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 #