data_OYE # _chem_comp.id OYE _chem_comp.name "bn7GpppG mRNA 5' cap analog" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H31 N10 O18 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate" _chem_comp.pdbx_formal_charge -2 _chem_comp.pdbx_initial_date 2020-04-07 _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 876.513 _chem_comp.one_letter_code ? _chem_comp.three_letter_code OYE _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 6YLR _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.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 OYE C1 CB1 C 0 1 Y N N 125.223 -51.135 -6.084 -6.723 1.159 -3.391 C1 OYE 1 OYE O1 OB1 O -1 1 N N N 125.067 -47.049 -10.936 -0.175 -3.595 -2.052 O1 OYE 2 OYE C2 CB2 C 0 1 Y N N 124.887 -51.826 -4.925 -5.464 0.687 -3.712 C2 OYE 3 OYE O2 OB2 O 0 1 N N N 123.630 -46.748 -12.940 0.883 -5.072 -0.302 O2 OYE 4 OYE C3 CB3 C 0 1 Y N N 123.909 -52.817 -4.950 -4.644 1.419 -4.549 C3 OYE 5 OYE O3 OG1 O -1 1 N N N 124.334 -49.969 -10.436 -1.135 -4.370 2.476 O3 OYE 6 OYE O4 OG2 O 0 1 N N N 125.193 -51.343 -12.319 -2.555 -4.402 0.391 O4 OYE 7 OYE C4 "C1'" C 0 1 N N R 129.922 -50.509 -9.356 -5.835 0.447 2.138 C4 OYE 8 OYE C5 C1P C 0 1 N N R 130.578 -47.313 -14.975 7.311 1.190 -0.749 C5 OYE 9 OYE C6 C2 C 0 1 N N N 130.886 -52.478 -5.681 -8.825 3.750 1.258 C6 OYE 10 OYE C7 "C2'" C 0 1 N N R 129.945 -51.873 -10.011 -6.659 -0.496 3.052 C7 OYE 11 OYE C8 C2G C 0 1 N N N 133.949 -45.645 -12.871 10.007 4.149 1.259 C8 OYE 12 OYE C9 C2P C 0 1 N N R 129.784 -48.602 -14.987 8.240 0.609 -1.845 C9 OYE 13 OYE C10 "C3'" C 0 1 N N S 128.799 -51.745 -10.939 -5.549 -1.239 3.835 C10 OYE 14 OYE C11 C3P C 0 1 N N S 129.450 -48.675 -16.454 7.224 0.096 -2.894 C11 OYE 15 OYE C12 C4 C 0 1 Y N N 129.486 -51.258 -7.079 -7.476 1.847 0.834 C12 OYE 16 OYE C13 "C4'" C 0 1 N N R 129.075 -50.378 -11.509 -4.292 -1.072 2.960 C13 OYE 17 OYE C14 C4G C 0 1 Y N N 131.685 -46.177 -13.131 8.792 2.197 1.035 C14 OYE 18 OYE C15 C4P C 0 1 N N R 129.108 -47.232 -16.819 5.912 -0.067 -2.101 C15 OYE 19 OYE C16 C5 C 0 1 Y N N 128.547 -51.197 -6.133 -7.967 1.810 -0.465 C16 OYE 20 OYE C17 "C5'" C 0 1 N N N 127.809 -49.945 -12.219 -3.743 -2.446 2.570 C17 OYE 21 OYE C18 C5G C 0 1 Y N N 131.380 -45.631 -11.953 9.212 1.774 2.301 C18 OYE 22 OYE C19 C5P C 0 1 N N N 127.577 -47.056 -16.916 5.430 -1.517 -2.186 C19 OYE 23 OYE C20 C6 C 0 1 N N N 128.793 -51.797 -4.961 -8.946 2.826 -0.864 C20 OYE 24 OYE C21 C6G C 0 1 N N N 132.327 -45.076 -11.196 10.067 2.618 3.048 C21 OYE 25 OYE C22 C8 C 0 1 Y N N 127.837 -50.142 -7.883 -6.574 0.167 -0.259 C22 OYE 26 OYE C23 C8G C 0 1 Y N N 129.555 -46.401 -12.826 7.925 0.225 1.501 C23 OYE 27 OYE C24 CB4 C 0 1 Y N N 123.251 -53.115 -6.138 -5.082 2.624 -5.065 C24 OYE 28 OYE C25 CB5 C 0 1 Y N N 123.578 -52.419 -7.298 -6.341 3.096 -4.745 C25 OYE 29 OYE C26 CB6 C 0 1 Y N N 