data_EXC # _chem_comp.id EXC _chem_comp.name ;3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-7,7,9,9-tetramethyl-7,8,9,11-tetrahydropyrimido[4',5' :5,6][1,4]oxazino[2,3-f]isoindol-2(3H)-one radical ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C21 H26 N4 O9 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms "nitroxide spin-labeled nucleotide C-spin" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-10-19 _chem_comp.pdbx_modified_date 2020-06-17 _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 509.426 _chem_comp.one_letter_code ? _chem_comp.three_letter_code EXC _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 Y _chem_comp.pdbx_model_coordinates_db_code 3OT0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 EXC P P P 0 1 N N N -0.153 -7.754 16.419 ? ? ? P EXC 1 EXC C1 C1 C 0 1 N N N -2.100 -5.974 10.714 ? ? ? C1 EXC 2 EXC N2 N2 N 0 1 N N N -1.503 -6.616 9.687 ? ? ? N2 EXC 3 EXC C3 C3 C 0 1 N N N -0.713 -7.690 9.932 ? ? ? C3 EXC 4 EXC N4 N4 N 0 1 N N N -0.500 -8.116 11.194 ? ? ? N4 EXC 5 EXC C5 C5 C 0 1 N N N -1.084 -7.521 12.243 ? ? ? C5 EXC 6 EXC C6 C6 C 0 1 N N N -1.895 -6.417 12.019 ? ? ? C6 EXC 7 EXC N7 N7 N 0 1 N N N -2.899 -4.908 10.469 ? ? ? N7 EXC 8 EXC C8 C8 C 0 1 Y N N -3.510 -4.260 11.505 ? ? ? C8 EXC 9 EXC C9 C9 C 0 1 Y N N -3.318 -4.701 12.818 ? ? ? C9 EXC 10 EXC "C1'" C1* C 0 1 N N R 0.326 -9.298 11.432 ? ? ? C1* EXC 11 EXC O10 O10 O 0 1 N N N -2.495 -5.775 13.075 ? ? ? O10 EXC 12 EXC C11 C11 C 0 1 Y N N -3.937 -4.051 13.887 ? ? ? C11 EXC 13 EXC C12 C12 C 0 1 Y N N -4.740 -2.954 13.614 ? ? ? C12 EXC 14 EXC C13 C13 C 0 1 Y N N -4.943 -2.519 12.331 ? ? ? C13 EXC 15 EXC C14 C14 C 0 1 Y N N -4.334 -3.153 11.251 ? ? ? C14 EXC 16 EXC C15 C15 C 0 1 N N N -5.857 -1.325 12.297 ? ? ? C15 EXC 17 EXC N16 N16 N 0 1 N N N -6.285 -1.294 13.700 ? ? ? N16 EXC 18 EXC C17 C17 C 0 1 N N N -5.511 -2.136 14.610 ? ? ? C17 EXC 19 EXC O18 O18 O 0 1 N N N -0.151 -8.273 8.967 ? ? ? O18 EXC 20 EXC C19 C19 C 0 1 N N N -5.066 -0.083 11.897 ? ? ? C19 EXC 21 EXC "C2'" C2* C 0 1 N N N 1.803 -8.988 11.487 ? ? ? C2* EXC 22 EXC C20 C20 C 0 1 N N N -7.027 -1.560 11.349 ? ? ? C20 EXC 23 EXC O21 O21 O 0 1 N N N -7.237 -0.634 14.089 ? ? ? O21 EXC 24 EXC C22 C22 C 0 1 N N N -4.586 -1.350 15.535 ? ? ? C22 EXC 25 EXC C23 C23 C 0 1 N N N -6.429 -3.064 15.398 ? ? ? C23 EXC 26 EXC "C3'" C3* C 0 1 N N S 2.124 -9.144 12.956 ? ? ? C3* EXC 27 EXC "O3'" O3* O 0 1 N N N 3.417 -9.708 13.111 ? ? ? O3* EXC 28 EXC "C4'" C4* C 0 1 N N R 1.082 -10.099 13.508 ? ? ? C4* EXC 29 EXC "O4'" O4* O 0 1 N N N -0.068 -9.876 12.687 ? ? ? O4* EXC 30 EXC "C5'" C5* C 0 1 N N N 0.767 -9.783 