data_8H2
# 
_chem_comp.id                                    8H2 
_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                     2023-03-28 
_chem_comp.pdbx_modified_date                    2025-12-15 
_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                     8H2 
_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        8ILH 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
8H2 P     P1  P  0 1 N N S N N N 20.640 23.281 76.710 -4.575 0.414  0.598  P     8H2 1  
8H2 OP2   O1  O  0 1 N N N N N N 19.094 22.962 76.683 -4.869 0.035  2.135  OP2   8H2 2  
8H2 "O5'" O2  O  0 1 N N N N N N 21.591 22.139 76.078 -3.073 0.988  0.677  "O5'" 8H2 3  
8H2 "C5'" C1  C  0 1 N N N N N N 22.934 22.193 76.117 -2.362 1.468  -0.466 "C5'" 8H2 4  
8H2 "C4'" C2  C  0 1 N N R N N N 23.352 20.846 75.583 -0.970 1.939  -0.041 "C4'" 8H2 5  
8H2 "C3'" C3  C  0 1 N N S N N N 22.530 20.336 74.400 -0.179 2.478  -1.261 "C3'" 8H2 6  
8H2 "O3'" O3  O  0 1 N N N N N N 22.750 21.047 73.166 -0.469 3.859  -1.486 "O3'" 8H2 7  
8H2 "C2'" C4  C  0 1 N N N N N N 22.841 18.852 74.461 1.288  2.288  -0.805 "C2'" 8H2 8  
8H2 "C1'" C5  C  0 1 N N R N N N 22.792 18.601 75.971 1.205  1.221  0.303  "C1'" 8H2 9  
8H2 "O4'" O4  O  0 1 N N N N N N 23.169 19.828 76.600 -0.172 0.824  0.411  "O4'" 8H2 10 
8H2 N9    N1  N  0 1 Y N N N N N 21.447 18.247 76.422 2.031  0.065  -0.054 N9    8H2 11 
8H2 C4    C6  C  0 1 Y N N N N N 20.991 16.980 76.696 3.373  -0.073 0.177  C4    8H2 12 
8H2 C5    C7  C  0 1 Y N N N N N 19.655 17.132 77.005 3.726  -1.328 -0.332 C5    8H2 13 
8H2 N7    N2  N  0 1 Y N N N N N 19.275 18.462 76.908 2.602  -1.888 -0.841 N7    8H2 14 
8H2 C8    C8  C  0 1 Y N N N N N 20.364 19.084 76.546 1.602  -1.072 -0.674 C8    8H2 15 
8H2 N3    N3  N  0 1 N N N N N N 21.729 15.849 76.679 4.306  0.700  0.743  N3    8H2 16 
8H2 C2    C9  C  0 1 N N N N N N 21.010 14.784 77.000 5.556  0.301  0.832  C2    8H2 17 
8H2 N2    N4  N  0 1 N N N N N N 21.585 13.571 77.018 6.478  1.128  1.422  N2    8H2 18 
8H2 N1    N5  N  0 1 N N N N N N 19.674 14.830 77.321 5.961  -0.910 0.356  N1    8H2 19 
8H2 C6    C10 C  0 1 N N N N N N 18.896 15.984 77.344 5.074  -1.745 -0.229 C6    8H2 20 
8H2 O6    O5  O  0 1 N N N N N N 17.695 15.913 77.635 5.427  -2.830 -0.658 O6    8H2 21 
8H2 SE1   SE1 SE 0 0 N N N N N N 21.191 24.881 75.908 -4.250 -1.628 -0.338 SE1   8H2 22 
8H2 H1    H1  H  0 1 N N N N N N 18.934 22.132 77.116 -5.749 -0.336 2.287  H1    8H2 23 
8H2 H2    H2  H  0 1 N N N N N N 23.293 22.337 77.147 -2.266 0.666  -1.198 H2    8H2 24 
8H2 H3    H3  H  0 1 N N N N N N 23.314 23.005 75.479 -2.907 2.301  -0.910 H3    8H2 25 
8H2 H4    H4  H  0 1 N N N N N N 24.410 20.890 75.286 -1.044 2.698  0.737  H4    8H2 26 
8H2 H5    H5  H  0 1 N N N N N N 21.471 20.453 74.674 -0.389 1.887  -2.152 H5    8H2 27 
8H2 H6    H6  H  0 1 N N N N N N 22.513 21.960 73.279 0.067  4.264  -2.181 H6    8H2 28 