124.556 -51.426 -7.271 -7.164 2.361 -3.913 C26 OYE 30 OYE C27 CBZ C 0 1 N N N 126.194 -50.129 -6.035 -7.617 0.360 -2.478 C27 OYE 31 OYE N1 N1 N 0 1 N N N 129.947 -52.433 -4.731 -9.319 3.747 0.038 N1 OYE 32 OYE N2 N1G N 0 1 N N N 133.657 -45.066 -11.637 10.449 3.792 2.498 N2 OYE 33 OYE N3 N2 N 0 1 N N N 132.037 -53.109 -5.459 -9.243 4.714 2.135 N3 OYE 34 OYE N4 N2G N 0 1 N N N 135.200 -45.655 -13.331 10.412 5.347 0.726 N4 OYE 35 OYE N5 N3 N 0 1 N N N 130.651 -51.884 -6.855 -7.920 2.829 1.682 N5 OYE 36 OYE N6 N3G N 0 1 N N N 132.952 -46.186 -13.586 9.208 3.376 0.558 N6 OYE 37 OYE N7 N7 N 1 1 Y N N 127.511 -50.511 -6.641 -7.381 0.762 -1.089 N7 OYE 38 OYE N8 N7G N 0 1 Y N N 130.066 -45.771 -11.770 8.648 0.563 2.528 N8 OYE 39 OYE N9 N9 N 0 1 Y N N 129.064 -50.587 -8.143 -6.603 0.809 0.945 N9 OYE 40 OYE N10 N9G N 0 1 Y N N 130.559 -46.659 -13.659 7.988 1.201 0.549 N10 OYE 41 OYE O5 "O2'" O 0 1 N N N 131.135 -51.944 -10.795 -7.494 0.253 3.937 O5 OYE 42 OYE O6 O2P O 0 1 N N N 130.641 -49.690 -14.627 9.074 1.628 -2.400 O6 OYE 43 OYE O7 "O3'" O 0 1 N N N 128.910 -52.715 -11.990 -5.352 -0.637 5.117 O7 OYE 44 OYE O8 O3P O 0 1 N N N 130.601 -49.107 -17.198 7.061 1.052 -3.943 O8 OYE 45 OYE O9 "O4'" O 0 1 N N N 129.323 -49.605 -10.324 -4.683 -0.347 1.780 O9 OYE 46 OYE O10 O4P O 0 1 N N N 129.752 -46.451 -15.768 6.193 0.277 -0.732 O10 OYE 47 OYE O11 "O5'" O 0 1 N N N 126.784 -49.742 -11.260 -2.515 -2.284 1.857 O11 OYE 48 OYE O12 O5P O 0 1 N N N 126.687 -47.484 -15.863 4.156 -1.633 -1.547 O12 OYE 49 OYE O13 O6 O 0 1 N N N 127.839 -51.750 -3.996 -9.408 2.838 -1.994 O13 OYE 50 OYE O14 O6G O 0 1 N N N 132.047 -44.571 -10.110 10.456 2.291 4.156 O14 OYE 51 OYE O15 OA1 O 0 1 N N N 126.007 -45.003 -15.238 3.164 -3.612 -2.864 O15 OYE 52 OYE O16 OA2 O -1 1 N N N 124.444 -46.913 -15.088 4.142 -4.018 -0.575 O16 OYE 53 OYE O17 OAB O 0 1 N N N 126.126 -46.706 -13.311 1.906 -2.757 -0.785 O17 OYE 54 OYE O18 OBG O 0 1 N N N 124.877 -48.903 -12.749 -0.413 -2.971 0.436 O18 OYE 55 OYE P1 PA P 0 1 N N N 125.876 -46.471 -14.893 3.349 -3.022 -1.449 P1 OYE 56 OYE P2 PB P 0 1 N N N 124.919 -47.341 -12.413 0.546 -3.614 -0.686 P2 OYE 57 OYE P3 PG P 0 1 N N N 125.259 -49.994 -11.633 -1.658 -3.525 1.293 P3 OYE 58 OYE H2 H2 H 0 1 N N N 125.389 -51.592 -3.998 -5.122 -0.255 -3.308 H2 OYE 59 OYE H3 H3 H 0 1 N N N 123.662 -53.354 -4.046 -3.660 1.051 -4.799 H3 OYE 60 OYE H5 H5 H 0 1 N N N 130.942 -50.193 -9.093 -5.531 1.340 2.683 H5 OYE 61 OYE H6 H6 H 0 1 N N N 131.594 -47.444 -15.377 6.982 2.194 -1.018 H6 OYE 62 OYE H7 H7 H 0 1 N N N 129.830 -52.694 -9.288 -7.250 -1.194 2.459 H7 OYE 63 OYE H8 H8 H 0 1 N N N 128.882 -48.534 -14.361 8.841 -0.211 -1.451 H8 OYE 64 OYE H9 H9 H 0 1 N N N 127.832 -51.784 -10.416 -5.800 -2.294 3.945 H9 OYE 65 OYE H10 H10 H 0 1 N N N 128.583 -49.331 -16.624 7.546 -0.863 -3.299 H10 OYE 66 OYE H11 H11 H 0 1 