data_DYF
# 
_chem_comp.id                                    DYF 
_chem_comp.name                                  "[(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H36 N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-09-19 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        465.478 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DYF 
_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        6KXF 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_chem_comp.pdbx_pcm                              Y 
# 
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 
DYF C29 C1  C 0 1 N N N N N N -15.652 -24.726 27.675 -13.019 -0.029 0.315  C29 DYF 1  
DYF C26 C2  C 0 1 N N N N N N -15.922 -22.531 24.422 -9.337  -1.077 0.408  C26 DYF 2  
DYF C25 C3  C 0 1 N N N N N N -16.463 -21.313 24.575 -8.241  -0.365 0.651  C25 DYF 3  
DYF O13 O1  O 0 1 N N N N N N -21.629 -15.986 27.615 3.732   2.487  0.369  O13 DYF 4  
DYF C21 C4  C 0 1 N N N N N N -15.665 -17.838 23.947 -4.533  -0.547 -0.131 C21 DYF 5  
DYF C17 C5  C 0 1 N N N N N N -19.150 -16.838 24.316 -1.038  0.716  0.021  C17 DYF 6  
DYF O11 O2  O 0 1 N N N N N N -19.685 -14.681 30.285 4.877   0.082  -1.939 O11 DYF 7  
DYF N22 N1  N 0 1 N N N N N N -15.818 -19.000 23.276 -5.829  -0.096 0.383  N22 DYF 8  
DYF C10 C6  C 0 1 N N R N N N -20.935 -15.038 29.725 5.101   1.115  -0.978 C10 DYF 9  
DYF N19 N2  N 0 1 N N N N N N -17.739 -16.629 24.205 -2.149  -0.006 -0.226 N19 DYF 10 
DYF C30 C7  C 0 1 N N N N N N -14.357 -25.341 28.258 -14.014 0.084  -0.841 C30 DYF 11 
DYF C31 C8  C 0 1 N N N N N N -14.528 -26.341 29.409 -15.367 0.555  -0.306 C31 DYF 12 
DYF N14 N3  N 0 1 N N N N N N -19.398 -16.148 28.040 2.678   0.793  -0.602 N14 DYF 13 
DYF C28 C9  C 0 1 N N N N N N -15.293 -23.625 26.666 -11.665 -0.500 -0.221 C28 DYF 14 
DYF C27 C10 C 0 1 N N N N N N -16.124 -23.696 25.404 -10.670 -0.613 0.936  C27 DYF 15 
DYF C23 C11 C 0 1 N N N N N N -16.254 -20.296 23.427 -6.939  -0.818 0.136  C23 DYF 16 
DYF C20 C12 C 0 1 N N N N N N -16.854 -17.130 23.181 -3.445  0.445  0.288  C20 DYF 17 
DYF C16 C13 C 0 1 N N N N N N -19.648 -16.151 25.574 0.294   0.252  -0.507 C16 DYF 18 
DYF C15 C14 C 0 1 N N N N N N -19.139 -16.862 26.806 1.382   1.244  -0.088 C15 DYF 19 
DYF C12 C15 C 0 1 N N N N N N -20.739 -15.753 28.377 3.789   1.515  -0.355 C12 DYF 20 
DYF C01 C16 C 0 1 N N N N N N -20.836 -17.226 31.046 6.410   1.751  1.053  C01 DYF 21 
DYF C02 C17 C 0 1 N N N N N N -21.609 -15.906 30.822 6.047   0.602  0.111  C02 DYF 22 
DYF C03 C18 C 0 1 N N N N N N -23.083 -16.231 30.508 5.357   -0.510 0.904  C03 DYF 23 
DYF C04 C19 C 0 1 N N N N N N -21.581 -15.058 32.121 7.319   0.052  -0.537 C04 DYF 24 
DYF O05 O3  O 0 1 N N N N N N -22.334 -13.882 31.916 8.202   -0.427 0.479  O05 DYF 25 
DYF P06 P1  P 0 1 N N N N N N -21.673 -12.364 31.888 9.640   -1.076 0.157  P06 DYF 26 
DYF O07 O4  O 0 1 N N N N N N -21.960 -11.716 33.234 10.301  -1.621 1.520  O07 DYF 27 
DYF O08 O5  O 0 1 N N N N N N -22.444 -11.604 30.822 9.473   -2.199 -0.793 O08 DYF 28 
DYF O09 O6  O 0 1 N N N N N N -20.159 -12.347 31.848 10.599  0.041  -0.495 O09 DYF 29 
DYF O18 O7  O 0 1 N N N N N N -19.859 -17.463 23.561 -1.112  1.739  0.669  O18 DYF 30 
DYF O24 O8  O 0 1 N N N N N N -16.318 -20.542 22.242 -6.866  -1.844 -0.513 O24 DYF 31 
DYF H1  H1  H 0 1 N N N N N N -16.251 -24.294 28.490 -12.902 0.945  0.791  H1  DYF 32 
DYF H2  H2  H 0 1 N N N N N N -16.234 -25.510 27.169 -13.390 -0.748 1.045  H2  DYF 33 
