data_X0K # _chem_comp.id X0K _chem_comp.name "[(2~{S})-2-oxidanyl-3-[[4-(2-pyren-1-ylethynyl)phenyl]methoxy]propyl] dihydrogen phosphite" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C28 H23 O5 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-05-26 _chem_comp.pdbx_modified_date 2024-01-12 _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 470.453 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X0K _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 8P69 _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 X0K C1 C1 C 0 1 Y N N N N N 20.800 17.343 24.745 -9.422 -1.977 -0.391 C1 X0K 1 X0K C2 C2 C 0 1 Y N N N N N 19.445 17.000 24.878 -8.869 -3.016 0.197 C2 X0K 2 X0K C3 C3 C 0 1 Y N N N N N 18.758 17.288 26.069 -7.458 -3.043 0.602 C3 X0K 3 X0K C4 C4 C 0 1 Y N N N N N 18.755 18.190 28.338 -5.243 -2.054 0.810 C4 X0K 4 X0K C5 C5 C 0 1 Y N N N N N 19.437 18.791 29.414 -4.464 -1.011 0.593 C5 X0K 5 X0K C6 C6 C 0 1 Y N N N N N 21.510 19.720 30.373 -4.256 1.249 -0.288 C6 X0K 6 X0K C7 C7 C 0 1 Y N N N N N 22.866 20.064 30.222 -4.788 2.453 -0.938 C7 X0K 7 X0K P P1 P 0 1 N N N N N N 14.302 24.278 38.236 10.501 -0.465 -0.939 P X0K 8 X0K OP1 O1 O 0 1 N N N N N N 13.152 23.346 38.200 10.792 -1.971 -0.450 OP1 X0K 9 X0K OP2 O2 O 0 1 N N N N N N 14.090 25.696 38.595 10.759 -0.572 -2.525 OP2 X0K 10 X0K "O5'" O3 O 0 1 N N N N N N 15.414 23.663 39.221 8.894 -0.393 -0.866 "O5'" X0K 11 X0K "C2'" C8 C 0 1 N N S N N N 16.697 21.837 40.267 6.681 -0.028 0.034 "C2'" X0K 12 X0K "C3'" C9 C 0 1 N N N N N N 18.116 22.372 39.967 5.927 0.531 1.242 "C3'" X0K 13 X0K "C4'" C10 C 0 1 N N N N N N 18.585 20.848 38.153 3.732 1.107 2.014 "C4'" X0K 14 X0K C12 C11 C 0 1 Y N N N N N 18.079 20.609 35.668 1.482 0.029 1.826 C12 X0K 15 X0K C11 C12 C 0 1 Y N N N N N 18.529 20.380 34.350 0.155 0.047 1.447 C11 X0K 16 X0K C14 C13 C 0 1 Y N N N N N 20.841 20.597 35.095 0.440 2.287 0.596 C14 X0K 17 X0K C13 C14 C 0 1 Y N N N N N 20.399 20.776 36.417 1.767 2.255 0.975 C13 X0K 18 X0K C15 C15 C 0 1 N N N N N N 20.410 20.154 32.740 -1.752 1.204 0.432 C15 X0K 19 X0K C16 C16 C 0 1 N N N N N N 20.891 19.957 31.652 -2.880 1.224 0.108 C16 X0K 20 X0K C8 C17 C 0 1 Y N N N N N 23.528 19.821 29.008 -6.040 2.557 -1.331 C8 X0K 21 X0K C8A C18 C 0 1 Y N N N N N 22.838 19.215 27.944 -6.958 1.424 -1.122 C8A X0K 22 X0K C3A C19 C 0 1 Y N N N N N 19.432 17.910 27.138 -6.657 -2.023 0.401 C3A X0K 23 X0K C5A C20 C 0 1 Y N N N N N 20.802 19.131 29.299 -5.003 0.194 -0.059 C5A X0K 24 X0K C10 C21 C 0 1 Y N N N N N 22.834 18.304 25.683 -9.090 0.290 -1.244 C10 X0K 25 X0K C9 C22 C 0 1 Y N N N