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 ? ?
#