DYF H3  H3  H 0 1 N N N N N N -15.305 -22.704 23.553 -9.272  -1.988 -0.169 H3  DYF 34 
DYF H4  H4  H 0 1 N N N N N N -17.021 -21.053 25.462 -8.306  0.546  1.227  H4  DYF 35 
DYF H5  H5  H 0 1 N N N N N N -14.689 -17.360 23.774 -4.303  -1.531 0.277  H5  DYF 36 
DYF H6  H6  H 0 1 N N N N N N -15.839 -17.934 25.029 -4.573  -0.604 -1.218 H6  DYF 37 
DYF H7  H7  H 0 1 N N N N N N -19.824 -14.241 31.116 4.480   -0.719 -1.571 H7  DYF 38 
DYF H8  H8  H 0 1 N N N N N N -15.502 -18.873 22.336 -5.887  0.723  0.900  H8  DYF 39 
DYF H9  H9  H 0 1 N N N N N N -21.551 -14.142 29.562 5.548   1.979  -1.470 H9  DYF 40 
DYF H10 H10 H 0 1 N N N N N N -17.317 -16.071 24.920 -2.091  -0.824 -0.743 H10 DYF 41 
DYF H11 H11 H 0 1 N N N N N N -13.837 -25.860 27.440 -13.642 0.803  -1.572 H11 DYF 42 
DYF H12 H12 H 0 1 N N N N N N -13.731 -24.514 28.625 -14.130 -0.890 -1.317 H12 DYF 43 
DYF H13 H13 H 0 1 N N N N N N -13.540 -26.702 29.731 -16.076 0.636  -1.129 H13 DYF 44 
DYF H14 H14 H 0 1 N N N N N N -15.031 -25.846 30.253 -15.739 -0.163 0.425  H14 DYF 45 
DYF H15 H15 H 0 1 N N N N N N -15.136 -27.192 29.068 -15.251 1.529  0.170  H15 DYF 46 
DYF H16 H16 H 0 1 N N N N N N -18.643 -15.930 28.658 2.736   -0.025 -1.119 H16 DYF 47 
DYF H17 H17 H 0 1 N N N N N N -14.232 -23.728 26.395 -11.782 -1.474 -0.697 H17 DYF 48 
DYF H18 H18 H 0 1 N N N N N N -15.456 -22.646 27.140 -11.293 0.219  -0.951 H18 DYF 49 
DYF H19 H19 H 0 1 N N N N N N -17.185 -23.716 25.695 -11.042 -1.332 1.666  H19 DYF 50 
DYF H20 H20 H 0 1 N N N N N N -15.870 -24.630 24.881 -10.553 0.361  1.411  H20 DYF 51 
DYF H21 H21 H 0 1 N N N N N N -16.473 -16.302 22.565 -3.675  1.429  -0.120 H21 DYF 52 
DYF H22 H22 H 0 1 N N N N N N -17.380 -17.852 22.540 -3.405  0.503  1.375  H22 DYF 53 
DYF H23 H23 H 0 1 N N N N N N -19.290 -15.111 25.583 0.524   -0.732 -0.099 H23 DYF 54 
DYF H24 H24 H 0 1 N N N N N N -20.748 -16.161 25.580 0.254   0.194  -1.594 H24 DYF 55 
DYF H25 H25 H 0 1 N N N N N N -19.627 -17.846 26.865 1.422   1.302  0.999  H25 DYF 56 
DYF H26 H26 H 0 1 N N N N N N -18.052 -16.997 26.705 1.152   2.228  -0.496 H26 DYF 57 
DYF H27 H27 H 0 1 N N N N N N -21.337 -17.817 31.827 5.499   2.190  1.459  H27 DYF 58 
DYF H28 H28 H 0 1 N N N N N N -20.814 -17.801 30.109 7.025   1.370  1.869  H28 DYF 59 
DYF H29 H29 H 0 1 N N N N N N -19.807 -16.999 31.362 6.966   2.510  0.503  H29 DYF 60 
DYF H30 H30 H 0 1 N N N N N N -23.504 -16.845 31.318 5.098   -1.328 0.232  H30 DYF 61 
DYF H31 H31 H 0 1 N N N N N N -23.655 -15.295 30.423 6.030   -0.875 1.679  H31 DYF 62 
DYF H32 H32 H 0 1 N N N N N N -23.142 -16.784 29.559 4.450   -0.118 1.365  H32 DYF 63 
DYF H33 H33 H 0 1 N N N N N N -22.017 -15.636 32.949 7.060   -0.767 -1.209 H33 DYF 64 
DYF H34 H34 H 0 1 N N N N N N -20.542 -14.793 32.367 7.811   0.844  -1.102 H34 DYF 65 
DYF H35 H35 H 0 1 N N N N N N -22.554 -10.984 33.113 11.171  -2.026 1.401  H35 DYF 66 
DYF H36 H36 H 0 1 N N N N N N -19.867 -11.826 31.109 10.753  0.807  0.073  H36 DYF 67 
# 
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 
DYF O24 C23 DOUB N N 1  
DYF C20 C21 SING N N 2  
DYF C20 N19 SING N N 3  
DYF N22 C23 SING N N 4  
DYF N22 C21 SING N N 5  
DYF C23 C25 SING N N 6  
DYF O18 C17 DOUB N N 7  
DYF N19 C17 SING N N 8  
DYF C17 C16 SING N N 9  
DYF C26 C25 DOUB N E 10 
DYF C26 C27 SING N N 11 
DYF C27 C28 SING N N 12 
DYF C16 C15 SING N N 13 
DYF C28 C29 SING N N 14 
DYF C15 N14 SING N N 15 
