data_DL5 # _chem_comp.id DL5 _chem_comp.name "Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H19 N8 O18 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms TNP-AMPPCP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-06-03 _chem_comp.pdbx_modified_date 2021-03-01 _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 716.297 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DL5 _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 5A3R _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 DL5 N1 N1 N 0 1 Y N N 1.198 0.881 14.137 -4.009 5.920 0.414 N1 DL5 1 DL5 C2 C2 C 0 1 Y N N 2.497 1.233 13.845 -4.317 4.785 1.015 C2 DL5 2 DL5 N3 N3 N 0 1 Y N N 2.836 2.538 13.563 -3.601 3.691 0.869 N3 DL5 3 DL5 C4 C4 C 0 1 Y N N 1.923 3.602 13.547 -2.520 3.687 0.096 C4 DL5 4 DL5 C5 C5 C 0 1 Y N N 0.597 3.280 13.838 -2.149 4.870 -0.566 C5 DL5 5 DL5 C6 C6 C 0 1 Y N N 0.212 1.921 14.136 -2.946 6.012 -0.378 C6 DL5 6 DL5 N6 N6 N 0 1 N N N -1.078 1.640 14.418 -2.631 7.206 -1.004 N6 DL5 7 DL5 N7 N7 N 0 1 Y N N -0.172 4.373 13.791 -1.029 4.596 -1.276 N7 DL5 8 DL5 C8 C8 C 0 1 Y N N 0.650 5.328 13.483 -0.696 3.351 -1.097 C8 DL5 9 DL5 N9 N9 N 0 1 Y N N 1.946 4.952 13.312 -1.585 2.747 -0.259 N9 DL5 10 DL5 PA PA P 0 1 N N N -0.582 7.780 10.265 3.450 -1.465 -0.825 PA DL5 11 DL5 PB PB P 0 1 N N N -2.967 6.552 11.742 6.241 -0.732 -0.148 PB DL5 12 DL5 PG PG P 0 1 N N N -4.064 3.716 11.801 8.799 0.135 1.104 PG DL5 13 DL5 C01 C01 C 0 1 N N N -3.261 5.029 12.670 7.015 -0.114 1.382 C01 DL5 14 DL5 "C1'" "C1'" C 0 1 N N R 3.186 5.732 12.958 -1.549 1.351 0.184 "C1'" DL5 15 DL5 O1A O1A O 0 1 N N N 0.209 7.500 8.922 3.595 -0.905 -2.187 O1A DL5 16 DL5 O1B O1B O 0 1 N N N -2.660 7.591 12.659 6.920 -2.131 -0.565 O1B DL5 17 DL5 C1F C1F C 0 1 N N N 5.739 6.408 10.760 -3.870 -1.058 0.125 C1F DL5 18 DL5 O1G O1G O 0 1 N N N -5.010 4.211 10.608 8.996 1.122 0.018 O1G DL5 19 DL5 "C2'" "C2'" C 0 1 N N R 3.644 5.675 11.469 -2.368 0.455 -0.776 "C2'" DL5 20 DL5 "O2'" "O2'" O 0 1 N N N 5.018 5.200 11.391 -3.701 0.317 -0.262 "O2'" DL5 21 DL5 O2A O2A O 0 1 N N N -1.477 9.003 10.239 3.476 -3.073 -0.900 O2A DL5 22 DL5 O2B O2B O 0 1 N N N -4.171 6.853 11.116 6.438 0.255 -1.234 O2B DL5 23 DL5 C2F C2F C 0 1 N N N 6.428 5.805 9.489 -4.423 -1.839 -1.027 C2F DL5 24 DL5 N2F N2F N 1 1 N N N 5.711 5.183 8.387 -3.899 -1.561 -2.384 N2F DL5 25 DL5 O2F O2F O 0 1 N N N 6.246 4.718 7.428 -4.346 -0.631 -3.030 O2F DL5 26 DL5 O2G O2G O 0 1 N N N -5.016 3.032 12.889 9.483 0.681 2.455 O2G DL5 27 DL5 "C3'" "C3'" C 0 1 N N R 3.505 7.148 10.880 -1.695 -0.936 -0.583 "C3'" DL5 28 DL5 "O3'" "O3'" O 0 1 N N N 4.828 7.596 10.453 -2.522 -1.556 0.428 "O3'" DL5 29 DL5 O3A O3A O 0 1 N N N -1.613 6.593 10.689 4.666 -0.952 0.098 O3A DL5 30 DL5 C3F C3F C 0 1 N N N 7.837 5.818 9.341 -5.355 -2.766 -0.889 C3F DL5 31 DL5 O3F O3F O -1 1 N N N 4.493 5.092 8.368 -3.022 -2.264 -2.854 O3F DL5 32 DL5 O3G O3G O 0 1 N N N -3.176 2.713 11.236 9.478 -1.264 0.687 O3G DL5 33 DL5 "C4'" "C4'" C 0 1 N N R 2.990 8.050 11.892 -0.324 -0.607 0.038 "C4'" DL5 34 DL5 "O4'" "O4'" O 0 1 N N N 2.865 7.088 13.010 -0.209 0.824 0.089 "O4'" DL5 35 DL5 C4F C4F C 0 1 N N R 8.784 6.335 10.218 -5.903 -3.050 0.456 C4F DL5 36 DL5 N4F N4F N 1 1 N N N 10.115 6.328 10.039 -6.571 -4.148 0.697 N4F DL5 37 DL5 O4F O4F O 0 1 N N N 10.916 6.797 10.840 -7.084 -4.394 1.993 O4F DL5 38 DL5 "C5'" "C5'" C 0 1 N N N 1.510 8.699 11.783 0.793 -1.188 -0.832 "C5'" DL5 39 DL5 "O5'" "O5'" O 0 1 N N N 0.514 7.671 11.517 2.052 -0.979 -0.190 "O5'" DL5 40 DL5 C5F C5F C 0 1 N N N 8.260 6.917 11.402 -5.667 -2.048 1.519 C5F DL5 41 DL5 O5F O5F O -1 1 N N N 10.625 5.845 9.046 -6.782 -5.089 -0.339 O5F DL5 42 DL5 C6F C6F C 0 1 N N N 6.796 7.013 11.755 -4.730 -1.132 1.349 C6F DL5 43 DL5 N6F N6F N 1 1 N N N 6.590 7.668 13.056 -4.520 -0.130 2.420 N6F DL5 44 DL5 O6F O6F O 0 1 N N N 7.572 8.073 13.713 -3.664 0.727 2.292 O6F DL5 45 DL5 O7F O7F O -1 1 N N N 5.555 7.875 13.585 -5.203 -0.164 3.427 O7F DL5 46 DL5 H2 H2 H 0 1 N N N 3.264 0.472 13.837 -5.190 4.754 1.651 H2 DL5 47 DL5 HN6 HN6 H 0 1 N N N -1.174 0.662 14.604 -1.853 7.261 -1.581 HN6 DL5 48 DL5 HN6A HN6A H 0 0 N N N -1.365 2.162 15.222 -3.189 7.988 -0.867 HN6A DL5 49 DL5 H8 H8 H 0 1 N N N 0.327 6.352 13.370 0.158 2.867 -1.547 H8 DL5 50 DL5 H01 H01 H 0 1 N N N -2.286 4.654 13.014 6.556 0.834 1.665 H01 DL5 51 DL5 H01A H01A H 0 0 N N N -3.884 5.283 13.540 6.870 -0.840 2.182 H01A DL5 52 DL5 "H1'" "H1'" H 0 1 N N N 4.021 5.467 13.623 -1.923 1.264 1.204 "H1'" DL5 53 DL5 HO1B HO1B H 0 0 N N N -3.345 8.249 12.633 6.829 -2.826 0.101 HO1B DL5 54 DL5 "H2'" "H2'" H 0 1 N N N 2.972 5.007 10.910 -2.344 0.804 -1.809 "H2'" DL5 55 DL5 HO2A HO2A H 0 0 N N N -1.417 9.421 9.388 3.385 -3.509 -0.041 HO2A DL5 56 DL5 HO2G HO2G H 0 0 N N N -5.917 3.071 12.591 10.434 0.837 2.380 HO2G DL5 57 DL5 "H3'" "H3'" H 0 1 N N N 2.822 7.113 10.018 -1.620 -1.512 -1.505 "H3'" DL5 58 DL5 H3F H3F H 0 1 N N N 8.223 5.372 8.436 -5.715 -3.310 -1.750 H3F DL5 59 DL5 HO3G HO3G H 0 0 N N N -3.372 2.600 10.313 9.387 -1.959 1.353 HO3G DL5 60 DL5 "H4'" "H4'" H 0 1 N N N 3.714 8.842 12.132 -0.265 -1.020 1.045 "H4'" DL5 61 DL5 "H5'" "H5'" H 0 1 N N N 1.266 9.201 12.731 0.627 -2.256 -0.970 "H5'" DL5 62 DL5 "H5'A" "H5'A" H 0 0 N N N 1.498 9.434 10.964 0.793 -0.692 -1.802 "H5'A" DL5 63 DL5 H5F H5F H 0 1 N N N 8.968 7.325 12.109 -6.254 -2.066 2.425 H5F DL5 64 DL5 H4F H4F H 0 1 N N N 11.799 6.683 10.509 -7.564 -5.230 2.074 H4F DL5 65 # # 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 DL5 C2 N1 DOUB Y N 1 DL5 C6 N1 SING Y N 2 DL5 N3 C2 SING Y N 3 DL5 C2 H2 SING N N 4 DL5 C4 N3 DOUB Y N 5 DL5 N9 C4 SING Y N 6 DL5 C4 C5 SING Y N 7 DL5 N7 C5 SING Y N 8 DL5 C5 C6 DOUB Y N 9 DL5 C6 N6 SING N N 10 DL5 N6 HN6 SING N N 11 DL5 N6 HN6A SING N N 12 DL5 C8 N7 DOUB Y N 13 DL5 N9 C8 SING Y N 14 DL5 C8 H8 SING N N 15 DL5 "C1'" N9 SING N N 16 DL5 O1A PA DOUB N N 17 DL5 O2A PA SING N N 18 DL5 PA O3A SING N N 19 DL5 PA "O5'" SING N N 20 DL5 O3A