data_365 # _chem_comp.id 365 _chem_comp.name "[(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl dihydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H27 B N6 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "3-AMINOMETHYL-7-(3-HYDROXY-PROPOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine" _chem_comp.pdbx_formal_charge -1 _chem_comp.pdbx_initial_date 2013-01-21 _chem_comp.pdbx_modified_date 2021-03-13 _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 565.258 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 365 _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 3ZJV _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 365 O3P O3P O 0 1 N N N 52.194 -19.417 30.287 6.479 1.104 -1.806 O3P 365 1 365 B B B -1 1 N N N 53.697 -26.635 32.889 -1.304 1.454 1.095 B 365 2 365 P P P 0 1 N N N 51.652 -20.043 31.671 5.709 1.563 -0.468 P 365 3 365 N1 N1 N 0 1 Y N N 57.039 -22.030 26.320 -2.136 -5.651 0.366 N1 365 4 365 O1 O1 O 0 1 N N N 54.570 -27.553 33.535 -1.603 1.673 2.415 O1 365 5 365 C2 C2 C 0 1 Y N N 55.964 -22.845 26.292 -2.492 -4.477 -0.121 C2 365 6 365 N3 N3 N 0 1 Y N N 55.445 -23.400 27.398 -1.690 -3.432 -0.104 N3 365 7 365 C4 C4 C 0 1 Y N N 56.037 -23.126 28.575 -0.470 -3.524 0.414 C4 365 8 365 C5 C5 C 0 1 Y N N 57.126 -22.269 28.639 -0.044 -4.754 0.945 C5 365 9 365 C6 C6 C 0 1 Y N N 57.637 -21.722 27.483 -0.936 -5.839 0.904 C6 365 10 365 N6 N6 N 0 1 N N N 58.703 -20.885 27.534 -0.572 -7.074 1.412 N6 365 11 365 N7 N7 N 0 1 Y N N 57.497 -22.159 29.924 1.219 -4.576 1.401 N7 365 12 365 C8 C8 C 0 1 Y N N 56.653 -22.936 30.630 1.587 -3.345 1.189 C8 365 13 365 N9 N9 N 0 1 Y N N 55.763 -23.527 29.810 0.579 -2.656 0.582 N9 365 14 365 "C1'" "C1'" C 0 1 N N R 54.674 -24.482 30.138 0.611 -1.247 0.182 "C1'" 365 15 365 C10 C10 C 0 1 N N S 53.991 -28.840 33.790 -2.296 2.934 2.459 C10 365 16 365 C11 C11 C 0 1 Y N N 52.584 -28.641 33.416 -2.996 3.088 1.130 C11 365 17 365 C12 C12 C 0 1 Y N N 52.398 -27.336 32.826 -2.396 2.183 0.264 C12 365 18 365 C13 C13 C 0 1 Y N N 51.546 -29.551 33.528 -4.022 3.892 0.686 C13 365 19 365 C14 C14 C 0 1 Y N N 50.284 -29.169 33.091 -4.454 3.802 -0.626 C14 365 20 365 C15 C15 C 0 1 Y N N 50.072 -27.911 32.528 -3.857 2.906 -1.492 C15 365 21 365 C16 C16 C 0 1 Y N N 51.125 -26.981 32.397 -2.824 2.093 -1.047 C16 365 22 365 C17 C17 C 0 1 N N N 54.587 -29.883 32.860 -3.321 2.930 3.594 C17 365 23 365 N18 N18 N 0 1 N N N 54.607 -29.409 31.469 -2.622 2.866 4.885 N18 365 24 365 O19 O19 O 0 1 N N N 50.868 -25.755 31.841 -2.235 1.212 -1.898 O19 365 25 365 O1P O1P O 0 1 N N N 52.513 -19.439 32.740 6.372 0.966 0.712 O1P 365 26 365 "C2'" "C2'" C 0 1 N N R 54.943 -25.244 31.416 -0.014 -0.363 1.282 "C2'" 365 27 365 "O2'" "O2'" O 0 1 N N N 54.180 -26.467 31.561 -1.299 0.109 0.819 "O2'" 365 28 365 C20 C20 C 0 1 N N N 49.512 -25.301 31.752 -2.729 1.174 -3.238 C20 365 29 365 C21 C21 C 0 1 N N N 49.453 -24.005 30.973 -1.950 0.130 -4.040 C21 365 30 365 C22 C22 C 0 1 N N N 48.837 -24.266 29.609 -2.479 