data_94O # _chem_comp.id 94O _chem_comp.name "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-2H-indeno[2',1':5,6]pyrido[2,3-d]pyrimidine-2,6(3H)-dione" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C19 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-12-14 _chem_comp.pdbx_modified_date 2018-11-16 _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 445.319 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 94O _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 5YTG _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 94O P P1 P 0 1 N N N -44.177 14.383 9.457 6.360 -1.757 -0.460 P 94O 1 94O OP2 O1 O 0 1 N N N -44.428 12.928 9.753 6.575 -2.533 -1.854 OP2 94O 2 94O OP1 O2 O 0 1 N N N -45.354 15.167 8.957 7.644 -1.167 -0.020 OP1 94O 3 94O "O5'" O3 O 0 1 N N N -43.531 15.000 10.785 5.272 -0.587 -0.658 "O5'" 94O 4 94O "C5'" C1 C 0 1 N N N -43.351 16.380 10.770 4.938 0.348 0.369 "C5'" 94O 5 94O "C4'" C2 C 0 1 N N R -42.532 16.912 11.923 3.876 1.319 -0.150 "C4'" 94O 6 94O "O4'" O4 O 0 1 N N N -41.493 17.702 11.318 2.614 0.637 -0.324 "O4'" 94O 7 94O "C1'" C3 C 0 1 N N R -41.509 19.055 11.797 1.615 1.680 -0.321 "C1'" 94O 8 94O N1 N1 N 0 1 N N N -41.914 19.981 10.723 0.298 1.123 -0.001 N1 94O 9 94O C2 C4 C 0 1 N N N -41.196 21.205 10.546 0.149 0.391 1.113 C2 94O 10 94O O2 O5 O 0 1 N N N -40.285 21.551 11.317 1.123 0.212 1.827 O2 94O 11 94O N3 N2 N 0 1 N N N -41.462 22.049 9.531 -1.010 -0.148 1.475 N3 94O 12 94O C4 C5 C 0 1 N N N -42.428 21.783 8.634 -2.099 0.023 0.723 C4 94O 13 94O N23 N3 N 0 1 N N N -42.693 22.666 7.620 -3.274 -0.512 1.063 N23 94O 14 94O C22 C6 C 0 1 N N N -43.688 22.357 6.742 -4.351 -0.349 0.319 C22 94O 15 94O C26 C7 C 0 1 Y N N -44.182 23.122 5.560 -5.745 -0.837 0.484 C26 94O 16 94O C27 C8 C 0 1 Y N N -43.752 24.341 5.032 -6.337 -1.613 1.473 C27 94O 17 94O C28 C9 C 0 1 Y N N -44.403 24.858 3.903 -7.682 -1.934 1.391 C28 94O 18 94O C29 C10 C 0 1 Y N N -45.450 24.153 3.278 -8.443 -1.486 0.328 C29 94O 19 94O C30 C11 C 0 1 Y N N -45.900 22.910 3.764 -7.869 -0.711 -0.665 C30 94O 20 94O C25 C12 C 0 1 Y N N -45.286 22.385 4.898 -6.519 -0.381 -0.596 C25 94O 21 94O C24 C13 C 0 1 N N N -45.422 21.149 5.728 -5.655 0.418 -1.499 C24 94O 22 94O C21 C14 C 0 1 N N N -44.460 21.093 6.870 -4.299 0.431 -0.916 C21 94O 23 94O C20 C15 C 0 1 N N N -44.212 20.187 7.886 -3.111 1.011 -1.321 C20 94O 24 94O C5 C16 C 0 1 N N N -43.200 20.504 8.789 -1.977 0.820 -0.507 C5 94O 25 94O C6 C17 C 0 1 N N N -42.892 19.653 9.846 -0.736 1.362 -0.827 C6 94O 26 94O O31 O6 O 0 1 N N N -46.276 20.222 5.502 -6.001 0.961 -2.530 O31 94O 27 94O "C2'" C18 C 0 1 N N N -42.371 19.014 13.011 2.069 2.658 0.784 "C2'" 94O 28 94O "C3'" C19 C 0 1 N N S -43.343 17.867 12.806 3.590 2.416 0.899 "C3'" 94O 29 94O "O3'" O7 O 0 1 N N N -43.965 17.295 13.991 4.313 3.608 0.587 "O3'" 94O 30 94O H1 H1 H 0 1 N N N -45.336 12.719 9.569 7.219 -3.253 -1.808 H1 94O 31 94O H3 H3 H 0 1 N N N -42.843 16.651 9.833 4.550 -0.187 1.235 H3 94O 32 94O H4 H4 H 0 1 N N N -44.342 16.857 10.802 5.830 0.905 0.656 H4 94O 33 94O H5 H5 H 0 1 N N N -42.122 16.087 12.524 4.199 1.767 -1.089 H5 94O 34 94O H6 H6 H 0 1 N N N -40.491 19.326 12.115 1.590 2.184 -1.287 H6 94O 35 94O H9 H9 H 0 1 N N N -42.931 24.877 5.486 -5.747 -1.967 2.306 H9 94O 36 94O H10 H10 H 0 1 N N N -44.096 25.814 3.505 -8.138 -2.537 2.162 H10 94O 37 94O H11 H11 H 0 1 N N N -45.920 24.577 