data_7S8
# 
_chem_comp.id                                    7S8 
_chem_comp.name                                  "[(2R,3S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphinous acid" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H14 N5 O5 P Se" 
_chem_comp.mon_nstd_parent_comp_id               DG 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-03-09 
_chem_comp.pdbx_modified_date                    2024-01-11 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   OBS 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        394.182 
_chem_comp.one_letter_code                       G 
_chem_comp.three_letter_code                     7S8 
_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        8ILI 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
# 
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 
7S8 P     P1  P  0 1 N N R N N N 20.649 23.504 77.257 -4.073 -1.387 0.048  P     7S8 1  
7S8 OP1   O1  O  0 1 N N N N N N 21.321 24.668 76.622 -4.319 -2.122 1.459  OP1   7S8 2  
7S8 "O5'" O2  O  0 1 N N N N N N 21.468 22.234 76.772 -2.747 -0.525 0.346  "O5'" 7S8 3  
7S8 "C5'" C1  C  0 1 N N N N N N 22.897 22.255 76.635 -2.125 0.311  -0.632 "C5'" 7S8 4  
7S8 "C4'" C2  C  0 1 N N R N N N 23.375 20.930 76.088 -0.893 0.982  -0.022 "C4'" 7S8 5  
7S8 "C3'" C3  C  0 1 N N S N N N 22.667 20.445 74.824 -0.206 1.907  -1.058 "C3'" 7S8 6  
7S8 "O3'" O3  O  0 1 N N N N N N 23.221 20.998 73.626 -0.796 3.209  -1.050 "O3'" 7S8 7  
7S8 "C2'" C4  C  0 1 N N N N N N 22.884 18.948 74.899 1.249  1.958  -0.532 "C2'" 7S8 8  
7S8 "C1'" C5  C  0 1 N N R N N N 22.788 18.679 76.400 1.375  0.703  0.354  "C1'" 7S8 9  
7S8 "O4'" O4  O  0 1 N N N N N N 23.144 19.888 77.064 0.122  0.002  0.281  "O4'" 7S8 10 
7S8 N9    N1  N  0 1 Y N N N N N 21.435 18.315 76.806 2.455  -0.152 -0.143 N9    7S8 11 
7S8 C4    C6  C  0 1 Y N N N N N 20.983 17.043 77.055 3.784  -0.037 0.163  C4    7S8 12 
7S8 C5    C7  C  0 1 Y N N N N N 19.642 17.181 77.345 4.433  -1.061 -0.536 C5    7S8 13 
7S8 N7    N2  N  0 1 Y N N N N N 19.253 18.510 77.257 3.484  -1.742 -1.225 N7    7S8 14 
7S8 C8    C8  C  0 1 Y N N N N N 20.343 19.144 76.922 2.319  -1.213 -0.990 C8    7S8 15 
7S8 N3    N3  N  0 1 N N N N N N 21.732 15.920 77.044 4.496  0.795  0.931  N3    7S8 16 
7S8 C2    C9  C  0 1 N N N N N N 21.018 14.846 77.341 5.799  0.669  1.043  C2    7S8 17 
7S8 N2    N4  N  0 1 N N N N N N 21.608 13.641 77.366 6.487  1.547  1.843  N2    7S8 18 
7S8 N1    N5  N  0 1 N N N N N N 19.674 14.875 77.626 6.488  -0.307 0.387  N1    7S8 19 
7S8 C6    C10 C  0 1 N N N N N N 18.887 16.023 77.655 5.836  -1.186 -0.407 C6    7S8 20 
7S8 O6    O5  O  0 1 N N N N N N 17.687 15.941 77.938 6.443  -2.063 -0.998 O6    7S8 21 
7S8 SE1   SE1 SE 0 0 N N N N N N 18.818 23.147 76.861 -5.686 0.210  0.061  SE1   7S8 22 
7S8 H1    H1  H  0 1 N N N N N N 20.875 25.468 76.874 -5.095 -2.700 1.472  H1    7S8 23 
7S8 H2    H2  H  0 1 N N N N N N 23.356 22.432 77.619 -1.824 -0.293 -1.488 H2    7S8 24 
7S8 H3    H3  H  0 1 N N N N N N 23.187 23.061 75.945 -2.831 1.075  -0.958 H3    7S8 25 
7S8 H4    H4  H  0 1 N N N N N N 24.452 21.004 75.877 -1.166 1.541  0.874  H4    7S8 26 
7S8 H5    H5  H  0 1 N N N N N N 21.592 20.667 74.897 -0.244 1.470  -2.055 H5    7S8 27 
7S8 H6    H6  H  0 1 N N N N N N 23.069 21.936 73.609 -0.344 3.849  -1.616 H6    7S8 28 
