data_DJF # _chem_comp.id DJF _chem_comp.name ;[(1S,5R,6R,8R)-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 "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C20 H24 B N5 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge -1 _chem_comp.pdbx_initial_date 2013-01-21 _chem_comp.pdbx_modified_date 2013-04-12 _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 536.217 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DJF _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 3ZJU _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 DJF B B B -1 1 N N N 28.626 27.843 33.223 0.974 1.593 -1.751 B DJF 1 DJF P P P 0 1 N N N 22.015 27.555 32.409 -5.732 0.698 0.671 P DJF 2 DJF N1 N1 N 0 1 Y N N 24.256 34.361 29.269 3.304 -4.978 0.010 N1 DJF 3 DJF O1 O1 O 0 1 N N N 29.594 28.561 34.165 1.095 1.616 -3.116 O1 DJF 4 DJF C2 C2 C 0 1 Y N N 24.836 33.363 28.563 3.457 -3.688 0.249 C2 DJF 5 DJF N3 N3 N 0 1 Y N N 25.340 32.281 29.170 2.461 -2.831 0.166 N3 DJF 6 DJF C4 C4 C 0 1 Y N N 25.269 32.145 30.527 1.241 -3.240 -0.168 C4 DJF 7 DJF C5 C5 C 0 1 Y N N 24.641 33.136 31.253 1.026 -4.603 -0.432 C5 DJF 8 DJF C6 C6 C 0 1 Y N N 24.143 34.272 30.604 2.121 -5.479 -0.330 C6 DJF 9 DJF N6 N6 N 0 1 N N N 23.522 35.281 31.283 1.970 -6.832 -0.579 N6 DJF 10 DJF N7 N7 N 0 1 Y N N 24.695 32.762 32.530 -0.284 -4.748 -0.742 N7 DJF 11 DJF C8 C8 C 0 1 Y N N 25.334 31.563 32.617 -0.873 -3.589 -0.687 C8 DJF 12 DJF N9 N9 N 0 1 Y N N 25.663 31.174 31.389 0.026 -2.626 -0.337 N9 DJF 13 DJF "C1'" "C1'" C 0 1 N N R 26.469 29.969 31.087 -0.254 -1.198 -0.170 "C1'" DJF 14 DJF C10 C10 C 0 1 N N N 30.882 27.916 34.249 1.508 2.952 -3.455 C10 DJF 15 DJF C11 C11 C 0 1 Y N N 30.688 26.696 33.371 2.286 3.475 -2.270 C11 DJF 16 DJF C12 C12 C 0 1 Y N N 29.434 26.645 32.797 1.969 2.652 -1.199 C12 DJF 17 DJF C13 C13 C 0 1 Y N N 31.649 25.695 33.172 3.165 4.523 -2.101 C13 DJF 18 DJF C14 C14 C 0 1 Y N N 31.322 24.596 32.366 3.729 4.758 -0.859 C14 DJF 19 DJF C15 C15 C 0 1 Y N N 30.050 24.523 31.778 3.413 3.944 0.212 C15 DJF 20 DJF C16 C16 C 0 1 Y N N 29.082 25.537 32.004 2.529 2.886 0.043 C16 DJF 21 DJF O17 O17 O 0 1 N N N 27.860 25.383 31.397 2.216 2.084 1.094 O17 DJF 22 DJF C18 C18 C 0 1 N N N 27.758 24.331 30.417 2.834 2.386 2.347 C18 DJF 23 DJF C19 C19 C 0 1 N N N 26.312 23.985 30.100 2.364 1.384 3.403 C19 DJF 24 DJF "C2'" "C2'" C 0 1 N N R 27.178 29.581 32.379 0.070 -0.432 -1.471 "C2'" DJF 25 DJF "O2'" "O2'" O 0 1 N N N 28.395 28.912 32.138 1.270 0.345 -1.262 "O2'" DJF 26 DJF C20 C20 C 0 1 N N N 25.690 25.052 29.206 3.025 1.708 4.744 C20 DJF 27 DJF O21 O21 O 0 1 N N N 24.293 25.117 29.506 2.586 0.771 5.730 O21 DJF 28 DJF "C3'" "C3'" C 0 1 N N S 26.392 28.443 32.964 -1.044 0.653 -1.551 "C3'" DJF 29 DJF "O3'" "O3'" O 0 1 N N N 27.363 27.626 33.607 -0.312 1.887 -1.375 "O3'" DJF 30 DJF "C4'" "C4'" C 0 1 N N R 25.875 27.803 31.679 -1.895 0.401 -0.288 "C4'" DJF 31 DJF "O4'" "O4'" O 0 1 N N N 25.707 28.849 30.706 -1.665 -0.985 0.045 "O4'" DJF 32 DJF "C5'" "C5'" C 0 1 N N N 24.543 27.099 31.870 -3.377 0.637 -0.589 "C5'" DJF 33 DJF "O5'" "O5'" O 0 1 N N N 23.529 28.049 32.187 -4.134 0.512 0.616 "O5'" DJF 34 DJF OP1 OP1 O 0 1 N N N 21.686 27.876 33.840 -6.229 0.619 2.201 OP1 DJF 35 DJF OP2 OP2 O 0 1 N N N 21.759 26.173 31.883 -6.095 2.015 0.102 OP2 DJF 36 DJF H2 H2 H 0 1 N N N 24.894 33.441 27.487 4.436 -3.323 0.522 H2 DJF 37 DJF HN6 HN6 H 0 1 N N N 23.224 35.984 30.637 2.733 -7.427 -0.506 HN6 DJF 38 DJF HN6A HN6A H 0 0 N N N 22.728 34.916 31.769 1.101 -7.186 -0.827 HN6A DJF 39 DJF H8 H8 H 0 1 N N N 25.539 31.020 33.528 -1.919 -3.415 -0.890 H8 DJF 40 DJF "H1'" "H1'" H 0 1 N N N 27.221 30.208 30.321 0.323 -0.793 0.661 "H1'" DJF 41 DJF H10 H10 H 0 1 N N N 31.679 28.565 33.859 2.143 2.934 -4.340 H10 DJF 42 DJF H10A H10A H 0 0 N N N 31.117 27.629 35.284 0.635 3.579 -3.634 H10A DJF 43 DJF H13 H13 H 0 1 N N N 32.624 25.769 33.631 3.413 5.160 -2.936 H13 DJF 44 DJF H14 H14 H 0 1 N N N 32.044 23.811 32.199 4.417 5.579 -0.727 H14 DJF 45 DJF H15 H15 H 0 1 N N N 29.804 23.684 31.145 3.853 4.130 1.180 H15 DJF 46 DJF H18 H18 H 0 1 N N N 28.256 24.658 29.492 3.917 2.323 2.243 H18 DJF 47 DJF H18A H18A H 0 0 N N N 28.261 23.433 30.806 2.557 3.395 2.655 H18A DJF 48 DJF H19 H19 H 0 1 N N N 26.277 23.015 29.583 1.280 1.447 3.507 H19 DJF 49 DJF H19A H19A H 0 0 N N N 25.741 23.921 31.038 2.641 0.375 3.095 H19A DJF 50 DJF "H2'" "H2'" H 0 1 N N N 27.265 30.430 33.073 0.125 -1.079 -2.347 "H2'" DJF 51 DJF H20 H20 H 0 1 N N N 26.161 26.026 29.404 4.108 1.644 4.640 H20 DJF 52 DJF H20A H20A H 0 0 N N N 25.833 24.784 28.149 2.748 2.716 5.052 H20A DJF 53 DJF HO21 HO21 H 0 0 N N N 23.882 25.777 28.960 2.966 0.916 6.607 HO21 DJF 54 DJF "H3'" "H3'" H 0 1 N N N 25.578 28.780 33.623 -1.614 0.621 -2.479 "H3'" DJF 55 DJF "H4'" "H4'" H 0 1 N N N 26.617 27.073 31.323 -1.566 1.046 0.526 "H4'" DJF 56 DJF "H5'" "H5'" H 0 1 N N N 24.272 26.574 30.942 -3.509 1.638 -1.000 "H5'" DJF 57 DJF "H5'A" "H5'A" H 0 0 N N N 24.630 26.372 32.691 -3.722 -0.101 -1.313 "H5'A" DJF 58 DJF HOP1 HOP1 H 0 0 N N N 21.330 27.104 34.264 -7.184 0.723 2.309 HOP1 DJF 59 DJF OP3 OP3 O 0 1 N Y N ? ? ? -6.438 -0.469 -0.184 OP3 DJF 60 DJF HOP3 HOP3 H 0 0 N N N ? ? ? -6.243 -1.362 0.133 HOP3 DJF 61 # 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 DJF B O1 SING N N 1 DJF B C12 SING