data_KBC # _chem_comp.id KBC _chem_comp.name "[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-methoxy-3-oxidanyl-oxolan-2-yl]methyl 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 ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-09-14 _chem_comp.pdbx_modified_date 2025-04-11 _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 338.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KBC _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 8GPA _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm ? # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 KBC "C2'" C1 C 0 1 N N N N N N 13.363 -4.244 -9.732 1.332 -1.926 1.153 "C2'" KBC 1 KBC "C3'" C2 C 0 1 N N S N N N 13.287 -3.695 -10.910 -0.158 -2.348 1.144 "C3'" KBC 2 KBC C6 C3 C 0 1 N N N N N N 16.737 -2.771 -8.816 3.704 -0.546 -1.008 C6 KBC 3 KBC C5 C4 C 0 1 N N N N N N 17.771 -3.044 -7.854 4.727 0.335 -1.002 C5 KBC 4 KBC C4 C5 C 0 1 N N N N N N 17.435 -3.041 -6.461 4.635 1.491 -0.190 C4 KBC 5 KBC N1 N1 N 0 1 N N N N N N 15.376 -2.664 -8.434 2.601 -0.310 -0.234 N1 KBC 6 KBC "O4'" O1 O 0 1 N N N N N N 15.590 -4.208 -10.817 0.233 -0.585 -0.436 "O4'" KBC 7 KBC C01 C6 C 0 1 N N N N N N 15.234 -6.153 -11.786 -1.957 -1.522 -2.032 C01 KBC 8 KBC "C4'" C7 C 0 1 N N R N N N 14.645 -4.025 -11.702 -0.797 -1.454 0.064 "C4'" KBC 9 KBC "C5'" C8 C 0 1 N N N N N N 15.117 -2.933 -12.633 -1.925 -0.623 0.678 "C5'" KBC 10 KBC "C1'" C9 C 0 1 N N R N N N 14.827 -4.244 -9.418 1.491 -1.266 -0.240 "C1'" KBC 11 KBC C2 C10 C 0 1 N N N N N N 14.998 -2.639 -6.915 2.526 0.793 0.534 C2 KBC 12 KBC N3 N2 N 0 1 N N N N N N 16.113 -2.884 -5.972 3.531 1.688 0.559 N3 KBC 13 KBC O02 O2 O 0 1 N N N N N N 14.475 -5.209 -12.437 -1.308 -2.263 -0.997 O02 KBC 14 KBC "O5'" O3 O 0 1 N N N N N N 16.316 -3.531 -13.110 -2.409 0.311 -0.289 "O5'" KBC 15 KBC OP2 O4 O 0 1 N N N N N N 18.436 -3.556 -14.634 -4.791 0.610 0.491 OP2 KBC 16 KBC OP3 O5 O 0 1 N N N N N N 17.435 -1.265 -13.805 -3.128 2.392 1.148 OP3 KBC 17 KBC "O3'" O6 O 0 1 N N N N N N 12.151 -4.407 -11.541 -0.285 -3.728 0.794 "O3'" KBC 18 KBC O4 O7 O 0 1 N N N N N N 18.264 -3.255 -5.676 5.545 2.300 -0.167 O4 KBC 19 KBC O2 O8 O 0 1 N N N N N N 13.963 -2.491 -6.422 1.536 0.984 1.214 O2 KBC 20 KBC P P1 P 0 1 N N N N N N 17.217 -2.706 -14.230 -3.601 1.350 0.015 P KBC 21 KBC OP1 O9 O 0 1 N Y N N N N 16.229 -2.402 -15.411 -3.970 2.153 -1.331 OP1 KBC 22 KBC H1 H1 H 0 1 N N N N N N 12.805 -3.654 -8.990 1.527 -1.207 1.949 H1 KBC 23 KBC H2 H2 H 0 1 N N N N N N 12.969 -5.271 -9.754 1.982 -2.796 1.249 H2 KBC 24 KBC H3 H3 H 0 1 N N N N N N 13.121 -2.608 -10.897 -0.614 -2.159 2.115 H3 KBC 25 KBC H4 H4 H 0 1 N N N N N N 17.004 -2.644 -9.855 3.754 -1.432 -1.624 H4 KBC 26 KBC H5 H5 H 0 1 N N N N N N 18.782 -3.247 -8.176 5.603 0.160 -1.608 