N N N 129.936 -50.392 -12.194 -3.534 -0.509 3.503 H11 OYE 67 OYE H12 H12 H 0 1 N N N 129.556 -46.992 -17.794 5.152 0.603 -2.500 H12 OYE 68 OYE H13 H13 H 0 1 N N N 127.995 -49.007 -12.764 -3.566 -3.036 3.469 H13 OYE 69 OYE H14 H14 H 0 1 N N N 127.499 -50.726 -12.929 -4.466 -2.960 1.936 H14 OYE 70 OYE H15 H15 H 0 1 N N N 127.399 -45.979 -17.050 5.339 -1.809 -3.232 H15 OYE 71 OYE H16 H16 H 0 1 N N N 127.263 -47.595 -17.822 6.147 -2.168 -1.687 H16 OYE 72 OYE H17 H17 H 0 1 N N N 127.212 -49.579 -8.560 -5.973 -0.701 -0.488 H17 OYE 73 OYE H18 H18 H 0 1 N N N 128.516 -46.656 -12.978 7.364 -0.693 1.412 H18 OYE 74 OYE H19 H19 H 0 1 N N N 122.491 -53.882 -6.161 -4.441 3.197 -5.719 H19 OYE 75 OYE H20 H20 H 0 1 N N N 123.072 -52.649 -8.224 -6.686 4.036 -5.152 H20 OYE 76 OYE H21 H21 H 0 1 N N N 124.797 -50.882 -8.172 -8.148 2.730 -3.662 H21 OYE 77 OYE H22 H22 H 0 1 N N N 126.364 -49.865 -4.981 -8.660 0.545 -2.738 H22 OYE 78 OYE H23 H23 H 0 1 N N N 125.808 -49.252 -6.575 -7.398 -0.701 -2.592 H23 OYE 79 OYE H24 H24 H 0 1 N N N 134.378 -44.654 -11.081 11.041 4.384 2.988 H24 OYE 80 OYE H25 H25 H 0 1 N N N 132.202 -53.552 -4.578 -9.891 5.379 1.853 H25 OYE 81 OYE H26 H26 H 0 1 N N N 132.736 -53.140 -6.173 -8.890 4.734 3.039 H26 OYE 82 OYE H27 H27 H 0 1 N N N 135.403 -46.069 -14.218 11.005 5.926 1.230 H27 OYE 83 OYE H28 H28 H 0 1 N N N 135.935 -45.248 -12.789 10.106 5.614 -0.155 H28 OYE 84 OYE H29 H29 H 0 1 N N N 131.348 -51.906 -7.571 -7.585 2.867 2.591 H29 OYE 85 OYE H30 H30 H 0 1 N N N 131.888 -52.027 -10.222 -8.029 -0.293 4.529 H30 OYE 86 OYE H31 H31 H 0 1 N N N 130.848 -49.638 -13.701 9.674 1.313 -3.090 H31 OYE 87 OYE H32 H32 H 0 1 N N N 128.738 -53.582 -11.641 -6.133 -0.664 5.687 H32 OYE 88 OYE H33 H33 H 0 1 N N N 130.809 -50.005 -16.967 7.872 1.235 -4.437 H33 OYE 89 # # 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 OYE O8 C11 SING N N 1 OYE C19 C15 SING N N 2 OYE C19 O12 SING N N 3 OYE C15 C11 SING N N 4 OYE C15 O10 SING N N 5 OYE C11 C9 SING N N 6 OYE O12 P1 SING N N 7 OYE O10 C5 SING N N 8 OYE O15 P1 DOUB N N 9 OYE O16 P1 SING N N 10 OYE C9 C5 SING N N 11 OYE C9 O6 SING N N 12 OYE C5 N10 SING N N 13 OYE P1 O17 SING N N 14 OYE N10 C14 SING Y N 15 OYE N10 C23 SING Y N 16 OYE N6 C14 SING N N 17 OYE N6 C8 DOUB N N 18 OYE N4 C8 SING N N 19 OYE O17 P2 SING N N 20 OYE C14 C18 DOUB Y N 21 OYE O2 P2 DOUB N N 22 OYE C8 N2 SING N N 23 OYE C23 N8 DOUB Y N 24 OYE O18 P2 SING N N 25 OYE O18 P3 SING N N 26 OYE P2 O1 SING N N 27 OYE O4 P3 DOUB N N 28 OYE C17 C13 SING N N 29 OYE C17 O11 SING N N 30 OYE O7 C10 SING N N 31 OYE C18 N8 SING Y N 32 OYE C18 C21 SING N N 33 OYE N2 C21 SING N N 34 OYE P3 O11 SING N N 35 OYE P3 O3 SING N N 36 OYE C13 C10 SING N N 37 OYE C13 O9 SING N N 38 OYE C21 O14 DOUB N N 39 OYE C10 C7 SING N N 40 OYE O5 C7 SING N N 41 OYE O9 C4 SING N N 42 OYE C7 C4 SING N N 43 OYE C4 N9 