N N 2 DJF B "O2'" SING N N 3 DJF B "O3'" SING N N 4 DJF P "O5'" SING N N 5 DJF P OP1 SING N N 6 DJF P OP2 DOUB N N 7 DJF N1 C2 DOUB Y N 8 DJF N1 C6 SING Y N 9 DJF O1 C10 SING N N 10 DJF C2 N3 SING Y N 11 DJF N3 C4 DOUB Y N 12 DJF C4 C5 SING Y N 13 DJF C4 N9 SING Y N 14 DJF C5 C6 DOUB Y N 15 DJF C5 N7 SING Y N 16 DJF C6 N6 SING N N 17 DJF N7 C8 DOUB Y N 18 DJF C8 N9 SING Y N 19 DJF N9 "C1'" SING N N 20 DJF "C1'" "C2'" SING N N 21 DJF "C1'" "O4'" SING N N 22 DJF C10 C11 SING N N 23 DJF C11 C12 DOUB Y N 24 DJF C11 C13 SING Y N 25 DJF C12 C16 SING Y N 26 DJF C13 C14 DOUB Y N 27 DJF C14 C15 SING Y N 28 DJF C15 C16 DOUB Y N 29 DJF C16 O17 SING N N 30 DJF O17 C18 SING N N 31 DJF C18 C19 SING N N 32 DJF C19 C20 SING N N 33 DJF "C2'" "O2'" SING N N 34 DJF "C2'" "C3'" SING N N 35 DJF C20 O21 SING N N 36 DJF "C3'" "O3'" SING N N 37 DJF "C3'" "C4'" SING N N 38 DJF "C4'" "O4'" SING N N 39 DJF "C4'" "C5'" SING N N 40 DJF "C5'" "O5'" SING N N 41 DJF C2 H2 SING N N 42 DJF N6 HN6 SING N N 43 DJF N6 HN6A SING N N 44 DJF C8 H8 SING N N 45 DJF "C1'" "H1'" SING N N 46 DJF C10 H10 SING N N 47 DJF C10 H10A SING N N 48 DJF C13 H13 SING N N 49 DJF C14 H14 SING N N 50 DJF C15 H15 SING N N 51 DJF C18 H18 SING N N 52 DJF C18 H18A SING N N 53 DJF C19 H19 SING N N 54 DJF C19 H19A SING N N 55 DJF "C2'" "H2'" SING N N 56 DJF C20 H20 SING N N 57 DJF C20 H20A SING N N 58 DJF O21 HO21 SING N N 59 DJF "C3'" "H3'" SING N N 60 DJF "C4'" "H4'" SING N N 61 DJF "C5'" "H5'" SING N N 62 DJF "C5'" "H5'A" SING N N 63 DJF HOP1 OP1 SING N N 64 DJF P OP3 SING N N 65 DJF HOP3 OP3 SING N N 66 # 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 DJF InChI InChI 1.03 "InChI=1S/C20H22BN5O9P/c22-18-15-19(24-9-23-18)26(10-25-15)20-17-16(13(33-20)8-32-36(28)29)34-21(35-17)14-11(7-31-21)3-1-4-12(14)30-6-2-5-27/h1,3-4,9-10,13,16-17,20,27H,2,5-8H2,(H2,22,23,24)/q-1/t13-,16-,17-,20-,21+/m1/s1" DJF InChIKey InChI 1.03 QAJGLUMMRUEBOV-PGBNIQHZSA-N DJF SMILES_CANONICAL CACTVS 3.370 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@H]4O[B-]5(OCc6cccc(OCCCO)c56)O[C@@H]34" DJF SMILES CACTVS 3.370 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH]4O[B-]5(OCc6cccc(OCCCO)c56)O[CH]34" DJF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[B-]12(c3c(cccc3OCCCO)CO1)O[C@@H]4[C@H](O[C@H]([C@@H]4O2)n5cnc6c5ncnc6N)COP(=O)(O)O" DJF SMILES "OpenEye OEToolkits" 1.7.6 "[B-]12(c3c(cccc3OCCCO)CO1)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 DJF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 ;[(1S,5R,6R,8R)-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 DJF "Create component" 2013-01-21 EBI DJF "Initial release" 2013-04-17 RCSB #