data_7RZ
# 
_chem_comp.id                                    7RZ 
_chem_comp.name                                  
;[(1R,3'S,5S,6R,8R)-3'-(aminomethyl)-8-(6-aminopurin-9-yl)-4'-bromanyl-7'-[3-[methyl-(phenylmethyl)amino]propoxy]spiro[2,4,7-trioxa-3$l^{4}-borabicyclo[3.3.0]octane-3,1'-3H-2,1$l^{4}-benzoxaborole]-6-yl]methyl dihydrogen phosphate
;
_chem_comp.type                                  "RNA OH 3 prime terminus" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C29 H35 B Br N7 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               A 
_chem_comp.pdbx_synonyms                         "AMP adduct with 3-[[(3S)-3-(aminomethyl)-4-bromanyl-1,3-dihydro-2,1-benzoxaborol-7-yl]oxy]-N-methyl-N-(phenylmethyl)propan-1-amine" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-07-12 
_chem_comp.pdbx_modified_date                    2024-06-07 
_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                        747.318 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ? 
_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        8POS 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
7RZ C2     C1  C  0 1 Y N N N N N 7.250  -25.846 6.731  -2.651  1.586  2.898  C2     7RZ 1  
7RZ C4     C2  C  0 1 Y N N N N N 8.234  -24.029 5.959  -1.900  -0.527 2.396  C4     7RZ 2  
7RZ C5     C3  C  0 1 Y N N N N N 9.116  -24.770 5.190  -2.794  -1.057 3.343  C5     7RZ 3  
7RZ C6     C4  C  0 1 Y N N N N N 9.001  -26.170 5.257  -3.605  -0.164 4.062  C6     7RZ 4  
7RZ C11    C5  C  0 1 Y N N N N N 7.191  -16.426 8.459  3.872   1.994  -0.146 C11    7RZ 5  
7RZ C22    C6  C  0 1 N N N N N N 3.503  -20.280 5.264  -3.153  2.894  -1.797 C22    7RZ 6  
7RZ N23    N1  N  0 1 N N N N N N 3.185  -21.263 6.369  -4.466  2.241  -1.701 N23    7RZ 7  
7RZ C26    C7  C  0 1 Y N N N N N 4.045  -23.499 5.288  -6.875  2.553  -1.735 C26    7RZ 8  
7RZ C28    C8  C  0 1 Y N N N N N 4.861  -23.541 4.166  -7.538  1.778  -2.668 C28    7RZ 9  
7RZ OP3    O1  O  0 1 N Y N N N N 3.983  -21.216 1.402  -0.121  -7.199 -2.624 OP3    7RZ 10 
7RZ P      P1  P  0 1 N N N N N N 5.138  -20.241 1.484  1.065   -6.650 -1.684 P      7RZ 11 
7RZ OP1    O2  O  0 1 N N N N N N 5.954  -20.176 0.209  1.060   -7.389 -0.401 OP1    7RZ 12 
7RZ OP2    O3  O  0 1 N N N N N N 4.725  -18.870 1.980  2.479   -6.865 -2.422 OP2    7RZ 13 
7RZ "O5'"  O4  O  0 1 N N N N N N 6.097  -20.880 2.629  0.842   -5.081 -1.399 "O5'"  7RZ 14 
7RZ "C5'"  C9  C  0 1 N N N N N N 7.287  -20.168 3.033  1.668   -4.325 -0.512 "C5'"  7RZ 15 
7RZ "C4'"  C10 C  0 1 N N R N N N 7.222  -19.931 4.521  1.183   -2.875 -0.474 "C4'"  7RZ 16 
7RZ "O4'"  O5  O  0 1 N N N N N N 6.854  -21.168 5.175  -0.120  -2.812 0.130  "O4'"  7RZ 17 
7RZ "C1'"  C11 C  0 1 N N R N N N 7.790  -21.537 6.172  -0.199  -1.552 0.827  "C1'"  7RZ 18 
7RZ N9     N2  N  0 1 Y N N N N N 8.533  -22.712 5.709  -1.236  -1.602 1.860  N9     7RZ 19 