0.090 -5.475 C22 365 31 365 O23 O23 O 0 1 N N N 48.022 -23.144 29.267 -1.751 -0.885 -6.224 O23 365 32 365 O2P O2P O 0 1 N N N 50.140 -19.839 31.736 5.748 3.168 -0.352 O2P 365 33 365 "C3'" "C3'" C 0 1 N N S 54.351 -24.365 32.467 0.861 0.925 1.265 "C3'" 365 34 365 "O3'" "O3'" O 0 1 N N N 53.837 -25.300 33.386 -0.055 1.938 0.795 "O3'" 365 35 365 "C4'" "C4'" C 0 1 N N R 53.254 -23.595 31.751 1.901 0.650 0.158 "C4'" 365 36 365 "O4'" "O4'" O 0 1 N N N 53.426 -23.839 30.342 1.975 -0.789 0.067 "O4'" 365 37 365 "C5'" "C5'" C 0 1 N N N 53.253 -22.103 31.974 3.262 1.229 0.551 "C5'" 365 38 365 "O5'" "O5'" O 0 1 N N N 52.035 -21.568 31.425 4.179 1.067 -0.533 "O5'" 365 39 365 H2 H2 H 0 1 N N N 55.502 -23.060 25.340 -3.477 -4.368 -0.550 H2 365 40 365 HN6 HN6 H 0 1 N N N 58.928 -20.575 26.610 -1.197 -7.815 1.377 HN6 365 41 365 HN6A HN6A H 0 0 N N N 58.480 -20.095 28.105 0.307 -7.198 1.802 HN6A 365 42 365 H8 H8 H 0 1 N N N 56.685 -23.067 31.702 2.548 -2.931 1.455 H8 365 43 365 "H1'" "H1'" H 0 1 N N N 54.584 -25.208 29.316 0.082 -1.110 -0.761 "H1'" 365 44 365 H10 H10 H 0 1 N N N 54.095 -29.144 34.842 -1.583 3.746 2.602 H10 365 45 365 H13 H13 H 0 1 N N N 51.714 -30.533 33.945 -4.490 4.593 1.362 H13 365 46 365 H14 H14 H 0 1 N N N 49.456 -29.855 33.189 -5.259 4.433 -0.973 H14 365 47 365 H15 H15 H 0 1 N N N 49.083 -27.643 32.186 -4.195 2.839 -2.516 H15 365 48 365 H17 H17 H 0 1 N N N 55.617 -30.101 33.179 -3.918 3.841 3.549 H17 365 49 365 H17A H17A H 0 0 N N N 53.983 -30.801 32.917 -3.974 2.062 3.491 H17A 365 50 365 HN18 HN18 H 0 0 N N N 55.003 -30.115 30.882 -1.963 3.624 4.977 HN18 365 51 365 HN1A HN1A H 0 0 N N N 53.673 -29.213 31.170 -3.279 2.862 5.652 HN1A 365 52 365 "H2'" "H2'" H 0 1 N N N 56.021 -25.399 31.573 -0.062 -0.856 2.253 "H2'" 365 53 365 H20 H20 H 0 1 N N N 48.905 -26.062 31.240 -3.787 0.909 -3.228 H20 365 54 365 H20A H20A H 0 0 N N N 49.115 -25.136 32.765 -2.605 2.154 -3.699 H20A 365 55 365 H21 H21 H 0 1 N N N 48.838 -23.275 31.520 -0.892 0.395 -4.050 H21 365 56 365 H21A H21A H 0 0 N N N 50.470 -23.606 30.846 -2.074 -0.850 -3.579 H21A 365 57 365 H22 H22 H 0 1 N N N 49.632 -24.392 28.859 -3.536 -0.175 -5.465 H22 365 58 365 H22A H22A H 0 0 N N N 48.221 -25.177 29.646 -2.355 1.070 -5.936 H22A 365 59 365 HO23 HO23 H 0 0 N N N 47.626 -23.287 28.415 -2.034 -0.965 -7.145 HO23 365 60 365 "H3'" "H3'" H 0 1 N N N 55.099 -23.688 32.906 1.302 1.162 2.234 "H3'" 365 61 365 "H4'" "H4'" H 0 1 N N N 52.282 -23.996 32.075 1.567 1.074 -0.789 "H4'" 365 62 365 "H5'" "H5'" H 0 1 N N N 53.302 -21.887 33.052 3.154 2.289 0.780 "H5'" 365 63 365 "H5'A" "H5'A" H 0 0 N N N 54.119 -21.650 31.470 3.640 0.705 1.429 "H5'A" 365 64 365 HOP3 HOP3 H 0 0 N N N 52.915 -18.826 30.467 7.409 1.370 -1.836 HOP3 365 65 365 HOP2 HOP2 H 0 0 N N N 49.923 -19.318 32.500 5.330 3.627 -1.093 HOP2 365 66 # # 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 365 O3P P SING N N 1 365 B O1 SING N N 2 365 B C12 SING N N 3 365 B "O2'" SING N N 4 365 B "O3'" SING N N 5 365 P O1P