PB SING N N 21 DL5 O2B PB DOUB N N 22 DL5 PB O1B SING N N 23 DL5 PB C01 SING N N 24 DL5 O1G PG DOUB N N 25 DL5 O3G PG SING N N 26 DL5 PG C01 SING N N 27 DL5 PG O2G SING N N 28 DL5 C01 H01 SING N N 29 DL5 C01 H01A SING N N 30 DL5 "C2'" "C1'" SING N N 31 DL5 "C1'" "O4'" SING N N 32 DL5 "C1'" "H1'" SING N N 33 DL5 O1B HO1B SING N N 34 DL5 C2F C1F SING N N 35 DL5 "O3'" C1F SING N N 36 DL5 C1F "O2'" SING N N 37 DL5 C1F C6F SING N N 38 DL5 "C3'" "C2'" SING N N 39 DL5 "O2'" "C2'" SING N N 40 DL5 "C2'" "H2'" SING N N 41 DL5 O2A HO2A SING N N 42 DL5 N2F C2F SING N N 43 DL5 C3F C2F DOUB N N 44 DL5 O2F N2F DOUB N N 45 DL5 O3F N2F SING N N 46 DL5 O2G HO2G SING N N 47 DL5 "O3'" "C3'" SING N N 48 DL5 "C3'" "C4'" SING N N 49 DL5 "C3'" "H3'" SING N N 50 DL5 C3F C4F SING N N 51 DL5 C3F H3F SING N N 52 DL5 O3G HO3G SING N N 53 DL5 "C5'" "C4'" SING N N 54 DL5 "C4'" "O4'" SING N N 55 DL5 "C4'" "H4'" SING N N 56 DL5 N4F C4F DOUB N N 57 DL5 C4F C5F SING N N 58 DL5 O5F N4F SING N N 59 DL5 N4F O4F SING N N 60 DL5 "O5'" "C5'" SING N N 61 DL5 "C5'" "H5'" SING N N 62 DL5 "C5'" "H5'A" SING N N 63 DL5 C5F C6F DOUB N N 64 DL5 C5F H5F SING N N 65 DL5 C6F N6F SING N N 66 DL5 N6F O7F SING N N 67 DL5 N6F O6F DOUB N N 68 DL5 H4F O4F SING N N 69 # # 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 DL5 InChI InChI 1.03 "InChI=1S/C17H19N8O18P3/c18-14-11-15(20-4-19-14)22(5-21-11)16-13-12(8(40-16)3-39-46(37,38)43-45(35,36)6-44(32,33)34)41-17(42-13)9(24(28)29)1-7(23(26)27)2-10(17)25(30)31/h1-2,4-5,8,12-13,16H,3,6H2,(H,26,27)(H,35,36)(H,37,38)(H2,18,19,20)(H2,32,33,34)/t8-,12-,13-,16-/m1/s1" DL5 InChIKey InChI 1.03 WOUJMFLAWZHYLK-KWDXPJCYSA-N DL5 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[C@H]4O[C]5(O[C@@H]34)C(=C[C@@](C=C5[N+]([O-])=O)=[N+](O)[O-])[N+]([O-])=O" DL5 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH]4O[C]5(O[CH]34)C(=C[C](C=C5[N+]([O-])=O)=[N+](O)[O-])[N+]([O-])=O" DL5 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)OC5(O4)C(=CC(=[N+](O)[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N" DL5 SMILES "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)C3C4C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)OC5(O4)C(=CC(=[N+](O)[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N" # _pdbx_chem_comp_identifier.comp_id DL5 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.7.6 _pdbx_chem_comp_identifier.identifier "(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-3',5'-dinitro-N-oxidanyl-6-[[oxidanyl-[oxidanyl(phosphonomethyl)phosphoryl]oxy-phosphoryl]oxymethyl]spiro[3a,4,6,6a-tetrahydrofuro[3,4-d][1,3]dioxole-2,4'-cyclohexa-2,5-diene]-1'-imine oxide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DL5 "Create component" 2015-06-03 EBI DL5 "Other modification" 2015-09-12 EBI DL5 "Initial release" 2016-04-13 RCSB DL5 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id DL5 _pdbx_chem_comp_synonyms.name TNP-AMPPCP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##