7RZ N3     N3  N  0 1 Y N N N N N 7.273  -24.509 6.752  -1.863  0.788  2.209  N3     7RZ 20 
7RZ N1     N4  N  0 1 Y N N N N N 8.033  -26.684 6.046  -3.502  1.136  3.802  N1     7RZ 21 
7RZ N6     N5  N  0 1 N N N N N N 9.844  -27.008 4.661  -4.504  -0.627 5.006  N6     7RZ 22 
7RZ N7     N6  N  0 1 Y N N N N N 9.957  -23.936 4.467  -2.630  -2.402 3.337  N7     7RZ 23 
7RZ C8     C12 C  0 1 Y N N N N N 9.570  -22.732 4.813  -1.718  -2.724 2.467  C8     7RZ 24 
7RZ "C2'"  C13 C  0 1 N N R N N N 8.645  -20.300 6.450  1.200   -1.390 1.468  "C2'"  7RZ 25 
7RZ "C3'"  C14 C  0 1 N N S N N N 8.519  -19.455 5.181  2.132   -2.029 0.393  "C3'"  7RZ 26 
7RZ "O3'"  O6  O  0 1 N N N N N N 8.389  -18.118 5.655  2.543   -0.866 -0.366 "O3'"  7RZ 27 
7RZ "O2'"  O7  O  0 1 N N N N N N 8.019  -19.511 7.456  1.559   0.004  1.435  "O2'"  7RZ 28 
7RZ B      B1  B  0 1 N N N N N N 8.025  -18.124 7.059  2.608   0.139  0.568  B      7RZ 29 
7RZ O1     O8  O  0 1 N N N N N N 9.118  -17.514 7.792  3.802   0.087  1.250  O1     7RZ 30 
7RZ C10    C15 C  0 1 N N S N N N 8.640  -16.608 8.773  4.711   0.928  0.517  C10    7RZ 31 
7RZ C17    C16 C  0 1 N N N N N N 8.905  -17.108 10.177 5.716   1.572  1.474  C17    7RZ 32 
7RZ N18    N7  N  0 1 N N N N N N 8.385  -18.491 10.339 6.603   0.537  2.022  N18    7RZ 33 
7RZ C12    C17 C  0 1 Y N N N N N 6.733  -17.298 7.476  2.564   1.528  -0.132 C12    7RZ 34 
7RZ C16    C18 C  0 1 Y N N N N N 5.407  -17.226 7.059  1.552   2.290  -0.684 C16    7RZ 35 
7RZ C15    C19 C  0 1 Y N N N N N 4.514  -16.330 7.633  1.847   3.525  -1.245 C15    7RZ 36 
7RZ C14    C20 C  0 1 Y N N N N N 4.964  -15.462 8.612  3.148   3.989  -1.251 C14    7RZ 37 
7RZ C13    C21 C  0 1 Y N N N N N 6.289  -15.502 9.012  4.163   3.218  -0.708 C13    7RZ 38 
7RZ BR     BR1 BR 0 0 N N N N N N 6.848  -14.223 10.304 5.945   3.849  -0.731 BR     7RZ 39 
7RZ O19    O9  O  0 1 N N N N N N 5.061  -18.077 6.036  0.273   1.831  -0.678 O19    7RZ 40 
7RZ C20    C22 C  0 1 N N N N N N 3.873  -17.796 5.263  -0.721  2.672  -1.266 C20    7RZ 41 
7RZ C21    C23 C  0 1 N N N N N N 2.869  -18.912 5.437  -2.089  1.993  -1.166 C21    7RZ 42 
7RZ C24    C24 C  0 1 N N N N N N 3.196  -20.637 7.727  -4.509  1.023  -2.520 C24    7RZ 43 
7RZ C25    C25 C  0 1 N N N N N N 4.190  -22.388 6.292  -5.542  3.168  -2.077 C25    7RZ 44 
7RZ C30    C26 C  0 1 Y N N N N N 4.893  -24.666 3.358  -8.764  1.220  -2.357 C30    7RZ 45 
7RZ C31    C27 C  0 1 Y N N N N N 4.108  -25.758 3.655  -9.326  1.436  -1.113 C31    7RZ 46 
7RZ C29    C28 C  0 1 Y N N N N N 3.290  -25.728 4.763  -8.663  2.211  -0.180 C29    7RZ 47 
7RZ C27    C29 C  0 1 Y N N N N N 3.255  -24.605 5.574  -7.438  2.770  -0.491 C27    7RZ 48 
7RZ H2     H1  H  0 1 N N N N N N 6.497  -26.311 7.351  -2.595  2.650  2.721  H2     7RZ 49 
