data_8EB
# 
_chem_comp.id                                    8EB 
_chem_comp.name                                  "[[(2R,3S,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphoryl] dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N5 O9 P2 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                    2024-01-05 
_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                        490.162 
_chem_comp.one_letter_code                       G 
_chem_comp.three_letter_code                     8EB 
_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 
# 
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 
8EB O3B   O1  O  0 1 N N N N N N 11.801 23.968 104.092 -5.159 2.478  -2.461 O3B   8EB 1  
8EB PB    P1  P  0 1 N N N N N N 10.405 23.358 103.582 -5.132 1.567  -1.134 PB    8EB 2  
8EB O1B   O2  O  0 1 N N N N N N 10.027 22.287 104.587 -5.247 2.508  0.167  O1B   8EB 3  
8EB O2B   O3  O  0 1 N N N N N N 9.452  24.521 103.409 -6.270 0.621  -1.161 O2B   8EB 4  
8EB O3A   O4  O  0 1 N N N N N N 10.800 22.662 102.154 -3.750 0.742  -1.078 O3A   8EB 5  
8EB PA    P2  P  0 1 N N R N N N 10.854 23.225 100.612 -3.270 -0.585 -0.302 PA    8EB 6  
8EB O1A   O5  O  0 1 N N N N N N 12.237 23.033 100.007 -4.121 -1.727 -0.704 O1A   8EB 7  
8EB "O5'" O6  O  0 1 N N N N N N 9.774  22.296 99.840  -1.736 -0.900 -0.677 "O5'" 8EB 8  
8EB "C5'" C1  C  0 1 N N N N N N 8.409  22.267 100.245 -0.925 -1.810 0.069  "C5'" 8EB 9  
8EB "C4'" C2  C  0 1 N N R N N N 7.966  20.863 100.606 0.471  -1.875 -0.554 "C4'" 8EB 10 
8EB "O4'" O7  O  0 1 N N N N N N 8.222  19.955 99.541  1.177  -0.634 -0.338 "O4'" 8EB 11 
8EB "C3'" C3  C  0 1 N N S N N N 8.671  20.261 101.813 1.328  -2.946 0.158  "C3'" 8EB 12 
8EB "O3'" O8  O  0 1 N N N N N N 8.144  20.690 103.073 1.333  -4.163 -0.591 "O3'" 8EB 13 
8EB "C2'" C4  C  0 1 N N N N N N 8.452  18.783 101.584 2.744  -2.329 0.196  "C2'" 8EB 14 
8EB "C1'" C5  C  0 1 N N R N N N 8.585  18.681 100.071 2.575  -0.959 -0.498 "C1'" 8EB 15 
8EB N9    N1  N  0 1 Y N N N N N 10.001 18.373 99.731  3.411  0.051  0.157  N9    8EB 16 
8EB C8    C6  C  0 1 Y N N N N N 11.013 19.252 99.609  3.032  0.874  1.177  C8    8EB 17 
8EB N7    N2  N  0 1 Y N N N N N 12.179 18.646 99.298  4.029  1.642  1.511  N7    8EB 18 
8EB C5    C7  C  0 1 Y N N N N N 11.911 17.336 99.244  5.093  1.353  0.727  C5    8EB 19 
8EB C6    C8  C  0 1 N N N N N N 12.693 16.128 98.976  6.464  1.865  0.626  C6    8EB 20 
8EB N1    N3  N  0 1 N N N N N N 12.058 14.948 99.007  7.281  1.333  -0.296 N1    8EB 21 
8EB C2    C9  C  0 1 N N N N N N 10.737 14.830 99.267  6.876  0.373  -1.098 C2    8EB 22 
8EB N2    N4  N  0 1 N N N N N N 10.155 13.602 99.277  7.754  -0.131 -2.019 N2    8EB 23 
8EB N3    N5  N  0 1 N N N N N N 9.958  15.916 99.530  5.618  -0.139 -1.048 N3    8EB 24 
8EB C4    C10 C  0 1 Y N N N N N 10.485 17.156 99.527  4.709  0.335  -0.137 C4    8EB 25 
8EB O6    O9  O  0 1 N N N N N N 13.914 16.227 98.725  6.852  2.756  1.364  O6    8EB 26 
8EB SEA   SE1 SE 0 0 N N N N N N 10.165 24.935 100.430 -3.450 -0.258 1.937  SEA   8EB 27 
8EB H1    H1  H  0 1 N N N N N N 11.724 24.911 104.172 -5.964 3.004  -2.560 H1    8EB 28 
8EB H2    H2  H  0 1 N N N N N N 9.196  22.510 104.990 -4.533 3.154  0.250  H2    8EB 29 
8EB H3    H3  H  0 1 N N N N N N 8.283  22.918 101.122 -0.847 -1.467 1.100  H3    8EB 30 
8EB H4    H4  H  0 1 N N N N N N 7.783  22.638 99.420  -1.378 -2.801 0.049  H4    8EB 31 
8EB H5    H5  H  0 1 N N N N N N 6.887  20.886 100.816 0.401  -2.093 -1.620 H5    8EB 32 
8EB H6    H6  H  0 1 N N N N N N 9.747  20.483 101.751 0.958  -3.121 1.168  H6    8EB 33 
8EB H7    H7  H  0 1 N N N N N N 8.630  20.277 103.777 1.856  -4.870 -0.189 H7    8EB 34 
