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 
# 