7RZ H1     H2  H  0 1 N N N N N N 3.149  -20.705 4.313  -2.908  3.066  -2.845 H1     7RZ 50 
7RZ H3     H3  H  0 1 N N N N N N 4.595  -20.150 5.223  -3.181  3.847  -1.269 H3     7RZ 51 
7RZ H5     H5  H  0 1 N N N N N N 5.477  -22.689 3.920  -7.099  1.609  -3.640 H5     7RZ 52 
7RZ HOP3   H6  H  0 0 N Y N N N N 3.974  -21.625 0.545  -0.051  -8.140 -2.837 HOP3   7RZ 53 
7RZ HOP2   H7  H  0 0 N N N N N N 5.059  -18.205 1.390  2.553   -6.408 -3.271 HOP2   7RZ 54 
7RZ "H5'"  H8  H  0 1 N N N N N N 8.178  -20.767 2.791  1.614   -4.753 0.489  "H5'"  7RZ 55 
7RZ "H5''" H9  H  0 0 N N N N N N 7.339  -19.204 2.506  2.700   -4.354 -0.864 "H5''" 7RZ 56 
7RZ "H4'"  H10 H  0 1 N N N N N N 6.445  -19.177 4.716  1.143   -2.471 -1.485 "H4'"  7RZ 57 
7RZ "H1'"  H11 H  0 1 N N N N N N 7.257  -21.797 7.098  -0.395  -0.740 0.127  "H1'"  7RZ 58 
7RZ H61    H12 H  0 1 N N N N N N 9.611  -27.948 4.909  -4.579  -1.579 5.179  H61    7RZ 59 
7RZ H62    H13 H  0 1 N N N N N N 9.777  -26.898 3.669  -5.060  -0.000 5.496  H62    7RZ 60 
7RZ H8     H14 H  0 1 N N N N N N 10.028 -21.834 4.426  -1.389  -3.731 2.257  H8     7RZ 61 
7RZ "H2'"  H15 H  0 1 N N N N N N 9.690  -20.560 6.673  1.279   -1.836 2.460  "H2'"  7RZ 62 
7RZ "H3'"  H16 H  0 1 N N N N N N 9.384  -19.596 4.516  2.968   -2.597 0.801  "H3'"  7RZ 63 
7RZ H17    H17 H  0 1 N N N N N N 9.146  -15.639 8.653  5.236   0.342  -0.237 H17    7RZ 64 
7RZ H18    H18 H  0 1 N N N N N N 9.989  -17.103 10.365 6.308   2.311  0.936  H18    7RZ 65 
7RZ H19    H19 H  0 1 N N N N N N 8.405  -16.445 10.899 5.180   2.059  2.289  H19    7RZ 66 
7RZ H20    H20 H  0 1 N N N N N N 8.566  -18.809 11.270 7.063   0.027  1.282  H20    7RZ 67 
7RZ H21    H21 H  0 1 N N N N N N 7.399  -18.498 10.170 7.277   0.937  2.657  H21    7RZ 68 
7RZ H23    H23 H  0 1 N N N N N N 3.481  -16.311 7.319  1.058   4.123  -1.678 H23    7RZ 69 
7RZ H24    H24 H  0 1 N N N N N N 4.283  -14.755 9.063  3.375   4.950  -1.687 H24    7RZ 70 
7RZ H25    H25 H  0 1 N N N N N N 4.142  -17.710 4.200  -0.750  3.625  -0.738 H25    7RZ 71 
7RZ H26    H26 H  0 1 N N N N N N 3.430  -16.850 5.607  -0.477  2.844  -2.315 H26    7RZ 72 
7RZ H27    H27 H  0 1 N N N N N N 2.436  -18.846 6.446  -2.333  1.820  -0.118 H27    7RZ 73 
7RZ H28    H28 H  0 1 N N N N N N 2.072  -18.793 4.688  -2.060  1.040  -1.695 H28    7RZ 74 
7RZ H29    H29 H  0 1 N N N N N N 2.959  -21.399 8.484  -3.747  0.325  -2.175 H29    7RZ 75 
7RZ H30    H30 H  0 1 N N N N N N 4.192  -20.217 7.929  -5.492  0.560  -2.431 H30    7RZ 76 
7RZ H31    H31 H  0 1 N N N N N N 2.445  -19.834 7.767  -4.322  1.279  -3.563 H31    7RZ 77 
7RZ H32    H32 H  0 1 N N N N N N 4.201  -22.864 7.284  -5.423  4.104  -1.531 H32    7RZ 78 
7RZ H33    H33 H  0 1 N N N N N N 5.167  -21.920 6.099  -5.496  3.363  -3.148 H33    7RZ 79 
7RZ H34    H34 H  0 1 N N N N N N 5.537  -24.687 2.491  -9.283  0.614  -3.086 H34    7RZ 80 