2.403 -9.491 -1.742 0.272 H11 94O 38 94O H12 H12 H 0 1 N N N -46.700 22.378 3.270 -8.468 -0.364 -1.494 H12 94O 39 94O H13 H13 H 0 1 N N N -44.779 19.272 7.975 -3.053 1.590 -2.230 H13 94O 40 94O H14 H14 H 0 1 N N N -43.435 18.727 9.967 -0.605 1.954 -1.722 H14 94O 41 94O H17 H17 H 0 1 N N N -41.758 18.838 13.907 1.868 3.688 0.489 H17 94O 42 94O H18 H18 H 0 1 N N N -42.918 19.962 13.121 1.571 2.428 1.726 H18 94O 43 94O H19 H19 H 0 1 N N N -44.153 18.257 12.172 3.846 2.064 1.899 H19 94O 44 94O H20 H20 H 0 1 N Y N -44.438 17.973 14.459 4.170 4.330 1.214 H20 94O 45 94O OP3 OP3 O 0 1 N Y N -42.998 14.483 8.419 5.836 -2.793 0.656 OP3 94O 46 94O H2 H2 H 0 1 N N N -43.268 15.020 7.683 4.997 -3.219 0.434 H2 94O 47 # 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 94O C29 C30 DOUB Y N 1 94O C29 C28 SING Y N 2 94O C30 C25 SING Y N 3 94O C28 C27 DOUB Y N 4 94O C25 C26 DOUB Y N 5 94O C25 C24 SING N N 6 94O C27 C26 SING Y N 7 94O O31 C24 DOUB N N 8 94O C26 C22 SING N N 9 94O C24 C21 SING N N 10 94O C22 C21 SING N N 11 94O C22 N23 DOUB N N 12 94O C21 C20 DOUB N N 13 94O N23 C4 SING N N 14 94O C20 C5 SING N N 15 94O C4 C5 SING N N 16 94O C4 N3 DOUB N N 17 94O C5 C6 DOUB N N 18 94O OP1 P DOUB N N 19 94O P OP2 SING N N 20 94O P "O5'" SING N N 21 94O N3 C2 SING N N 22 94O C6 N1 SING N N 23 94O C2 N1 SING N N 24 94O C2 O2 DOUB N N 25 94O N1 "C1'" SING N N 26 94O "C5'" "O5'" SING N N 27 94O "C5'" "C4'" SING N N 28 94O "O4'" "C1'" SING N N 29 94O "O4'" "C4'" SING N N 30 94O "C1'" "C2'" SING N N 31 94O "C4'" "C3'" SING N N 32 94O "C3'" "C2'" SING N N 33 94O "C3'" "O3'" SING N N 34 94O OP2 H1 SING N N 35 94O "C5'" H3 SING N N 36 94O "C5'" H4 SING N N 37 94O "C4'" H5 SING N N 38 94O "C1'" H6 SING N N 39 94O C27 H9 SING N N 40 94O C28 H10 SING N N 41 94O C29 H11 SING N N 42 94O C30 H12 SING N N 43 94O C20 H13 SING N N 44 94O C6 H14 SING N N 45 94O "C2'" H17 SING N N 46 94O "C2'" H18 SING N N 47 94O "C3'" H19 SING N N 48 94O "O3'" H20 SING N N 49 94O P OP3 SING N N 50 94O OP3 H2 SING N N 51 # 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 94O SMILES ACDLabs 12.01 "P(O)(OCC1C(CC(O1)N5C(=O)N=C2C(C=C4C(=N2)c3ccccc3C4=O)=C5)O)(O)=O" 94O InChI InChI 1.03 "InChI=1S/C19H16N3O8P/c23-13-6-15(30-14(13)8-29-31(26,27)28)22-7-9-5-12-16(20-18(9)21-19(22)25)10-3-1-2-4-11(10)17(12)24/h1-5,7,13-15,23H,6,8H2,(H2,26,27,28)/t13-,14+,15+/m0/s1" 94O InChIKey InChI 1.03 WDLPMEJMNGIHMS-RRFJBIMHSA-N 94O SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C3C=C4C(=O)c5ccccc5C4=NC3=NC2=O" 94O SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C3C=C4C(=O)c5ccccc5C4=NC3=NC2=O" 94O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)C3=NC4=NC(=O)N(C=C4C=C3C2=O)[C@H]5C[C@@H]([C@H](O5)COP(=O)(O)O)O" 94O SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)C3=NC4=NC(=O)N(C=C4C=C3C2=O)C5CC(C(O5)COP(=O)(O)O)O" # 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 94O "SYSTEMATIC NAME" ACDLabs 12.01 "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-2H-indeno[2',1':5,6]pyrido[2,3-d]pyrimidine-2,6(3H)-dione" 94O "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[6,17-bis(oxidanylidene)-5,7,9-triazatetracyclo[8.7.0.0^{3,8}.0^{11,16}]heptadeca-1,3,7,9,11(16),12,14-heptaen-5-yl]-3-oxidanyl-oxolan-2-yl]methyl 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 94O "Create component" 2017-12-14 PDBJ 94O "Initial release" 2018-11-21 RCSB #