data_A52 # _chem_comp.id A52 _chem_comp.name "3-AMINOMETHYL-7-(ETHOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H23 B N6 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge -3 _chem_comp.pdbx_initial_date 2015-02-03 _chem_comp.pdbx_modified_date 2016-02-26 _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 533.216 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A52 _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 5AGR _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 A52 B B B -1 1 N N N 15.573 5.681 11.165 1.571 -1.304 0.654 B A52 1 A52 P P P 0 1 N N N 22.331 4.646 9.952 -5.526 -1.996 -0.244 P A52 2 A52 N1 N1 N 0 1 Y N N 20.854 6.230 17.928 1.774 5.815 -0.335 N1 A52 3 A52 O1 O1 O 0 1 N N N 14.434 6.632 11.216 2.005 -1.457 1.945 O1 A52 4 A52 C2 C2 C 0 1 Y N N 20.133 5.168 17.524 2.174 4.655 -0.822 C2 A52 5 A52 N3 N3 N 0 1 Y N N 19.508 5.144 16.334 1.462 3.554 -0.702 N3 A52 6 A52 C4 C4 C 0 1 Y N N 19.606 6.233 15.531 0.290 3.571 -0.075 C4 A52 7 A52 C5 C5 C 0 1 Y N N 20.335 7.346 15.926 -0.180 4.781 0.461 C5 A52 8 A52 C6 C6 C 0 1 Y N N 20.964 7.336 17.161 0.616 5.929 0.308 C6 A52 9 A52 N6 N6 N 0 1 N N N 21.682 8.406 17.584 0.205 7.149 0.816 N6 A52 10 A52 N7 N7 N 0 1 Y N N 20.245 8.265 14.945 -1.379 4.523 1.038 N7 A52 11 A52 C8 C8 C 0 1 Y N N 19.491 7.731 13.967 -1.667 3.263 0.893 C8 A52 12 A52 N9 N9 N 0 1 Y N N 19.100 6.493 14.325 -0.668 2.632 0.213 N9 A52 13 A52 "C1'" "C1'" C 0 1 N N R 18.211 5.552 13.572 -0.626 1.212 -0.146 "C1'" A52 14 A52 C10 C10 C 0 1 N N S 13.146 6.017 11.027 2.795 -2.660 1.958 C10 A52 15 A52 C11 C11 C 0 1 Y N N 13.507 4.704 10.445 3.381 -2.804 0.573 C11 A52 16 A52 C12 C12 C 0 1 Y N N 14.868 4.513 10.512 2.636 -1.977 -0.256 C12 A52 17 A52 C13 C13 C 0 1 Y N N 12.624 3.765 9.893 4.423 -3.543 0.056 C13 A52 18 A52 C14 C14 C 0 1 Y N N 13.164 2.574 9.416 4.725 -3.464 -1.292 C14 A52 19 A52 C15 C15 C 0 1 Y N N 14.542 2.366 9.476 3.983 -2.645 -2.122 C15 A52 20 A52 C16 C16 C 0 1 Y N N 15.408 3.320 10.028 2.934 -1.898 -1.604 C16 A52 21 A52 O1P O1P O -1 1 N N N 23.045 5.899 10.377 -6.255 -1.200 0.891 O1P A52 22 A52 "C2'" "C2'" C 0 1 N N R 17.174 6.328 12.777 0.165 0.414 0.913 "C2'" A52 23 A52 "O2'" "O2'" O 0 1 N N N 16.040 5.500 12.520 1.435 0.026 0.345 "O2'" A52 24 A52 O2P O2P O 0 1 N N N 23.003 3.347 10.298 -5.413 -3.504 0.166 O2P A52 25 A52 "C3'" "C3'" C 0 1 N N S 17.772 6.484 11.396 -0.605 -0.936 1.012 "C3'" A52 26 A52 "O3'" "O3'" O 0 1 N N N 16.654 6.348 10.511 0.342 -1.892 0.485 "O3'" A52 27 A52 C33 C33 C 0 1 N N N 12.481 5.838 12.391 3.916 -2.540 2.992 C33 A52 28 A52 N34 N34 N 0 1 N N N 13.345 5.095 13.316 3.336 -2.486 4.340 N34 A52 29 A52 O35 O35 O 0 1 N N N 