H5 KBC 27 KBC H6 H6 H 0 1 N N N N N N 15.150 -7.117 -12.310 -1.313 -0.702 -2.352 H6 KBC 28 KBC H7 H7 H 0 1 N N N N N N 16.286 -5.833 -11.775 -2.157 -2.178 -2.879 H7 KBC 29 KBC H8 H8 H 0 1 N N N N N N 14.873 -6.264 -10.753 -2.897 -1.119 -1.655 H8 KBC 30 KBC H9 H9 H 0 1 N N N N N N 15.313 -1.993 -12.096 -2.737 -1.283 0.984 H9 KBC 31 KBC H10 H10 H 0 1 N N N N N N 14.399 -2.748 -13.446 -1.548 -0.084 1.547 H10 KBC 32 KBC H11 H11 H 0 1 N N N N N N 15.131 -5.119 -8.824 1.641 -2.024 -1.009 H11 KBC 33 KBC H12 H12 H 0 1 N N N N N N 15.934 -2.939 -4.990 3.460 2.478 1.117 H12 KBC 34 KBC H13 H13 H 0 1 N N N N N N 18.361 -1.059 -13.846 -2.351 2.913 0.904 H13 KBC 35 KBC H14 H14 H 0 1 N N N N N N 11.351 -4.209 -11.069 0.151 -4.332 1.411 H14 KBC 36 KBC H15 H15 H 0 1 N N N N N N 16.554 -2.804 -16.208 -4.682 2.798 -1.221 H15 KBC 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 KBC OP2 P DOUB N N 1 KBC P OP3 SING N N 2 KBC P "O5'" SING N N 3 KBC "O5'" "C5'" SING N N 4 KBC "C5'" "C4'" SING N N 5 KBC O02 C01 SING N N 6 KBC O02 "C4'" SING N N 7 KBC "C4'" "C3'" SING N N 8 KBC "C4'" "O4'" SING N N 9 KBC "O3'" "C3'" SING N N 10 KBC "C3'" "C2'" SING N N 11 KBC "O4'" "C1'" SING N N 12 KBC "C2'" "C1'" SING N N 13 KBC C6 N1 SING N N 14 KBC C6 C5 DOUB N N 15 KBC N1 C2 SING N N 16 KBC C5 C4 SING N N 17 KBC C2 O2 DOUB N N 18 KBC C2 N3 SING N N 19 KBC C4 N3 SING N N 20 KBC C4 O4 DOUB N N 21 KBC "C1'" N1 SING N N 22 KBC P OP1 SING N N 23 KBC "C2'" H1 SING N N 24 KBC "C2'" H2 SING N N 25 KBC "C3'" H3 SING N N 26 KBC C6 H4 SING N N 27 KBC C5 H5 SING N N 28 KBC C01 H6 SING N N 29 KBC C01 H7 SING N N 30 KBC C01 H8 SING N N 31 KBC "C5'" H9 SING N N 32 KBC "C5'" H10 SING N N 33 KBC "C1'" H11 SING N N 34 KBC N3 H12 SING N N 35 KBC OP3 H13 SING N N 36 KBC "O3'" H14 SING N N 37 KBC OP1 H15 SING 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 KBC InChI InChI 1.06 "InChI=1S/C10H15N2O9P/c1-19-10(5-20-22(16,17)18)6(13)4-8(21-10)12-3-2-7(14)11-9(12)15/h2-3,6,8,13H,4-5H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,8+,10+/m0/s1" KBC InChIKey InChI 1.06 VHPFXSSAHQFLOL-SKWCMTHISA-N KBC SMILES_CANONICAL CACTVS 3.385 "CO[C@]1(CO[P](O)(O)=O)O[C@H](C[C@@H]1O)N2C=CC(=O)NC2=O" KBC SMILES CACTVS 3.385 "CO[C]1(CO[P](O)(O)=O)O[CH](C[CH]1O)N2C=CC(=O)NC2=O" KBC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@]1([C@H](C[C@@H](O1)N2C=CC(=O)NC2=O)O)COP(=O)(O)O" KBC SMILES "OpenEye OEToolkits" 2.0.7 "COC1(C(CC(O1)N2C=CC(=O)NC2=O)O)COP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id KBC _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~{S},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-methoxy-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 KBC "Create component" 2022-09-14 PDBJ KBC "Initial release" 2025-04-16 RCSB #