data_D8E
# 
_chem_comp.id                                    D8E 
_chem_comp.name                                  "~{N}-[(2~{S},5~{S},14~{S})-2-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-9-methyl-3,8,15-tris(oxidanylidene)-1,4,9-triazacyclopentadec-14-yl]-5-methyl-1,2-oxazole-3-carboxamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H34 F N5 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "LIPID FRAGMENT" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-01-09 
_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                        531.576 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D8E 
_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        6FFS 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
D8E C2  C1  C 0 1 N N S N N N -28.295 4.670  0.221  1.447  0.812  0.160  C2  D8E 1  
D8E C3  C2  C 0 1 N N N N N N -28.306 5.532  1.508  2.315  1.045  1.398  C3  D8E 2  
D8E C13 C3  C 0 1 N N S N N N -26.279 6.419  -2.550 1.420  -2.300 -2.038 C13 D8E 3  
D8E C14 C4  C 0 1 N N N N N N -26.277 7.925  -2.612 2.243  -2.150 -3.319 C14 D8E 4  
D8E C15 C5  C 0 1 N N N N N N -26.304 5.756  -3.969 0.135  -3.073 -2.339 C15 D8E 5  
D8E C17 C6  C 0 1 N N N N N N -25.625 4.363  -3.954 -0.226 -3.948 -1.136 C17 D8E 6  
D8E C18 C7  C 0 1 N N N N N N -25.823 3.515  -5.183 -1.549 -3.501 -0.569 C18 D8E 7  
D8E C21 C8  C 0 1 Y N N N N N -29.584 5.455  2.338  3.734  1.321  0.973  C21 D8E 8  
D8E C22 C9  C 0 1 Y N N N N N -29.493 5.266  3.725  4.107  2.597  0.594  C22 D8E 9  
D8E C23 C10 C 0 1 Y N N N N N -30.647 5.192  4.509  5.408  2.851  0.205  C23 D8E 10 
D8E C24 C11 C 0 1 Y N N N N N -31.900 5.315  3.906  6.339  1.826  0.193  C24 D8E 11 
D8E C25 C12 C 0 1 Y N N N N N -31.992 5.524  2.530  5.965  0.548  0.573  C25 D8E 12 
D8E C26 C13 C 0 1 Y N N N N N -30.836 5.597  1.745  4.664  0.298  0.967  C26 D8E 13 
D8E C27 C14 C 0 1 N N N N N N -24.348 2.143  -3.859 -3.453 -3.767 0.868  C27 D8E 14 
D8E C28 C15 C 0 1 N N N N N N -24.837 1.053  -2.858 -3.191 -2.945 2.132  C28 D8E 15 
D8E C29 C16 C 0 1 N N N N N N -25.582 1.606  -1.598 -3.006 -1.474 1.755  C29 D8E 16 
D8E N1  N1  N 0 1 N N N N N N -28.024 3.235  0.415  0.019  0.875  0.537  N1  D8E 17 
D8E C4  C17 C 0 1 N N N N N N -28.051 2.263  -0.543 -0.273 0.538  1.826  C4  D8E 18 
D8E O5  O1  O 0 1 N N N N N N -28.356 2.564  -1.691 0.607  0.201  2.589  O5  D8E 19 
D8E C6  C18 C 0 1 N N S N N N -27.719 0.782  -0.353 -1.707 0.593  2.286  C6  D8E 20 
D8E N7  N2  N 0 1 N N N N N N -28.598 0.027  -1.234 -2.566 0.978  1.164  N7  D8E 21 
