey InChI 1.03 QYPVHBKFTXARRD-LKEWCRSYSA-N J0X SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=NC2=O)NCC(O)=O" J0X SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=NC2=O)NCC(O)=O" J0X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)NCC(=O)O)COP(=O)(O)O)O" J0X SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(OC1N2C=CC(=NC2=O)NCC(=O)O)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id J0X _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-[[2-oxidanylidene-1-[(2~{R},4~{S},5~{R})-4-oxidanyl-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidin-4-yl]amino]ethanoic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site J0X "Create component" 2021-03-17 PDBJ J0X "Initial release" 2022-03-09 RCSB ##