7S8 H7    H7  H  0 1 N N N N N N 22.104 18.404 74.346 1.956  1.911  -1.361 H7    7S8 29 
7S8 H8    H8  H  0 1 N N N N N N 23.873 18.669 74.507 1.411  2.860  0.058  H8    7S8 30 
7S8 H9    H9  H  0 1 N N N N N N 23.489 17.874 76.665 1.578  0.996  1.384  H9    7S8 31 
7S8 H10   H10 H  0 1 N N N N N N 20.384 20.210 76.753 1.385  -1.560 -1.407 H10   7S8 32 
7S8 H11   H11 H  0 1 N N N N N N 22.583 13.557 77.161 6.011  2.247  2.316  H11   7S8 33 
7S8 H12   H12 H  0 1 N N N N N N 21.073 12.827 77.590 7.450  1.467  1.936  H12   7S8 34 
7S8 H13   H13 H  0 1 N N N N N N 19.227 14.004 77.828 7.450  -0.373 0.491  H13   7S8 35 
7S8 H14   H14 H  0 1 N N N N N N 18.382 21.964 77.597 -6.957 -0.647 -0.229 H14   7S8 36 
# 
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 
7S8 "O3'" "C3'" SING N N 1  
7S8 "C3'" "C2'" SING N N 2  
7S8 "C3'" "C4'" SING N N 3  
7S8 "C2'" "C1'" SING N N 4  
7S8 "C4'" "C5'" SING N N 5  
7S8 "C4'" "O4'" SING N N 6  
7S8 "C1'" N9    SING N N 7  
7S8 "C1'" "O4'" SING N N 8  
7S8 OP1   P     SING N N 9  
7S8 "C5'" "O5'" SING N N 10 
7S8 "O5'" P     SING N N 11 
7S8 N9    C8    SING Y N 12 
7S8 N9    C4    SING Y N 13 
7S8 SE1   P     SING N N 14 
7S8 C8    N7    DOUB Y N 15 
7S8 N3    C4    SING N N 16 
7S8 N3    C2    DOUB N N 17 
7S8 C4    C5    DOUB Y N 18 
7S8 N7    C5    SING Y N 19 
7S8 C2    N2    SING N N 20 
7S8 C2    N1    SING N N 21 
7S8 C5    C6    SING N N 22 
7S8 N1    C6    SING N N 23 
7S8 C6    O6    DOUB N N 24 
7S8 OP1   H1    SING N N 25 
7S8 "C5'" H2    SING N N 26 
7S8 "C5'" H3    SING N N 27 
7S8 "C4'" H4    SING N N 28 
7S8 "C3'" H5    SING N N 29 
7S8 "O3'" H6    SING N N 30 
7S8 "C2'" H7    SING N N 31 
7S8 "C2'" H8    SING N N 32 
7S8 "C1'" H9    SING N N 33 
7S8 C8    H10   SING N N 34 
7S8 N2    H11   SING N N 35 
7S8 N2    H12   SING N N 36 
7S8 N1    H13   SING N N 37 
7S8 SE1   H14   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 
7S8 InChI            InChI                1.06  "InChI=1S/C10H14N5O5PSe/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(20-6)2-19-21(18)22/h3-6,16,18,22H,1-2H2,(H3,11,13,14,17)/t4-,5+,6+,21+/m0/s1" 
7S8 InChIKey         InChI                1.06  VRWXFLMARXKZIY-HIJHWTOVSA-N                                                                                                                         
7S8 SMILES_CANONICAL CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)[SeH])O3"                                                                                     
7S8 SMILES           CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)[SeH])O3"                                                                                           
7S8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](O)[SeH])O)N=C(NC2=O)N"                                                                                     
7S8 SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3CC(C(O3)COP(O)[SeH])O)N=C(NC2=O)N"                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           7S8 
_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-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphinous 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 
7S8 "Create component"   2023-03-09 PDBC 
7S8 "Initial release"    2024-01-10 RCSB 
7S8 "Obsolete component" 2024-01-11 PDBC 
# 
