data_8DD # _chem_comp.id 8DD _chem_comp.name "8-oxo-7,8-dihydro-2'-deoxy-adenosine-5'-diphosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N5 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-01-09 _chem_comp.pdbx_modified_date 2011-06-04 _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 427.201 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8DD _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 3ACA _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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.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 8DD N1 N1 N 0 1 Y N N -18.632 23.299 78.850 -6.313 2.128 0.971 N1 8DD 1 8DD C2 C2 C 0 1 Y N N -18.188 22.260 78.133 -5.670 1.567 1.977 C2 8DD 2 8DD N3 N3 N 0 1 Y N N -18.876 21.237 77.632 -4.641 0.765 1.794 N3 8DD 3 8DD C4 C4 C 0 1 Y N N -20.180 21.343 77.932 -4.207 0.488 0.569 C4 8DD 4 8DD C5 C5 C 0 1 Y N N -20.784 22.350 78.656 -4.859 1.061 -0.525 C5 8DD 5 8DD C6 C6 C 0 1 Y N N -19.949 23.379 79.134 -5.944 1.903 -0.288 C6 8DD 6 8DD N6 N6 N 0 1 N N N -20.395 24.416 79.849 -6.624 2.496 -1.342 N6 8DD 7 8DD N7 N7 N 0 1 N N N -22.145 22.122 78.761 -4.207 0.607 -1.668 N7 8DD 8 8DD C8 C8 C 0 1 N N N -22.341 20.998 78.109 -3.203 -0.205 -1.282 C8 8DD 9 8DD O8 O8 O 0 1 N N N -23.439 20.485 77.993 -2.431 -0.772 -2.033 O8 8DD 10 8DD N9 N9 N 0 1 N N N -21.187 20.474 77.581 -3.183 -0.291 0.062 N9 8DD 11 8DD PA PA P 0 1 N N N -23.458 18.048 71.949 3.503 -0.586 -0.299 PA 8DD 12 8DD PB PB P 0 1 N N N -25.959 17.956 73.477 5.371 1.651 0.248 PB 8DD 13 8DD "C1'" "C1'" C 0 1 N N R -20.985 19.240 76.793 -2.236 -1.079 0.854 "C1'" 8DD 14 8DD O1A O1A O 0 1 N N N -23.075 16.661 72.306 3.333 -0.149 -1.702 O1A 8DD 15 8DD O1B O1B O 0 1 N N N -25.762 16.626 74.311 5.955 2.217 1.637 O1B 8DD 16 8DD "C2'" "C2'" C 0 1 N N N -22.192 18.331 76.638 -2.436 -2.580 0.569 "C2'" 8DD 17 8DD O2A O2A O 0 1 N N N -23.903 18.326 70.552 4.438 -1.895 -0.254 O2A 8DD 18 8DD O2B O2B O 0 1 N N N -26.777 17.929 72.293 6.453 0.979 -0.505 O2B 8DD 19 8DD "C3'" "C3'" C 0 1 N N S -21.921 17.643 75.305 -1.057 -3.055 0.049 "C3'" 8DD 20 8DD "O3'" "O3'" O 0 1 N N N -20.996 16.576 75.483 -0.720 -4.334 0.589 "O3'" 8DD 21 8DD O3A O3A O 0 1 N N N -24.577 18.585 73.007 4.193 0.595 0.551 O3A 8DD 22 8DD O3B O3B O 0 1 N N N -26.507 18.991 74.366 4.787 2.870 -0.626 O3B 8DD 23 8DD "C4'" "C4'" C 0 1 N N R -21.249 18.751 74.505 -0.109 -1.957 0.596 "C4'" 8DD 24 8DD "O4'" "O4'" O 0 1 N N N -20.597 19.599 75.476 -0.889 -0.748 0.477 "O4'" 8DD 25 8DD "C5'" "C5'" C 0 1 N N N -22.222 19.571 73.688 1.159 -1.866 -0.257 "C5'" 8DD 26 8DD "O5'" "O5'" O 0 1 N N N -22.294 19.053 72.348 2.064 -0.932 0.334 "O5'" 8DD 27 8DD H2 H2 H 0 1 N N N -17.127 22.250 77.934 -5.999 1.772 2.985 H2 8DD 28 8DD HN6 HN6 H 0 1 N N N -19.629 25.016 80.080 -7.378 3.080 -1.166 HN6 8DD 29 8DD HN6A HN6A H 0 0 N N N -21.068 24.926 79.313 -6.346 2.325 -2.256 HN6A 8DD 30 8DD HN7 HN7 H 0 1 N N N -22.826 22.686 79.228 -4.435 0.836 -2.583 HN7 8DD 31 8DD "H1'" "H1'" H 0 1 N N N -20.230 18.678 77.363 -2.385 -0.881 1.915 "H1'" 