16.751 3.092 10.085 2.203 -1.092 -2.418 O35 A52 30 A52 C36 C36 C 0 1 N N N 17.301 1.870 9.585 2.569 -1.062 -3.799 C36 A52 31 A52 C37 C37 C 0 1 N N N 18.792 1.852 9.827 1.640 -0.107 -4.552 C37 A52 32 A52 O3P O3P O -1 1 N N N 21.848 4.712 8.527 -6.344 -1.876 -1.575 O3P A52 33 A52 "C4'" "C4'" C 0 1 N N R 18.760 5.322 11.305 -1.760 -0.777 0.000 "C4'" A52 34 A52 "O4'" "O4'" O 0 1 N N N 18.903 4.764 12.619 -1.954 0.648 -0.122 "O4'" A52 35 A52 "C5'" "C5'" C 0 1 N N N 20.125 5.781 10.840 -3.030 -1.444 0.533 "C5'" A52 36 A52 "O5'" "O5'" O 0 1 N N N 20.990 4.647 10.831 -4.051 -1.388 -0.464 "O5'" A52 37 A52 H2 H2 H 0 1 N N N 20.054 4.310 18.175 3.122 4.607 -1.338 H2 A52 38 A52 HN6 HN6 H 0 1 N N N 22.067 8.214 18.487 0.764 7.934 0.704 HN6 A52 39 A52 HN6A HN6A H 0 0 N N N 22.423 8.587 16.937 -0.642 7.219 1.283 HN6A A52 40 A52 H8 H8 H 0 1 N N N 19.238 8.220 13.038 -2.565 2.786 1.258 H8 A52 41 A52 "H1'" "H1'" H 0 1 N N N 17.689 4.903 14.290 -0.176 1.084 -1.130 "H1'" A52 42 A52 H10 H10 H 0 1 N N N 12.502 6.597 10.349 2.164 -3.518 2.188 H10 A52 43 A52 H13 H13 H 0 1 N N N 11.563 3.959 9.840 5.004 -4.183 0.703 H13 A52 44 A52 H14 H14 H 0 1 N N N 12.519 1.814 9.001 5.541 -4.044 -1.696 H14 A52 45 A52 H15 H15 H 0 1 N N N 14.952 1.446 9.087 4.220 -2.586 -3.174 H15 A52 46 A52 "H2'" "H2'" H 0 1 N N N 16.926 7.294 13.241 0.262 0.941 1.862 "H2'" A52 47 A52 "H3'" "H3'" H 0 1 N N N 18.284 7.451 11.287 -0.936 -1.173 2.023 "H3'" A52 48 A52 H33 H33 H 0 1 N N N 12.269 6.829 12.818 4.576 -3.404 2.914 H33 A52 49 A52 H33A H33A H 0 0 N N N 11.539 5.286 12.260 4.487 -1.630 2.805 H33A A52 50 A52 HN34 HN34 H 0 0 N N N 12.883 4.995 14.197 2.749 -3.289 4.513 HN34 A52 51 A52 HN3A HN3A H 0 0 N N N 13.539 4.190 12.937 4.056 -2.407 5.041 HN3A A52 52 A52 H36 H36 H 0 1 N N N 16.835 1.019 10.104 3.598 -0.718 -3.894 H36 A52 53 A52 H36A H36A H 0 0 N N N 17.104 1.794 8.505 2.480 -2.063 -4.220 H36A A52 54 A52 H37 H37 H 0 1 N N N 19.215 0.912 9.442 1.919 -0.084 -5.605 H37 A52 55 A52 H37A H37A H 0 0 N N N 19.258 2.703 9.308 0.610 -0.451 -4.456 H37A A52 56 A52 H37B H37B H 0 0 N N N 18.989 1.928 10.907 1.729 0.894 -4.130 H37B A52 57 A52 "H4'" "H4'" H 0 1 N N N 18.369 4.568 10.606 -1.482 -1.205 -0.962 "H4'" A52 58 A52 "H5'" "H5'" H 0 1 N N N 20.052 6.203 9.827 -2.818 -2.484 0.779 "H5'" A52 59 A52 "H5'A" "H5'A" H 0 0 N N N 20.517 6.544 11.528 -3.366 -0.921 1.428 "H5'A" A52 60 # 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 A52 B O1 SING N N 1 A52 B C12 SING N N 2 A52 B "O2'" SING N N 3 A52 B "O3'" SING N N 4 A52 P O1P SING N N 5 A52 P O2P DOUB N N 6 A52 P O3P SING N N 7 A52 P "O5'" SING N N 8 A52 N1 C2 DOUB Y N 9 A52 N1 C6 SING Y N 10 A52 O1 C10 SING N N 11 