N N 23.507 18.943 26.740 -8.218 1.458 -1.488 C9 X0K 26 X0K "C1'" C23 C 0 1 N N N N N N 15.693 22.279 39.173 8.186 0.019 0.305 "C1'" X0K 27 X0K "O3'" O4 O 0 1 N N N N N N 16.861 20.434 40.474 6.280 -1.380 -0.194 "O3'" X0K 28 X0K "O1'" O5 O 0 1 N N N N N N 18.573 22.192 38.623 4.531 0.596 0.945 "O1'" X0K 29 X0K C12A C24 C 0 0 Y N N N N N 19.026 20.785 36.706 2.286 1.131 1.592 C12A X0K 30 X0K C14A C25 C 0 0 Y N N N N N 19.907 20.390 34.065 -0.375 1.179 0.828 C14A X0K 31 X0K C10A C26 C 0 0 Y N N N N N 21.476 17.963 25.811 -8.606 -0.780 -0.661 C10A X0K 32 X0K C10C C27 C 0 0 Y N N N N N 21.476 18.867 28.086 -6.419 0.218 -0.467 C10C X0K 33 X0K C10B C28 C 0 0 Y N N N N N 20.795 18.248 27.013 -7.189 -0.813 -0.252 C10B X0K 34 X0K H1 H1 H 0 1 N N N N N N 21.323 17.131 23.824 -10.464 -2.002 -0.676 H1 X0K 35 X0K H2 H2 H 0 1 N N N N N N 18.930 16.514 24.063 -9.479 -3.886 0.390 H2 X0K 36 X0K H3 H3 H 0 1 N N N N N N 17.713 17.032 26.165 -7.067 -3.929 1.081 H3 X0K 37 X0K H4 H4 H 0 1 N N N N N N 17.708 17.943 28.435 -4.841 -2.935 1.289 H4 X0K 38 X0K H5 H5 H 0 1 N N N N N N 18.911 18.993 30.335 -3.428 -1.041 0.896 H5 X0K 39 X0K H7 H6 H 0 1 N N N N N N 23.400 20.517 31.044 -4.124 3.290 -1.099 H7 X0K 40 X0K H6 H7 H 0 1 N N N N N N 13.454 22.479 37.954 10.684 -2.102 0.502 H6 X0K 41 X0K H15 H8 H 0 1 N N N N N N 14.921 26.157 38.572 11.693 -0.626 -2.769 H15 X0K 42 X0K "H2'" H9 H 0 1 N N N N N N 16.370 22.296 41.212 6.452 0.573 -0.847 "H2'" X0K 43 X0K "H3''" H10 H 0 0 N N N N N N 18.821 21.856 40.636 6.086 -0.120 2.102 "H3''" X0K 44 X0K "H3'" H11 H 0 1 N N N N N N 18.125 23.450 40.186 6.297 1.531 1.471 "H3'" X0K 45 X0K "H4'" H12 H 0 1 N N N N N N 17.572 20.427 38.239 3.845 0.468 2.889 "H4'" X0K 46 X0K "H4''" H13 H 0 0 N N N N N N 19.281 20.258 38.767 4.056 2.118 2.258 "H4''" X0K 47 X0K H12 H14 H 0 1 N N N N N N 17.021 20.650 35.883 1.893 -0.845 2.309 H12 X0K 48 X0K H11 H15 H 0 1 N N N N N N 17.816 20.197 33.560 -0.471 -0.814 1.629 H11 X0K 49 X0K H14 H16 H 0 1 N N N N N N 21.897 20.618 34.871 0.036 3.165 0.114 H14 X0K 50 X0K H13 H17 H 0 1 N N N N N N 21.118 20.907 37.212 2.401 3.108 0.788 H13 X0K 51 X0K H8 H18 H 0 1 N N N N N N 24.565 20.099 28.892 -6.389 3.463 -1.804 H8 X0K 52 X0K H10 H19 H 0 1 N N N N N N 23.362 18.074 24.770 -10.127 0.319 -1.545 H10 X0K 53 X0K H9 H20 H 0 1 N N N N N N 24.543 19.226 26.625 -8.617 2.340 -1.967 H9 X0K 54 X0K "H1''" H21 H 0 0 N N N N N N 14.753 21.725 39.312 8.427 -0.651 1.130 "H1''" X0K 55 X0K "H1'" H22 H 0 1 N N N N N N 16.118 22.039 38.187 8.477 1.036 0.566 "H1'" X0K 56 X0K H16 H23 H 0 1 N N N N N N 17.497 20.288 41.164 