SING N N 44 OYE N9 C22 SING Y N 45 OYE N9 C12 SING Y N 46 OYE C22 N7 DOUB Y N 47 OYE C25 C26 DOUB Y N 48 OYE C25 C24 SING Y N 49 OYE C26 C1 SING Y N 50 OYE C12 N5 SING N N 51 OYE C12 C16 DOUB Y N 52 OYE N5 C6 SING N N 53 OYE N7 C16 SING Y N 54 OYE N7 C27 SING N N 55 OYE C24 C3 DOUB Y N 56 OYE C16 C20 SING N N 57 OYE C1 C27 SING N N 58 OYE C1 C2 DOUB Y N 59 OYE C6 N3 SING N N 60 OYE C6 N1 DOUB N N 61 OYE C20 N1 SING N N 62 OYE C20 O13 DOUB N N 63 OYE C3 C2 SING Y N 64 OYE C2 H2 SING N N 65 OYE C3 H3 SING N N 66 OYE C4 H5 SING N N 67 OYE C5 H6 SING N N 68 OYE C7 H7 SING N N 69 OYE C9 H8 SING N N 70 OYE C10 H9 SING N N 71 OYE C11 H10 SING N N 72 OYE C13 H11 SING N N 73 OYE C15 H12 SING N N 74 OYE C17 H13 SING N N 75 OYE C17 H14 SING N N 76 OYE C19 H15 SING N N 77 OYE C19 H16 SING N N 78 OYE C22 H17 SING N N 79 OYE C23 H18 SING N N 80 OYE C24 H19 SING N N 81 OYE C25 H20 SING N N 82 OYE C26 H21 SING N N 83 OYE C27 H22 SING N N 84 OYE C27 H23 SING N N 85 OYE N2 H24 SING N N 86 OYE N3 H25 SING N N 87 OYE N3 H26 SING N N 88 OYE N4 H27 SING N N 89 OYE N4 H28 SING N N 90 OYE N5 H29 SING N N 91 OYE O5 H30 SING N N 92 OYE O6 H31 SING N N 93 OYE O7 H32 SING N N 94 OYE O8 H33 SING N N 95 # # 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 OYE InChI InChI 1.03 "InChI=1S/C27H33N10O18P3/c28-26-31-20-14(22(42)33-26)30-9-36(20)24-18(40)16(38)12(52-24)7-50-56(44,45)54-58(48,49)55-57(46,47)51-8-13-17(39)19(41)25(53-13)37-10-35(6-11-4-2-1-3-5-11)15-21(37)32-27(29)34-23(15)43/h1-5,9-10,12-13,16-19,24-25,38-41H,6-8H2,(H8-,28,29,31,32,33,34,42,43,44,45,46,47,48,49)/p-2/t12-,13-,16-,17-,18-,19-,24-,25-/m1/s1" OYE InChIKey InChI 1.03 DBIWUCQKTGTGGL-JIUDXVAXSA-L OYE SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5c[n+](Cc6ccccc6)c7C(=O)N=C(N)Nc57)[C@@H](O)[C@H]3O" OYE SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5c[n+](Cc6ccccc6)c7C(=O)N=C(N)Nc57)[CH](O)[CH]3O" OYE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C[n+]2cn(c3c2C(=O)N=C(N3)N)[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OC[C@@H]5[C@H]([C@H]([C@@H](O5)n6cnc7c6N=C(NC7=O)N)O)O)O)O" OYE SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C[n+]2cn(c3c2C(=O)N=C(N3)N)C4C(C(C(O4)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OCC5C(C(C(O5)n6cnc7c6N=C(NC7=O)N)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id OYE _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 "[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-3~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-phosphoryl] 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 OYE "Create component" 2020-04-07 PDBE OYE "Other modification" 2020-04-09 PDBE OYE "Initial release" 2020-04-15 RCSB OYE "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id OYE _pdbx_chem_comp_synonyms.name "[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##