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 #