A52 C2 N3 SING Y N 12 A52 N3 C4 DOUB Y N 13 A52 C4 C5 SING Y N 14 A52 C4 N9 SING Y N 15 A52 C5 C6 DOUB Y N 16 A52 C5 N7 SING Y N 17 A52 C6 N6 SING N N 18 A52 N7 C8 DOUB Y N 19 A52 C8 N9 SING Y N 20 A52 N9 "C1'" SING N N 21 A52 "C1'" "C2'" SING N N 22 A52 "C1'" "O4'" SING N N 23 A52 C10 C11 SING N N 24 A52 C10 C33 SING N N 25 A52 C11 C12 DOUB Y N 26 A52 C11 C13 SING Y N 27 A52 C12 C16 SING Y N 28 A52 C13 C14 DOUB Y N 29 A52 C14 C15 SING Y N 30 A52 C15 C16 DOUB Y N 31 A52 C16 O35 SING N N 32 A52 "C2'" "O2'" SING N N 33 A52 "C2'" "C3'" SING N N 34 A52 "C3'" "O3'" SING N N 35 A52 "C3'" "C4'" SING N N 36 A52 C33 N34 SING N N 37 A52 O35 C36 SING N N 38 A52 C36 C37 SING N N 39 A52 "C4'" "O4'" SING N N 40 A52 "C4'" "C5'" SING N N 41 A52 "C5'" "O5'" SING N N 42 A52 C2 H2 SING N N 43 A52 N6 HN6 SING N N 44 A52 N6 HN6A SING N N 45 A52 C8 H8 SING N N 46 A52 "C1'" "H1'" SING N N 47 A52 C10 H10 SING N N 48 A52 C13 H13 SING N N 49 A52 C14 H14 SING N N 50 A52 C15 H15 SING N N 51 A52 "C2'" "H2'" SING N N 52 A52 "C3'" "H3'" SING N N 53 A52 C33 H33 SING N N 54 A52 C33 H33A SING N N 55 A52 N34 HN34 SING N N 56 A52 N34 HN3A SING N N 57 A52 C36 H36 SING N N 58 A52 C36 H36A SING N N 59 A52 C37 H37 SING N N 60 A52 C37 H37A SING N N 61 A52 C37 H37B SING N N 62 A52 "C4'" "H4'" SING N N 63 A52 "C5'" "H5'" SING N N 64 A52 "C5'" "H5'A" 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 A52 InChI InChI 1.03 "InChI=1S/C20H25BN6O9P/c1-2-31-11-5-3-4-10-12(6-22)34-21(14(10)11)35-16-13(7-32-37(28,29)30)33-20(17(16)36-21)27-9-26-15-18(23)24-8-25-19(15)27/h3-5,8-9,12-13,16-17,20H,2,6-7,22H2,1H3,(H2,23,24,25)(H2,28,29,30)/q-1/p-2/t12-,13-,16-,17-,20-,21+/m1/s1" A52 InChIKey InChI 1.03 WLOBNXOMDQETEC-IMBSHPNCSA-L A52 SMILES_CANONICAL CACTVS 3.385 "CCOc1cccc2[C@@H](CN)O[B-]3(O[C@@H]4[C@@H](CO[P]([O-])([O-])=O)O[C@H]([C@@H]4O3)n5cnc6c(N)ncnc56)c12" A52 SMILES CACTVS 3.385 "CCOc1cccc2[CH](CN)O[B-]3(O[CH]4[CH](CO[P]([O-])([O-])=O)O[CH]([CH]4O3)n5cnc6c(N)ncnc56)c12" A52 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[B-]12(c3c(cccc3OCC)[C@H](O1)CN)O[C@@H]4[C@H](O[C@H]([C@@H]4O2)n5cnc6c5ncnc6N)COP(=O)([O-])[O-]" A52 SMILES "OpenEye OEToolkits" 1.7.6 "[B-]12(c3c(cccc3OCC)C(O1)CN)OC4C(OC(C4O2)n5cnc6c5ncnc6N)COP(=O)([O-])[O-]" # 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 A52 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 ;[(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-6-(6-aminopurin-9-yl)-2'-ethoxy-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 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 A52 "Create component" 2015-02-03 EBI A52 "Other modification" 2015-06-18 EBI A52 "Initial release" 2016-03-02 RCSB #