data_DPB # _chem_comp.id DPB _chem_comp.name "(S)-1-[2'-DEOXY-3',5'-O-(1-PHOSPHONO)BENZYLIDENE-B-D-THREO-PENTOFURANOSYL]THYMINE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C17 H19 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms DPB-T _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-09-17 _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 410.315 _chem_comp.one_letter_code T _chem_comp.three_letter_code DPB _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _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 DPB C11 C11 C 0 1 Y N N 15.733 41.697 23.918 0.652 -2.395 -0.497 C11 DPB 1 DPB C12 C12 C 0 1 Y N N 14.414 41.924 23.702 -0.204 -1.350 -0.792 C12 DPB 2 DPB C7 C7 C 0 1 Y N N 13.729 41.019 22.771 -1.104 -0.905 0.158 C7 DPB 3 DPB C8 C8 C 0 1 Y N N 14.409 39.916 22.108 -1.155 -1.511 1.400 C8 DPB 4 DPB C9 C9 C 0 1 Y N N 15.786 39.737 22.379 -0.302 -2.558 1.693 C9 DPB 5 DPB C10 C10 C 0 1 Y N N 16.548 40.577 23.271 0.602 -3.000 0.745 C10 DPB 6 DPB C2 C2 C 0 1 N N N 9.461 38.614 27.114 2.916 0.361 1.291 C2 DPB 7 DPB N1 N1 N 0 1 N N N 10.051 39.745 26.573 2.338 1.136 0.356 N1 DPB 8 DPB C6 C6 C 0 1 N N N 11.265 40.341 27.035 2.546 0.895 -0.975 C6 DPB 9 DPB C5 C5 C 0 1 N N N 11.830 39.655 28.127 3.340 -0.130 -1.352 C5 DPB 10 DPB C4 C4 C 0 1 N N N 11.177 38.464 28.670 3.938 -0.940 -0.358 C4 DPB 11 DPB N3 N3 N 0 1 N N N 10.065 38.000 28.166 3.711 -0.667 0.943 N3 DPB 12 DPB O2 O2 O 0 1 N N N 8.406 38.104 26.714 2.716 0.593 2.468 O2 DPB 13 DPB O4 O4 O 0 1 N N N 11.722 37.888 29.657 4.658 -1.870 -0.674 O4 DPB 14 DPB C5M C5M C 0 1 N N N 13.228 40.277 28.736 3.582 -0.411 -2.813 C5M DPB 15 DPB "C1'" C1* C 0 1 N N S 9.339 40.366 25.454 1.476 2.249 0.765 "C1'" DPB 16 DPB "O4'" O4* O 0 1 N N N 9.493 41.773 25.032 0.942 2.918 -0.380 "O4'" DPB 17 DPB "C4'" C4* C 0 1 N N S 9.617 41.576 23.574 -0.437 2.546 -0.564 "C4'" DPB 18 DPB "C3'" C3* C 0 1 N N S 9.586 40.535 22.994 -0.955 2.152 0.824 "C3'" DPB 19 DPB "C2'" C2* C 0 1 N N N 9.465 39.760 24.179 0.297 1.723 1.605 "C2'" DPB 20 DPB "C5'" C5* C 0 1 N N N 10.673 42.506 23.730 -0.481 1.343 -1.509 "C5'" DPB 21 DPB "O5'" O5* O 0 1 N N N 11.750 41.700 23.743 -1.760 0.738 -1.461 "O5'" DPB 22 DPB "C6'" C6* C 0 1 N N S 12.217 41.233 22.459 -2.035 0.237 -0.161 "C6'" DPB 23 DPB "O3'" O3* O 0 1 N N N 10.913 40.290 22.395 -1.982 1.216 0.844 "O3'" DPB 24 DPB P P P 0 1 N N N 12.126 42.651 21.108 -3.740 -0.452 -0.188 P DPB 25 DPB OP2 O2P O 0 1 N N N 12.776 41.746 19.977 -4.776 0.699 -0.629 OP2 DPB 26 DPB OP1 O1P O 0 1 N N N 13.051 43.751 21.404 -4.095 -0.943 1.163 OP1 DPB 27 DPB OP3 O3P O 0 1 N Y N 10.688 42.990 20.726 -3.811 -1.670 -1.237 OP3 DPB 28 DPB H11 H11 H 0 1 N N N 16.148 42.432 24.628 1.358 -2.739 -1.238 H11 DPB 29 DPB H12 H12 H 0 1 N N N 13.942 42.767 24.234 -0.165 -0.877 -1.762 H12 DPB 30 DPB H8 H8 H 0 1 N N N 13.892 39.231 21.415 -1.861 -1.166 2.141 H8 DPB 31 DPB H9 H9 H 0 1 N N N 16.291 38.900 21.869 -0.341 -3.031 2.663 H9 DPB 32 DPB H10 H10 H 0 1 N N N 17.622 40.386 23.438 1.269 -3.818 0.974 H10 DPB 33 DPB H6 H6 H 0 1 N N N 11.721 41.242 26.592 2.079 1.522 -1.720 H6 DPB 34 DPB H3 H3 H 0 1 N N N 9.670 37.162 28.592 4.120 -1.216 1.631 H3 DPB 35 DPB H71 1H5M H 0 1 N N N 13.078 41.349 29.002 4.455 0.147 -3.151 H71 DPB 36 DPB H72 2H5M H 0 1 N N N 13.675 39.734 29.601 3.756 -1.478 -2.954 H72 DPB 37 DPB H73 3H5M H 0 1 N N N 13.983 40.374 27.921 2.709 -0.106 -3.391 H73 DPB 38 DPB "H1'" H1* H 