14.966 ? ? ? C5* EXC 31 EXC "O5'" O5* O 0 1 N N N 0.350 -8.419 15.041 ? ? ? O5* EXC 32 EXC OP1 OP1 O 0 1 N N N 0.822 -8.172 17.499 ? ? ? OP1 EXC 33 EXC OP2 OP2 O 0 1 N N N -0.429 -6.301 16.123 ? ? ? OP2 EXC 34 EXC OP3 OP3 O 0 1 N Y N -1.553 -8.485 16.708 ? ? ? OP3 EXC 35 EXC H5 H5 H 0 1 N N N -0.927 -7.894 13.244 ? ? ? H5 EXC 36 EXC "H1'" H1* H 0 1 N N N 0.170 -9.988 10.590 ? ? ? H1* EXC 37 EXC H11 H11 H 0 1 N N N -3.794 -4.394 14.901 ? ? ? H11 EXC 38 EXC H14 H14 H 0 1 N N N -4.492 -2.801 10.242 ? ? ? H14 EXC 39 EXC H19 H19 H 0 1 N N N -5.737 0.788 11.873 ? ? ? H19 EXC 40 EXC H19A H19A H 0 0 N N N -4.264 0.092 12.629 ? ? ? H19A EXC 41 EXC H19B H19B H 0 0 N N N -4.626 -0.234 10.900 ? ? ? H19B EXC 42 EXC "H2'" H2* H 0 1 N N N 2.389 -9.682 10.866 ? ? ? H2* EXC 43 EXC "H2'A" H2*A H 0 0 N N N 2.020 -7.971 11.128 ? ? ? H2*A EXC 44 EXC H20 H20 H 0 1 N N N -7.678 -0.674 11.343 ? ? ? H20 EXC 45 EXC H20A H20A H 0 0 N N N -6.645 -1.741 10.333 ? ? ? H20A EXC 46 EXC H20B H20B H 0 0 N N N -7.602 -2.435 11.686 ? ? ? H20B EXC 47 EXC H22 H22 H 0 1 N N N -5.188 -0.766 16.247 ? ? ? H22 EXC 48 EXC H22A H22A H 0 0 N N N -3.940 -2.048 16.088 ? ? ? H22A EXC 49 EXC H22B H22B H 0 0 N N N -3.963 -0.669 14.937 ? ? ? H22B EXC 50 EXC H23 H23 H 0 1 N N N -7.001 -2.478 16.132 ? ? ? H23 EXC 51 EXC H23A H23A H 0 0 N N N -7.124 -3.565 14.708 ? ? ? H23A EXC 52 EXC H23B H23B H 0 0 N N N -5.825 -3.819 15.922 ? ? ? H23B EXC 53 EXC "H3'" H3* H 0 1 N N N 2.111 -8.176 13.479 ? ? ? H3* EXC 54 EXC "HO3'" HO3* H 0 0 N N N 3.613 -9.803 14.036 ? ? ? HO3* EXC 55 EXC "H4'" H4* H 0 1 N N N 1.423 -11.145 13.488 ? ? ? H4* EXC 56 EXC "H5'" H5* H 0 1 N N N -0.036 -10.442 15.328 ? ? ? H5* EXC 57 EXC "H5'A" H5*A H 0 0 N N N 1.663 -9.937 15.586 ? ? ? H5*A EXC 58 EXC HOP1 HOP1 H 0 0 N N N 1.189 -7.399 17.912 ? ? ? HOP1 EXC 59 EXC HOP3 HOP3 H 0 0 N Y N -2.261 -7.856 16.633 ? ? ? HOP3 EXC 60 EXC H26 H26 H 0 1 N N N -3.042 -4.595 9.530 ? ? ? H26 EXC 61 # # 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 EXC P OP3 SING N N 1 EXC P OP1 SING N N 2 EXC C1 C6 SING N N 3 EXC N2 C1 DOUB N N 4 EXC N2 C3 SING N N 5 EXC C3 N4 SING N N 6 EXC N4 "C1'" SING N N 7 EXC N4 C5 SING N N 8 EXC C5 H5 SING N N 9 EXC C6 C5 DOUB N N 10 EXC C6 O10 SING N N 11 EXC N7 C1 SING N N 12 EXC N7 C8 SING N N 13 EXC C8 C9 SING Y N 14 EXC C9 O10 SING N N 15 EXC C9 C11 DOUB Y N 16 EXC "C1'" "C2'" SING N N 17 EXC "C1'" "O4'" SING N N 18 EXC "C1'" "H1'" SING N N 19 EXC C11 H11 SING N N 20 EXC C12 C11 SING Y N 21 EXC C12 C17 SING N N 22 EXC C13 C12 DOUB Y N 23 EXC C14 C8 DOUB Y N 24 EXC C14 C13 SING Y N 25 EXC C14 H14 SING N N 26 EXC C15 C13 SING N N 27 EXC