8EB H8    H8  H  0 1 N N N N N N 7.453  18.469 101.921 3.076  -2.197 1.226  H8    8EB 35 
8EB H9    H9  H  0 1 N N N N N N 9.217  18.180 102.095 3.448  -2.953 -0.354 H9    8EB 36 
8EB H10   H10 H  0 1 N N N N N N 7.922  17.890 99.692  2.829  -1.035 -1.555 H10   8EB 37 
8EB H11   H11 H  0 1 N N N N N N 10.905 20.318 99.744  2.055  0.886  1.637  H11   8EB 38 
8EB H12   H12 H  0 1 N N N N N N 10.704 12.787 99.092  8.657  0.221  -2.071 H12   8EB 39 
8EB H13   H13 H  0 1 N N N N N N 9.178  13.513 99.469  7.475  -0.840 -2.620 H13   8EB 40 
8EB H14   H14 H  0 1 N N N N N N 8.986  15.792 99.727  5.362  -0.847 -1.659 H14   8EB 41 
8EB H15   H15 H  0 1 N N N N N N 11.051 25.890 101.089 -2.497 0.961  2.138  H15   8EB 42 
# 
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 
8EB O6    C6    DOUB N N 1  
8EB C6    N1    SING N N 2  
8EB C6    C5    SING N N 3  
8EB N1    C2    DOUB N N 4  
8EB C5    N7    SING Y N 5  
8EB C5    C4    DOUB Y N 6  
8EB C2    N2    SING N N 7  
8EB C2    N3    SING N N 8  
8EB N7    C8    DOUB Y N 9  
8EB C4    N3    SING N N 10 
8EB C4    N9    SING Y N 11 
8EB "O4'" "C1'" SING N N 12 
8EB "O4'" "C4'" SING N N 13 
8EB C8    N9    SING Y N 14 
8EB N9    "C1'" SING N N 15 
8EB "O5'" "C5'" SING N N 16 
8EB "O5'" PA    SING N N 17 
8EB O1A   PA    DOUB N N 18 
8EB "C1'" "C2'" SING N N 19 
8EB "C5'" "C4'" SING N N 20 
8EB SEA   PA    SING N N 21 
8EB "C4'" "C3'" SING N N 22 
8EB PA    O3A   SING N N 23 
8EB "C2'" "C3'" SING N N 24 
8EB "C3'" "O3'" SING N N 25 
8EB O3A   PB    SING N N 26 
8EB O2B   PB    DOUB N N 27 
8EB PB    O3B   SING N N 28 
8EB PB    O1B   SING N N 29 
8EB O3B   H1    SING N N 30 
8EB O1B   H2    SING N N 31 
8EB "C5'" H3    SING N N 32 
8EB "C5'" H4    SING N N 33 
8EB "C4'" H5    SING N N 34 
8EB "C3'" H6    SING N N 35 
8EB "O3'" H7    SING N N 36 
8EB "C2'" H8    SING N N 37 
8EB "C2'" H9    SING N N 38 
8EB "C1'" H10   SING N N 39 
8EB C8    H11   SING N N 40 
8EB N2    H12   SING N N 41 
8EB N2    H13   SING N N 42 
8EB N3    H14   SING N N 43 
8EB SEA   H15   SING N N 44 
# 
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 
8EB InChI            InChI                1.06  "InChI=1S/C10H15N5O9P2Se/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(23-6)2-22-26(21,27)24-25(18,19)20/h3-6,16H,1-2H2,(H,21,27)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+,26+/m0/s1" 
8EB InChIKey         InChI                1.06  XCFKPSIHHMJWLO-PDRQRWKTSA-N                                                                                                                                                         
8EB SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)c2ncn([C@H]3C[C@H](O)[C@@H](CO[P@]([SeH])(=O)O[P](O)(O)=O)O3)c2N1"                                                                                                       
8EB SMILES           CACTVS               3.385 "NC1=NC(=O)c2ncn([CH]3C[CH](O)[CH](CO[P]([SeH])(=O)O[P](O)(O)=O)O3)c2N1"                                                                                                            
8EB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(OP(=O)(O)O)[SeH])O)NC(=NC2=O)N"                                                                                                         
8EB SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3CC(C(O3)COP(=O)(OP(=O)(O)O)[SeH])O)NC(=NC2=O)N"                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           8EB 
_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-3~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphoryl] 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 
8EB "Create component" 2023-03-28 PDBC 
8EB "Initial release"  2024-01-10 RCSB 
# 