6.454 -1.973 0.550 H16 X0K 57 # 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 X0K C1 C2 DOUB Y N 1 X0K C1 C10A SING Y N 2 X0K C2 C3 SING Y N 3 X0K C10 C10A DOUB Y N 4 X0K C10 C9 SING Y N 5 X0K C10A C10B SING Y N 6 X0K C3 C3A DOUB Y N 7 X0K C9 C8A DOUB Y N 8 X0K C10B C3A SING Y N 9 X0K C10B C10C DOUB Y N 10 X0K C3A C4 SING Y N 11 X0K C8A C10C SING Y N 12 X0K C8A C8 SING Y N 13 X0K C10C C5A SING Y N 14 X0K C4 C5 DOUB Y N 15 X0K C8 C7 DOUB Y N 16 X0K C5A C5 SING Y N 17 X0K C5A C6 DOUB Y N 18 X0K C7 C6 SING Y N 19 X0K C6 C16 SING N N 20 X0K C16 C15 TRIP N N 21 X0K C15 C14A SING N N 22 X0K C14A C11 DOUB Y N 23 X0K C14A C14 SING Y N 24 X0K C11 C12 SING Y N 25 X0K C14 C13 DOUB Y N 26 X0K C12 C12A DOUB Y N 27 X0K C13 C12A SING Y N 28 X0K C12A "C4'" SING N N 29 X0K "C4'" "O1'" SING N N 30 X0K OP1 P SING N N 31 X0K P OP2 SING N N 32 X0K P "O5'" SING N N 33 X0K "O1'" "C3'" SING N N 34 X0K "C1'" "O5'" SING N N 35 X0K "C1'" "C2'" SING N N 36 X0K "C3'" "C2'" SING N N 37 X0K "C2'" "O3'" SING N N 38 X0K C1 H1 SING N N 39 X0K C2 H2 SING N N 40 X0K C3 H3 SING N N 41 X0K C4 H4 SING N N 42 X0K C5 H5 SING N N 43 X0K C7 H7 SING N N 44 X0K OP1 H6 SING N N 45 X0K OP2 H15 SING N N 46 X0K "C2'" "H2'" SING N N 47 X0K "C3'" "H3''" SING N N 48 X0K "C3'" "H3'" SING N N 49 X0K "C4'" "H4'" SING N N 50 X0K "C4'" "H4''" SING N N 51 X0K C12 H12 SING N N 52 X0K C11 H11 SING N N 53 X0K C14 H14 SING N N 54 X0K C13 H13 SING N N 55 X0K C8 H8 SING N N 56 X0K C10 H10 SING N N 57 X0K C9 H9 SING N N 58 X0K "C1'" "H1''" SING N N 59 X0K "C1'" "H1'" SING N N 60 X0K "O3'" H16 SING N N 61 # 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 X0K InChI InChI 1.06 "InChI=1S/C28H23O5P/c29-25(18-33-34(30)31)17-32-16-20-6-4-19(5-7-20)8-9-21-10-11-24-13-12-22-2-1-3-23-14-15-26(21)28(24)27(22)23/h1-7,10-15,25,29-31H,16-18H2/t25-/m0/s1" X0K InChIKey InChI 1.06 XBSOHNNZYGCRHJ-VWLOTQADSA-N X0K SMILES_CANONICAL CACTVS 3.385 "O[C@@H](COCc1ccc(cc1)C#Cc2ccc3ccc4cccc5ccc2c3c45)COP(O)O" X0K SMILES CACTVS 3.385 "O[CH](COCc1ccc(cc1)C#Cc2ccc3ccc4cccc5ccc2c3c45)COP(O)O" X0K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2ccc3ccc(c4c3c2c(c1)cc4)C#Cc5ccc(cc5)COC[C@@H](COP(O)O)O" X0K SMILES "OpenEye OEToolkits" 2.0.7 "c1cc2ccc3ccc(c4c3c2c(c1)cc4)C#Cc5ccc(cc5)COCC(COP(O)O)O" # _pdbx_chem_comp_identifier.comp_id X0K _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~{S})-2-oxidanyl-3-[[4-(2-pyren-1-ylethynyl)phenyl]methoxy]propyl] dihydrogen phosphite" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site X0K "Create component" 2023-05-26 PDBE X0K "Initial release" 2024-01-17 RCSB #