7RZ H35    H35 H  0 1 N N N N N N 4.134  -26.633 3.023  -10.285 1.001  -0.870 H35    7RZ 81 
7RZ H36    H36 H  0 1 N N N N N N 2.674  -26.583 5.000  -9.102  2.381  0.792  H36    7RZ 82 
7RZ H37    H37 H  0 1 N N N N N N 2.607  -24.590 6.438  -6.922  3.380  0.236  H37    7RZ 83 
# 
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 
7RZ OP1   P      DOUB N N 1  
7RZ OP3   P      SING N N 2  
7RZ P     OP2    SING N N 3  
7RZ P     "O5'"  SING N N 4  
7RZ "O5'" "C5'"  SING N N 5  
7RZ "C5'" "C4'"  SING N N 6  
7RZ C30   C31    DOUB Y N 7  
7RZ C30   C28    SING Y N 8  
7RZ C31   C29    SING Y N 9  
7RZ C28   C26    DOUB Y N 10 
7RZ N7    C8     DOUB Y N 11 
7RZ N7    C5     SING Y N 12 
7RZ "C4'" "O4'"  SING N N 13 
7RZ "C4'" "C3'"  SING N N 14 
7RZ N6    C6     SING N N 15 
7RZ C29   C27    DOUB Y N 16 
7RZ C8    N9     SING Y N 17 
7RZ "O4'" "C1'"  SING N N 18 
7RZ "C3'" "O3'"  SING N N 19 
7RZ "C3'" "C2'"  SING N N 20 
7RZ C5    C6     DOUB Y N 21 
7RZ C5    C4     SING Y N 22 
7RZ C6    N1     SING Y N 23 
7RZ C20   C21    SING N N 24 
7RZ C20   O19    SING N N 25 
7RZ C22   C21    SING N N 26 
7RZ C22   N23    SING N N 27 
7RZ C26   C27    SING Y N 28 
7RZ C26   C25    SING N N 29 
7RZ "O3'" B      SING N N 30 
7RZ N9    C4     SING Y N 31 
7RZ N9    "C1'"  SING N N 32 
7RZ C4    N3     DOUB Y N 33 
7RZ O19   C16    SING N N 34 
7RZ N1    C2     DOUB Y N 35 
7RZ "C1'" "C2'"  SING N N 36 
7RZ C25   N23    SING N N 37 
7RZ N23   C24    SING N N 38 
7RZ "C2'" "O2'"  SING N N 39 
7RZ C2    N3     SING Y N 40 
7RZ B     "O2'"  SING N N 41 
7RZ B     C12    SING N N 42 
7RZ B     O1     SING N N 43 
7RZ C16   C12    DOUB Y N 44 
7RZ C16   C15    SING Y N 45 
7RZ C12   C11    SING Y N 46 
7RZ C15   C14    DOUB Y N 47 
7RZ O1    C10    SING N N 48 
7RZ C11   C10    SING N N 49 
7RZ C11   C13    DOUB Y N 50 
7RZ C14   C13    SING Y N 51 
7RZ C10   C17    SING N N 52 
7RZ C13   BR     SING N N 53 
7RZ C17   N18    SING N N 54 
7RZ C2    H2     SING N N 55 
7RZ C22   H1     SING N N 56 
7RZ C22   H3     SING N N 57 
7RZ C28   H5     SING N N 58 
7RZ OP3   HOP3   SING N N 59 
7RZ OP2   HOP2   SING N N 60 
7RZ "C5'" "H5'"  SING N N 61 
7RZ "C5'" "H5''" SING N N 62 
7RZ "C4'" "H4'"  SING N N 63 
7RZ "C1'" "H1'"  SING N N 64 
7RZ N6    H61    SING N N 65 
7RZ N6    H62    SING N N 66 
7RZ C8    H8     SING N N 67 
7RZ "C2'" "H2'"  SING N N 68 
7RZ "C3'" "H3'"  SING N N 69 
7RZ C10   H17    SING N N 70 
7RZ C17   H18    SING N N 71 
7RZ C17   H19    SING N N 72 
7RZ N18   H20    SING N N 73 
7RZ N18   H21    SING N N 74 
7RZ C15   H23    SING N N 75 
7RZ C14   H24    SING N N 76 
7RZ C20   H25    SING N N 77 
7RZ C20   H26    SING N N 78 
7RZ C21   H27    SING N N 79 
7RZ C21   H28    SING N N 80 
7RZ C24   H29    SING N N 81 
7RZ C24   H30    SING N N 82 
7RZ C24   H31    SING N N 83 
7RZ C25   H32    SING N N 84 