8H2 H7    H7  H  0 1 N N N N N N 22.083 18.259 73.929 1.901  1.931  -1.633 H7    8H2 29 
8H2 H8    H8  H  0 1 N N N N N N 23.836 18.631 74.048 1.688  3.221  -0.408 H8    8H2 30 
8H2 H9    H9  H  0 1 N N N N N N 23.501 17.800 76.228 1.547  1.642  1.249  H9    8H2 31 
8H2 H10   H10 H  0 1 N N N N N N 20.409 20.147 76.363 0.585  -1.266 -0.982 H10   8H2 32 
8H2 H11   H11 H  0 1 N N N N N N 22.554 13.473 76.789 6.205  1.993  1.766  H11   8H2 33 
8H2 H12   H12 H  0 1 N N N N N N 21.045 12.765 77.260 7.404  0.848  1.495  H12   8H2 34 
8H2 H13   H13 H  0 1 N N N N N N 19.226 13.967 77.556 6.891  -1.173 0.438  H13   8H2 35 
8H2 H14   H14 H  0 1 N N N N N N 20.384 25.985 76.418 -5.714 -2.162 -0.403 H14   8H2 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 
8H2 "O3'" "C3'" SING N N 1  
8H2 "C3'" "C2'" SING N N 2  
8H2 "C3'" "C4'" SING N N 3  
8H2 "C2'" "C1'" SING N N 4  
8H2 "C4'" "C5'" SING N N 5  
8H2 "C4'" "O4'" SING N N 6  
8H2 SE1   P     SING N N 7  
8H2 "C1'" N9    SING N N 8  
8H2 "C1'" "O4'" SING N N 9  
8H2 "O5'" "C5'" SING N N 10 
8H2 "O5'" P     SING N N 11 
8H2 N9    C8    SING Y N 12 
8H2 N9    C4    SING Y N 13 
8H2 C8    N7    DOUB Y N 14 
8H2 N3    C4    SING N N 15 
8H2 N3    C2    DOUB N N 16 
8H2 OP2   P     SING N N 17 
8H2 C4    C5    DOUB Y N 18 
8H2 N7    C5    SING Y N 19 
8H2 C2    N2    SING N N 20 
8H2 C2    N1    SING N N 21 
8H2 C5    C6    SING N N 22 
8H2 N1    C6    SING N N 23 
8H2 C6    O6    DOUB N N 24 
8H2 OP2   H1    SING N N 25 
8H2 "C5'" H2    SING N N 26 
8H2 "C5'" H3    SING N N 27 
8H2 "C4'" H4    SING N N 28 
8H2 "C3'" H5    SING N N 29 
8H2 "O3'" H6    SING N N 30 
8H2 "C2'" H7    SING N N 31 
8H2 "C2'" H8    SING N N 32 
8H2 "C1'" H9    SING N N 33 
8H2 C8    H10   SING N N 34 
8H2 N2    H11   SING N N 35 
8H2 N2    H12   SING N N 36 
8H2 N1    H13   SING N N 37 
8H2 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 
8H2 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" 
8H2 InChIKey         InChI                1.06  VRWXFLMARXKZIY-LPPWAWCDSA-N                                                                                                                         
8H2 SMILES_CANONICAL CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)[SeH])O3"                                                                                      
8H2 SMILES           CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)[SeH])O3"                                                                                           
8H2 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"                                                                                      
8H2 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           8H2 
_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 
8H2 "Create component"   2023-03-28 PDBC 
8H2 "Initial release"    2024-01-10 RCSB 
8H2 "Obsolete component" 2024-01-11 PDBC 
8H2 "Modify formula"     2025-12-15 PDBE 
# 