DOUB N N 6 365 P O2P SING N N 7 365 P "O5'" SING N N 8 365 N1 C2 DOUB Y N 9 365 N1 C6 SING Y N 10 365 O1 C10 SING N N 11 365 C2 N3 SING Y N 12 365 N3 C4 DOUB Y N 13 365 C4 C5 SING Y N 14 365 C4 N9 SING Y N 15 365 C5 C6 DOUB Y N 16 365 C5 N7 SING Y N 17 365 C6 N6 SING N N 18 365 N7 C8 DOUB Y N 19 365 C8 N9 SING Y N 20 365 N9 "C1'" SING N N 21 365 "C1'" "C2'" SING N N 22 365 "C1'" "O4'" SING N N 23 365 C10 C11 SING N N 24 365 C10 C17 SING N N 25 365 C11 C12 DOUB Y N 26 365 C11 C13 SING Y N 27 365 C12 C16 SING Y N 28 365 C13 C14 DOUB Y N 29 365 C14 C15 SING Y N 30 365 C15 C16 DOUB Y N 31 365 C16 O19 SING N N 32 365 C17 N18 SING N N 33 365 O19 C20 SING N N 34 365 "C2'" "O2'" SING N N 35 365 "C2'" "C3'" SING N N 36 365 C20 C21 SING N N 37 365 C21 C22 SING N N 38 365 C22 O23 SING N N 39 365 "C3'" "O3'" SING N N 40 365 "C3'" "C4'" SING N N 41 365 "C4'" "O4'" SING N N 42 365 "C4'" "C5'" SING N N 43 365 "C5'" "O5'" SING N N 44 365 C2 H2 SING N N 45 365 N6 HN6 SING N N 46 365 N6 HN6A SING N N 47 365 C8 H8 SING N N 48 365 "C1'" "H1'" SING N N 49 365 C10 H10 SING N N 50 365 C13 H13 SING N N 51 365 C14 H14 SING N N 52 365 C15 H15 SING N N 53 365 C17 H17 SING N N 54 365 C17 H17A SING N N 55 365 N18 HN18 SING N N 56 365 N18 HN1A SING N N 57 365 "C2'" "H2'" SING N N 58 365 C20 H20 SING N N 59 365 C20 H20A SING N N 60 365 C21 H21 SING N N 61 365 C21 H21A SING N N 62 365 C22 H22 SING N N 63 365 C22 H22A SING N N 64 365 O23 HO23 SING N N 65 365 "C3'" "H3'" SING N N 66 365 "C4'" "H4'" SING N N 67 365 "C5'" "H5'" SING N N 68 365 "C5'" "H5'A" SING N N 69 365 O3P HOP3 SING N N 70 365 O2P HOP2 SING N N 71 # # 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 365 InChI InChI 1.03 "InChI=1S/C21H27BN6O10P/c23-7-13-11-3-1-4-12(33-6-2-5-29)15(11)22(36-13)37-17-14(8-34-39(30,31)32)35-21(18(17)38-22)28-10-27-16-19(24)25-9-26-20(16)28/h1,3-4,9-10,13-14,17-18,21,29H,2,5-8,23H2,(H2,24,25,26)(H2,30,31,32)/q-1/p-2/t13-,14-,17-,18-,21-,22+/m1/s1" 365 InChIKey InChI 1.03 SQCWYVPZBCHHDX-ZKDXOGESSA-L 365 SMILES_CANONICAL CACTVS 3.370 "NC[C@H]1O[B-]2(O[C@@H]3[C@@H](CO[P](O)(O)=O)O[C@H]([C@@H]3O2)n4cnc5c(N)ncnc45)c6c(OCCCO)cccc16" 365 SMILES CACTVS 3.370 "NC[CH]1O[B-]2(O[CH]3[CH](CO[P](O)(O)=O)O[CH]([CH]3O2)n4cnc5c(N)ncnc45)c6c(OCCCO)cccc16" 365 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[B-]12(c3c(cccc3OCCCO)[C@H](O1)CN)O[C@@H]4[C@H](O[C@H]([C@@H]4O2)n5cnc6c5ncnc6N)COP(=O)(O)O" 365 SMILES "OpenEye OEToolkits" 1.7.6 "[B-]12(c3c(cccc3OCCCO)C(O1)CN)OC4C(OC(C4O2)n5cnc6c5ncnc6N)COP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id 365 _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 "[(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-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 365 "Create component" 2013-01-21 EBI 365 "Initial release" 2013-04-17 RCSB 365 "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 365 _pdbx_chem_comp_synonyms.name "3-AMINOMETHYL-7-(3-HYDROXY-PROPOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##