data_T0P # _chem_comp.id T0P _chem_comp.name "[(2~{R},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-7-phenacyl-1~{H}-purin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C18 H20 F N5 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-03-16 _chem_comp.pdbx_modified_date 2022-02-04 _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 484.352 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _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 7LCD _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 T0P N N1 N 0 1 Y N N -56.958 -5.307 -19.390 ? ? ? N T0P 1 T0P CA C1 C 0 1 N N N -55.618 -5.342 -18.744 ? ? ? CA T0P 2 T0P C C2 C 0 1 N N N -54.474 -5.163 -19.747 ? ? ? C T0P 3 T0P O O1 O 0 1 N N N -54.652 -4.968 -20.955 ? ? ? O T0P 4 T0P CAA C3 C 0 1 Y N N -57.535 -4.327 -20.096 ? ? ? CAA T0P 5 T0P CAB C4 C 0 1 Y N N -58.755 -4.763 -20.455 ? ? ? CAB T0P 6 T0P CAD C5 C 0 1 N N N -59.212 -2.779 -21.574 ? ? ? CAD T0P 7 T0P CAF C6 C 0 1 N N N -57.122 -3.104 -20.465 ? ? ? CAF T0P 8 T0P CAH C7 C 0 1 Y N N -57.819 -6.323 -19.306 ? ? ? CAH T0P 9 T0P CAK C8 C 0 1 N N R -60.137 -6.875 -20.124 ? ? ? CAK T0P 10 T0P CAN C9 C 0 1 N N R -61.651 -8.011 -21.365 ? ? ? CAN T0P 11 T0P CAO C10 C 0 1 N N R -62.307 -7.490 -20.081 ? ? ? CAO T0P 12 T0P CAP C11 C 0 1 N N S -61.471 -6.264 -19.787 ? ? ? CAP T0P 13 T0P CAS C12 C 0 1 N N N -62.586 -7.837 -22.563 ? ? ? CAS T0P 14 T0P CAW C13 C 0 1 Y N N -53.200 -5.238 -19.197 ? ? ? CAW T0P 15 T0P CAY C14 C 0 1 Y N N -53.017 -5.769 -17.924 ? ? ? CAY T0P 16 T0P CAZ C15 C 0 1 Y N N -51.729 -5.847 -17.385 ? ? ? CAZ T0P 17 T0P CBA C16 C 0 1 Y N N -50.626 -5.394 -18.101 ? ? ? CBA T0P 18 T0P CBB C17 C 0 1 Y N N -50.824 -4.862 -19.374 ? ? ? CBB T0P 19 T0P CBC C18 C 0 1 Y N N -52.104 -4.785 -19.923 ? ? ? CBC T0P 20 T0P FAQ F1 F 0 1 N N N -61.705 -5.284 -20.709 ? ? ? FAQ T0P 21 T0P NAC N2 N 0 1 N N N -59.581 -4.000 -21.183 ? ? ? NAC T0P 22 T0P NAE N3 N 0 1 N N N -57.960 -2.296 -21.223 ? ? ? NAE T0P 23 T0P NAI N4 N 0 1 Y N N -58.932 -5.987 -19.964 ? ? ? NAI T0P 24 T0P NAL N5 N 0 1 N N N -60.042 -2.034 -22.297 ? ? ? NAL T0P 25 T0P OAJ O2 O 0 1 N N N -56.020 -2.656 -20.160 ? ? ? OAJ T0P 26 T0P OAM O3 O 0 1 N N N -60.427 -7.211 -21.494 ? ? ? OAM T0P 27 T0P OAR O4 O 0 1 N N N -62.050 -8.444 -19.076 ? ? ? OAR T0P 28 T0P OAT O5 O 0 1 N N N -62.854 -6.439 -22.721 ? ? ? OAT T0P 29 T0P OBE O6 O 0 1 N N N -63.845 -4.437 -23.900 ? ? ? OBE T0P 30 T0P OBF O7 O 0 1 N N N -65.379 -6.251 -22.918 ? ? ? OBF T0P 31 T0P PBD P1 P 0 1 N N N -64.113 -5.871 -23.604 ? ? ? PBD T0P 32 T0P O1 O8 O 0 1 N Y N -64.141 -6.303 -25.109 ? ? ? O1 T0P 33 T0P H1 H1 H 0 1 N N N -55.496 -6.312 -18.240 ? ? ? H1 T0P 34 T0P H2 H2 H 0 1 N N N -55.564 -4.533 -18.001 ? ? ? H2 T0P 35 T0P H3 H3 H 0 1 N N N -57.646 -7.258 -18.793 ? ? ? H3 T0P 36 T0P H4 H4 H 0 1 N N N -59.996 -7.790 -19.530 ? ? ? H4 T0P 37 T0P H5 H5 H 0 1 N N N -61.402 -9.076 -21.244 ? ? ? H5 T0P 38 T0P H6 H6 H 0 1 N N N -63.372 -7.253 -20.222 ? ? ? H6 T0P 39 T0P H7 H7 H 0 1 N N N -61.540 -5.946 -18.736 ? ? ? H7 T0P 40 T0P H8 H8 H 0 1 N N N -63.526 -8.379 -22.383 ? ? ? H8 T0P 41 T0P H9 H9 H 0 1 N N N -62.105 -8.229 -23.471 ? ? ? H9 T0P 42 T0P H10 H10 H 0 1 N N N -53.866 -6.119 -17.355 ? ? ? H10 T0P 43 T0P H11 H11 H 0 1 N N N -51.589 -6.265 -16.399 ? ? ? H11 T0P 44 T0P H12 H12 H 0 1 N N N -49.634 -5.453 -17.678 ? ? ? H12 T0P 45 T0P H13 H13 H 0 1 N N N -49.977 -4.505 -19.942 ? ? ? H13 T0P 46 T0P H14 H14 H 0 1 N N N -52.244 -4.374 -20.912 ? ? ? H14 T0P 47 T0P H15 H15 H 0 1 N N N -57.666 -1.384 -21.510 ? ? ? H15 T0P 48 T0P H16 H16 H 0 1 N N N -60.943 -2.389 -22.548 ? ? ? H16 T0P 49 T0P H17 H17 H 0 1 N N N -59.766 -1.119 -22.590 ? ? ? H17 T0P 50 T0P H18 H18 H 0 1 N N N -62.442 -8.158 -18.259 ? ? ? H18 T0P 51 T0P H19 H19 H 0 1 N N N -65.892 -5.471 -22.744 ? ? ? H19 T0P 52 T0P H20 H20 H 0 1 N N N -63.986 -5.544 -25.660 ? ? ? H20 T0P 53 # # 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 T0P OBE PBD DOUB N N 1 T0P PBD OBF SING N N 2 T0P PBD OAT SING N N 3 T0P OAT CAS SING N N 4 T0P CAS CAN SING N N 5 T0P NAL CAD SING N N 6 T0P CAD NAE SING N N 7 T0P CAD NAC DOUB N N 8 T0P OAM CAN SING N N 9 T0P OAM CAK SING N N 10 T0P CAN CAO SING N N 11 T0P NAE CAF SING N N 12 T0P NAC CAB SING N N 13 T0P O C DOUB N N 14 T0P FAQ CAP SING N N 15 T0P CAF OAJ DOUB N N 16 T0P CAF CAA SING N N 17 T0P CAB CAA DOUB Y N 18 T0P CAB NAI SING Y N 19 T0P CAK NAI SING N N 20 T0P CAK CAP SING N N 21 T0P CAA N SING Y N 22 T0P CAO CAP SING N N 23 T0P CAO OAR SING N N 24 T0P NAI CAH DOUB Y N 25 T0P CBC CBB DOUB Y N 26 T0P CBC CAW SING Y N 27 T0P C CAW SING N N 28 T0P C CA SING N N 29 T0P N CAH SING Y N 30 T0P N CA SING N N 31 T0P CBB CBA SING Y N 32 T0P CAW CAY DOUB Y N 33 T0P CBA CAZ DOUB Y N 34 T0P CAY CAZ SING Y N 35 T0P PBD O1 SING N N 36 T0P CA H1 SING N N 37 T0P CA H2 SING N N 38 T0P CAH H3 SING N N 39 T0P CAK H4 SING N N 40 T0P CAN H5 SING N N 41 T0P CAO H6 SING N N 42 T0P CAP H7 SING N N 43 T0P CAS H8 SING N N 44 T0P CAS H9 SING N N 45 T0P CAY H10 SING N N 46 T0P CAZ H11 SING N N 47 T0P CBA H12 SING N N 48 T0P CBB H13 SING N N 49 T0P CBC H14 SING N N 50 T0P NAE H15 SING N N 51 T0P NAL H16 SING N N 52 T0P NAL H17 SING N N 53 T0P OAR H18 SING N N 54 T0P OBF H19 SING N N 55 T0P O1 H20 SING N N 56 # # 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 T0P InChI InChI 1.03 "InChI=1S/C18H20FN5O8P/c19-12-14(26)11(7-31-33(28,29)30)32-17(12)24-8-23(6-10(25)9-4-2-1-3-5-9)13-15(24)21-18(20)22-16(13)27/h1-5,8,11-12,14,17,26H,6-7H2,(H2,28,29,30)(H3,20,21,22,27)/t11-,12+,14-,17-/m1/s1" T0P InChIKey InChI 1.03 RRUAIQFWCYLDFU-DMVWFOPNSA-N T0P SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2c(n(CC(=O)c3ccccc3)c[n]2[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]4F)C(=O)N1" T0P SMILES CACTVS 3.385 "NC1=Nc2c(n(CC(=O)c3ccccc3)c[n]2[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4F)C(=O)N1" T0P SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C(=O)CN2C=[N](C3=C2C(=O)NC(=N3)N)[C@H]4[C@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)F" T0P SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C(=O)CN2C=[N](C3=C2C(=O)NC(=N3)N)C4C(C(C(O4)COP(=O)(O)O)O)F" # _pdbx_chem_comp_identifier.comp_id T0P _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~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-7-phenacyl-1~{H}-purin-9-yl)-4-fluoranyl-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 T0P "Create component" 2020-03-16 RCSB T0P "Modify model coordinates code" 2021-12-08 RCSB T0P "Initial release" 2022-02-09 RCSB ##