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 
# 