DYF O13 C12 DOUB N N 16 
DYF C29 C30 SING N N 17 
DYF N14 C12 SING N N 18 
DYF C30 C31 SING N N 19 
DYF C12 C10 SING N N 20 
DYF C10 O11 SING N N 21 
DYF C10 C02 SING N N 22 
DYF C03 C02 SING N N 23 
DYF O08 P06 DOUB N N 24 
DYF C02 C01 SING N N 25 
DYF C02 C04 SING N N 26 
DYF O09 P06 SING N N 27 
DYF P06 O05 SING N N 28 
DYF P06 O07 SING N N 29 
DYF O05 C04 SING N N 30 
DYF C29 H1  SING N N 31 
DYF C29 H2  SING N N 32 
DYF C26 H3  SING N N 33 
DYF C25 H4  SING N N 34 
DYF C21 H5  SING N N 35 
DYF C21 H6  SING N N 36 
DYF O11 H7  SING N N 37 
DYF N22 H8  SING N N 38 
DYF C10 H9  SING N N 39 
DYF N19 H10 SING N N 40 
DYF C30 H11 SING N N 41 
DYF C30 H12 SING N N 42 
DYF C31 H13 SING N N 43 
DYF C31 H14 SING N N 44 
DYF C31 H15 SING N N 45 
DYF N14 H16 SING N N 46 
DYF C28 H17 SING N N 47 
DYF C28 H18 SING N N 48 
DYF C27 H19 SING N N 49 
DYF C27 H20 SING N N 50 
DYF C20 H21 SING N N 51 
DYF C20 H22 SING N N 52 
DYF C16 H23 SING N N 53 
DYF C16 H24 SING N N 54 
DYF C15 H25 SING N N 55 
DYF C15 H26 SING N N 56 
DYF C01 H27 SING N N 57 
DYF C01 H28 SING N N 58 
DYF C01 H29 SING N N 59 
DYF C03 H30 SING N N 60 
DYF C03 H31 SING N N 61 
DYF C03 H32 SING N N 62 
DYF C04 H33 SING N N 63 
DYF C04 H34 SING N N 64 
DYF O07 H35 SING N N 65 
DYF O09 H36 SING N N 66 
# 
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 
DYF InChI            InChI                1.03  "InChI=1S/C19H36N3O8P/c1-4-5-6-7-8-9-15(23)20-12-13-21-16(24)10-11-22-18(26)17(25)19(2,3)14-30-31(27,28)29/h8-9,17,25H,4-7,10-14H2,1-3H3,(H,20,23)(H,21,24)(H,22,26)(H2,27,28,29)/b9-8+/t17-/m0/s1" 
DYF InChIKey         InChI                1.03  KFHBREMVHHVYJE-IJDCCNJMSA-N                                                                                                                                                                         
DYF SMILES_CANONICAL CACTVS               3.385 "CCCCC\C=C\C(=O)NCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(O)=O"                                                                                                                                      
DYF SMILES           CACTVS               3.385 "CCCCCC=CC(=O)NCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(O)=O"                                                                                                                                         
DYF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCC/C=C/C(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O"                                                                                                                                       
DYF SMILES           "OpenEye OEToolkits" 2.0.7 "CCCCCC=CC(=O)NCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)O)O"                                                                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           DYF 
_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        "[(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen 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 
DYF "Create component" 2019-09-19 PDBJ 
DYF "Initial release"  2020-05-06 RCSB 
DYF "Modify PCM"       2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1 DYF CYS None Crosslinker "Amino-acid side chain" "Any position" C26 SG ? ? 
2 DYF SER None Crosslinker "Amino-acid side chain" "Any position" O07 CB ? ? 
3 DYF SER None Crosslinker "Amino-acid side chain" "Any position" P06 OG ? ? 
# 