8DD 32 8DD HO1B HO1B H 0 0 N N N -26.243 15.919 73.898 6.669 2.860 1.530 HO1B 8DD 33 8DD "H2'" "H2'" H 0 1 N N N -22.268 17.608 77.463 -2.701 -3.111 1.484 "H2'" 8DD 34 8DD "H2'A" "H2'A" H 0 0 N N N -23.133 18.900 76.621 -3.201 -2.726 -0.193 "H2'A" 8DD 35 8DD HO2A HO2A H 0 0 N N N -23.879 17.522 70.046 4.593 -2.238 0.637 HO2A 8DD 36 8DD "H3'" "H3'" H 0 1 N N N -22.822 17.220 74.837 -1.039 -3.078 -1.041 "H3'" 8DD 37 8DD "HO3'" "HO3'" H 0 0 N N N -20.834 16.154 74.647 -1.339 -5.038 0.348 "HO3'" 8DD 38 8DD HO3B HO3B H 0 0 N N N -27.263 19.394 73.955 4.072 3.357 -0.193 HO3B 8DD 39 8DD "H4'" "H4'" H 0 1 N N N -20.550 18.308 73.780 0.142 -2.151 1.639 "H4'" 8DD 40 8DD "H5'" "H5'" H 0 1 N N N -23.218 19.522 74.151 1.632 -2.847 -0.310 "H5'" 8DD 41 8DD "H5'A" "H5'A" H 0 0 N N N -21.881 20.616 73.657 0.898 -1.534 -1.262 "H5'A" 8DD 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 8DD N1 C2 DOUB Y N 1 8DD N1 C6 SING Y N 2 8DD C2 N3 SING Y N 3 8DD N3 C4 DOUB Y N 4 8DD C4 C5 SING Y N 5 8DD C4 N9 SING N N 6 8DD C5 C6 DOUB Y N 7 8DD C5 N7 SING N N 8 8DD C6 N6 SING N N 9 8DD N7 C8 SING N N 10 8DD C8 O8 DOUB N N 11 8DD C8 N9 SING N N 12 8DD N9 "C1'" SING N N 13 8DD PA O1A DOUB N N 14 8DD PA O2A SING N N 15 8DD PA O3A SING N N 16 8DD PA "O5'" SING N N 17 8DD PB O1B SING N N 18 8DD PB O2B DOUB N N 19 8DD PB O3A SING N N 20 8DD PB O3B SING N N 21 8DD "C1'" "C2'" SING N N 22 8DD "C1'" "O4'" SING N N 23 8DD "C2'" "C3'" SING N N 24 8DD "C3'" "O3'" SING N N 25 8DD "C3'" "C4'" SING N N 26 8DD "C4'" "O4'" SING N N 27 8DD "C4'" "C5'" SING N N 28 8DD "C5'" "O5'" SING N N 29 8DD C2 H2 SING N N 30 8DD N6 HN6 SING N N 31 8DD N6 HN6A SING N N 32 8DD N7 HN7 SING N N 33 8DD "C1'" "H1'" SING N N 34 8DD O1B HO1B SING N N 35 8DD "C2'" "H2'" SING N N 36 8DD "C2'" "H2'A" SING N N 37 8DD O2A HO2A SING N N 38 8DD "C3'" "H3'" SING N N 39 8DD "O3'" "HO3'" SING N N 40 8DD O3B HO3B SING N N 41 8DD "C4'" "H4'" SING N N 42 8DD "C5'" "H5'" SING N N 43 8DD "C5'" "H5'A" 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 8DD SMILES_CANONICAL CACTVS 3.352 "Nc1ncnc2N([C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)Nc12" 8DD SMILES CACTVS 3.352 "Nc1ncnc2N([CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)Nc12" 8DD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)N(C(=O)N2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)N" 8DD SMILES "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)N(C(=O)N2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)O)O)N" 8DD InChI InChI 1.03 "InChI=1S/C10H15N5O10P2/c11-8-7-9(13-3-12-8)15(10(17)14-7)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,14,17)(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,5+,6+/m0/s1" 8DD InChIKey InChI 1.03 FEPFWQCDWZFLGY-KVQBGUIXSA-N # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier 8DD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl phosphono hydrogen 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 8DD "Create component" 2010-01-09 PDBJ 8DD "Modify aromatic_flag" 2011-06-04 RCSB 8DD "Modify descriptor" 2011-06-04 RCSB #