7RZ C25   H33    SING N N 85 
7RZ C30   H34    SING N N 86 
7RZ C31   H35    SING N N 87 
7RZ C29   H36    SING N N 88 
7RZ C27   H37    SING N N 89 
# 
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 
7RZ InChI            InChI                1.06  "InChI=1S/C29H35BBrN7O9P/c1-37(13-17-6-3-2-4-7-17)10-5-11-42-19-9-8-18(31)22-20(12-32)45-30(23(19)22)46-25-21(14-43-48(39,40)41)44-29(26(25)47-30)38-16-36-24-27(33)34-15-35-28(24)38/h2-4,6-9,15-16,20-21,25-26,29H,5,10-14,32H2,1H3,(H2,33,34,35)(H2,39,40,41)/t20-,21-,25-,26-,29-/m1/s1" 
7RZ InChIKey         InChI                1.06  OOVYGSSPEYCEFD-LIBJEQSZSA-N                                                                                                                                                                                                                                                                  
7RZ SMILES_CANONICAL CACTVS               3.385 "CN(CCCOc1ccc(Br)c2[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)Cc7ccccc7"                                                                                                                                                                             
7RZ SMILES           CACTVS               3.385 "CN(CCCOc1ccc(Br)c2[CH](CN)O[B]3(O[CH]4[CH](CO[P](O)(O)=O)O[CH]([CH]4O3)n5cnc6c(N)ncnc56)c12)Cc7ccccc7"                                                                                                                                                                                      
7RZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "B12(c3c(ccc(c3[C@H](O1)CN)Br)OCCCN(C)Cc4ccccc4)O[C@@H]5[C@H](O[C@H]([C@@H]5O2)n6cnc7c6ncnc7N)COP(=O)(O)O"                                                                                                                                                                                   
7RZ SMILES           "OpenEye OEToolkits" 2.0.7 "B12(c3c(ccc(c3C(O1)CN)Br)OCCCN(C)Cc4ccccc4)OC5C(OC(C5O2)n6cnc7c6ncnc7N)COP(=O)(O)O"                                                                                                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           7RZ 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        
;[(1~{R},3'~{S},5~{S},6~{R},8~{R})-3'-(aminomethyl)-8-(6-aminopurin-9-yl)-4'-bromanyl-7'-[3-[methyl-(phenylmethyl)amino]propoxy]spiro[2,4,7-trioxa-3$l^{4}-borabicyclo[3.3.0]octane-3,1'-3~{H}-2,1$l^{4}-benzoxaborole]-6-yl]methyl dihydrogen phosphate
;
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      7RZ 
_pdbx_chem_comp_synonyms.name         "AMP adduct with 3-[[(3S)-3-(aminomethyl)-4-bromanyl-1,3-dihydro-2,1-benzoxaborol-7-yl]oxy]-N-methyl-N-(phenylmethyl)propan-1-amine" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
7RZ "Create component" 2023-07-12 PDBE 
7RZ "Initial release"  2024-06-12 RCSB 
# 