0 1 N N N 8.399 40.226 26.037 2.063 2.953 1.364 "H1'" DPB 39 DPB "H4'" H4* H 0 1 N N N 8.817 41.680 22.805 -1.020 3.383 -0.983 "H4'" DPB 40 DPB "H3'" H3* H 0 1 N N N 8.838 40.391 22.180 -1.339 3.079 1.309 "H3'" DPB 41 DPB "H2'" 1H2* H 0 1 N N N 8.606 39.062 24.045 0.353 0.644 1.721 "H2'" DPB 42 DPB "H2''" 2H2* H 0 0 N N N 10.330 39.057 24.218 0.302 2.195 2.594 "H2''" DPB 43 DPB "H5'" 1H5* H 0 1 N N N 10.580 43.186 24.609 0.315 0.648 -1.275 "H5'" DPB 44 DPB "H5''" 2H5* H 0 0 N N N 10.701 43.322 22.971 -0.308 1.709 -2.533 "H5''" DPB 45 DPB HOP2 2HOP H 0 0 N N N 12.732 42.433 19.322 -4.510 0.990 -1.512 HOP2 DPB 46 DPB HOP3 3HOP H 0 0 N N N 10.644 43.677 20.071 -4.719 -2.001 -1.220 HOP3 DPB 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 DPB C11 C12 DOUB Y N 1 DPB C11 C10 SING Y N 2 DPB C11 H11 SING N N 3 DPB C12 C7 SING Y N 4 DPB C12 H12 SING N N 5 DPB C7 C8 DOUB Y N 6 DPB C7 "C6'" SING N N 7 DPB C8 C9 SING Y N 8 DPB C8 H8 SING N N 9 DPB C9 C10 DOUB Y N 10 DPB C9 H9 SING N N 11 DPB C10 H10 SING N N 12 DPB C2 N1 SING N N 13 DPB C2 N3 SING N N 14 DPB C2 O2 DOUB N N 15 DPB N1 C6 SING N N 16 DPB N1 "C1'" SING N N 17 DPB C6 C5 DOUB N N 18 DPB C6 H6 SING N N 19 DPB C5 C4 SING N N 20 DPB C5 C5M SING N N 21 DPB C4 N3 SING N N 22 DPB C4 O4 DOUB N N 23 DPB N3 H3 SING N N 24 DPB C5M H71 SING N N 25 DPB C5M H72 SING N N 26 DPB C5M H73 SING N N 27 DPB "C1'" "O4'" SING N N 28 DPB "C1'" "C2'" SING N N 29 DPB "C1'" "H1'" SING N N 30 DPB "O4'" "C4'" SING N N 31 DPB "C4'" "C3'" SING N N 32 DPB "C4'" "C5'" SING N N 33 DPB "C4'" "H4'" SING N N 34 DPB "C3'" "C2'" SING N N 35 DPB "C3'" "O3'" SING N N 36 DPB "C3'" "H3'" SING N N 37 DPB "C2'" "H2'" SING N N 38 DPB "C2'" "H2''" SING N N 39 DPB "C5'" "O5'" SING N N 40 DPB "C5'" "H5'" SING N N 41 DPB "C5'" "H5''" SING N N 42 DPB "O5'" "C6'" SING N N 43 DPB "C6'" "O3'" SING N N 44 DPB "C6'" P SING N N 45 DPB P OP2 SING N N 46 DPB P OP1 DOUB N N 47 DPB P OP3 SING N N 48 DPB OP2 HOP2 SING N N 49 DPB OP3 HOP3 SING N N 50 # # 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 DPB SMILES ACDLabs 10.04 "O=C1C(=CN(C(=O)N1)C4OC2C(OC(OC2)(c3ccccc3)P(=O)(O)O)C4)C" DPB SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2C[C@@H]3O[C@@](OC[C@@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O" DPB SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O" DPB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]3[C@@H](O2)CO[C@](O3)(c4ccccc4)P(=O)(O)O" DPB SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC3C(O2)COC(O3)(c4ccccc4)P(=O)(O)O" DPB InChI InChI 1.03 "InChI=1S/C17H19N2O8P/c1-10-8-19(16(21)18-15(10)20)14-7-12-13(26-14)9-25-17(27-12,28(22,23)24)11-5-3-2-4-6-11/h2-6,8,12-14H,7,9H2,1H3,(H,18,20,21)(H2,22,23,24)/t12-,13-,14-,17-/m0/s1" DPB InChIKey InChI 1.03 WTZFKHNHHRPQOU-WSMBLCCSSA-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 DPB "SYSTEMATIC NAME" ACDLabs 10.04 "1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-L-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione" DPB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,4aS,6S,7aS)-6-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2-phenyl-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DPB "Create component" 2003-09-17 RCSB DPB "Modify descriptor" 2011-06-04 RCSB DPB "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id DPB _pdbx_chem_comp_synonyms.name DPB-T _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##