C15 N16 SING N N 28 EXC N16 O21 SING N N 29 EXC N16 C17 SING N N 30 EXC C17 C23 SING N N 31 EXC C17 C22 SING N N 32 EXC O18 C3 DOUB N N 33 EXC C19 C15 SING N N 34 EXC C19 H19 SING N N 35 EXC C19 H19A SING N N 36 EXC C19 H19B SING N N 37 EXC "C2'" "C3'" SING N N 38 EXC "C2'" "H2'" SING N N 39 EXC "C2'" "H2'A" SING N N 40 EXC C20 C15 SING N N 41 EXC C20 H20 SING N N 42 EXC C20 H20A SING N N 43 EXC C20 H20B SING N N 44 EXC C22 H22 SING N N 45 EXC C22 H22A SING N N 46 EXC C22 H22B SING N N 47 EXC C23 H23 SING N N 48 EXC C23 H23A SING N N 49 EXC C23 H23B SING N N 50 EXC "C3'" "O3'" SING N N 51 EXC "C3'" "C4'" SING N N 52 EXC "C3'" "H3'" SING N N 53 EXC "O3'" "HO3'" SING N N 54 EXC "C4'" "C5'" SING N N 55 EXC "C4'" "H4'" SING N N 56 EXC "O4'" "C4'" SING N N 57 EXC "C5'" "O5'" SING N N 58 EXC "C5'" "H5'" SING N N 59 EXC "C5'" "H5'A" SING N N 60 EXC "O5'" P SING N N 61 EXC OP1 HOP1 SING N N 62 EXC OP2 P DOUB N N 63 EXC OP3 HOP3 SING N N 64 EXC N7 H26 SING N N 65 # # 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 EXC SMILES ACDLabs 12.01 "O=P(O)(O)OCC5OC(N4C(=O)N=C2C(Oc1cc3c(cc1N2)C(N(O)C3(C)C)(C)C)=C4)CC5O" EXC SMILES_CANONICAL CACTVS 3.370 "CC1(C)N([O])C(C)(C)c2cc3OC4=CN([C@H]5C[C@H](O)[C@@H](CO[P](O)(O)=O)O5)C(=O)N=C4Nc3cc12" EXC SMILES CACTVS 3.370 "CC1(C)N([O])C(C)(C)c2cc3OC4=CN([CH]5C[CH](O)[CH](CO[P](O)(O)=O)O5)C(=O)N=C4Nc3cc12" EXC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1(c2cc3c(cc2C(N1[O])(C)C)OC4=CN(C(=O)N=C4N3)[C@H]5C[C@@H]([C@H](O5)COP(=O)(O)O)O)C" EXC SMILES "OpenEye OEToolkits" 1.7.0 "CC1(c2cc3c(cc2C(N1[O])(C)C)OC4=CN(C(=O)N=C4N3)C5CC(C(O5)COP(=O)(O)O)O)C" EXC InChI InChI 1.03 "InChI=1S/C21H27N4O9P/c1-20(2)10-5-12-14(6-11(10)21(3,4)25(20)28)33-15-8-24(19(27)23-18(15)22-12)17-7-13(26)16(34-17)9-32-35(29,30)31/h5-6,8,13,16-17,26,28H,7,9H2,1-4H3,(H,22,23,27)(H2,29,30,31)/t13-,16+,17+/m0/s1" EXC InChIKey InChI 1.03 LNDMWSVZTMCXNG-IAOVAPTHSA-N # _pdbx_chem_comp_identifier.comp_id EXC _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program ACDLabs _pdbx_chem_comp_identifier.program_version 12.01 _pdbx_chem_comp_identifier.identifier "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-7,7,9,9-tetramethyl-7,8,9,11-tetrahydropyrimido[4',5':5,6][1,4]oxazino[2,3-f]isoindol-2(3H)-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site EXC "Create component" 2010-10-19 RCSB EXC "Modify aromatic_flag" 2011-06-04 RCSB EXC "Modify descriptor" 2011-06-04 RCSB EXC "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id EXC _pdbx_chem_comp_synonyms.name "nitroxide spin-labeled nucleotide C-spin" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##