D8E C8  C19 C 0 1 N N N N N N -26.228 0.504  -0.704 -2.130 -0.784 2.802  C8  D8E 22 
D8E C9  C20 C 0 1 N N N N N N -29.636 -0.679 -0.740 -2.746 2.281  0.870  C9  D8E 23 
D8E C10 C21 C 0 1 N N N N N N -27.176 5.158  -0.651 1.742  -0.549 -0.414 C10 D8E 24 
D8E N11 N3  N 0 1 N N N N N N -27.405 5.937  -1.733 1.060  -0.963 -1.520 N11 D8E 25 
D8E O12 O2  O 0 1 N N N N N N -26.048 4.837  -0.293 2.574  -1.267 0.101  O12 D8E 26 
D8E O16 O3  O 0 1 N N N N N N -26.193 8.680  -1.519 3.488  -1.517 -3.014 O16 D8E 27 
D8E O19 O4  O 0 1 N N N N N N -26.521 3.917  -6.143 -2.066 -2.467 -0.937 O19 D8E 28 
D8E N20 N4  N 0 1 N N N N N N -25.139 2.337  -5.095 -2.155 -4.292 0.373  N20 D8E 29 
D8E F30 F1  F 0 1 N N N N N N -33.008 5.247  4.640  7.611  2.073  -0.188 F30 D8E 30 
D8E C31 C22 C 0 1 Y N N N N N -30.503 -1.398 -1.686 -3.615 2.672  -0.267 C31 D8E 31 
D8E O32 O5  O 0 1 N N N N N N -29.919 -0.754 0.440  -2.196 3.136  1.536  O32 D8E 32 
D8E N33 N5  N 0 1 Y N N N N N -30.191 -1.545 -2.909 -4.274 1.870  -1.066 N33 D8E 33 
D8E O34 O6  O 0 1 Y N N N N N -31.265 -2.270 -3.491 -4.900 2.488  -1.895 O34 D8E 34 
D8E C35 C23 C 0 1 Y N N N N N -32.148 -2.460 -2.517 -4.740 3.811  -1.757 C35 D8E 35 
D8E C36 C24 C 0 1 Y N N N N N -31.803 -1.964 -1.340 -3.907 3.993  -0.705 C36 D8E 36 
D8E C37 C25 C 0 1 N N N N N N -33.417 -3.195 -2.837 -5.364 4.887  -2.607 C37 D8E 37 
D8E C38 C26 C 0 1 N N N N N N -25.152 1.336  -6.140 -1.571 -5.548 0.851  C38 D8E 38 
D8E H1  H1  H 0 1 N N N N N N -29.253 4.802  -0.303 1.662  1.578  -0.585 H1  D8E 39 
D8E H2  H2  H 0 1 N N N N N N -27.469 5.205  2.143  1.931  1.899  1.956  H2  D8E 40 
D8E H3  H3  H 0 1 N N N N N N -28.155 6.581  1.215  2.291  0.158  2.031  H3  D8E 41 
D8E H4  H4  H 0 1 N N N N N N -25.344 6.103  -2.064 2.003  -2.837 -1.290 H4  D8E 42 
D8E H5  H5  H 0 1 N N N N N N -25.422 8.205  -3.245 2.432  -3.134 -3.747 H5  D8E 43 
D8E H6  H6  H 0 1 N N N N N N -27.213 8.213  -3.113 1.692  -1.541 -4.036 H6  D8E 44 
D8E H7  H7  H 0 1 N N N N N N -25.770 6.407  -4.678 -0.675 -2.370 -2.533 H7  D8E 45 
D8E H8  H8  H 0 1 N N N N N N -27.349 5.641  -4.292 0.286  -3.704 -3.214 H8  D8E 46 
D8E H9  H9  H 0 1 N N N N N N -26.022 3.805  -3.093 -0.300 -4.988 -1.452 H9  D8E 47 
D8E H10 H10 H 0 1 N N N N N N -24.544 4.518  -3.823 0.546  -3.854 -0.373 H10 D8E 48 
D8E H11 H11 H 0 1 N N N N N N -28.523 5.177  4.191  3.380  3.396  0.603  H11 D8E 49 
D8E H12 H12 H 0 1 N N N N N N -30.570 5.040  5.576  5.698  3.848  -0.091 H12 D8E 50 
D8E H13 H13 H 0 1 N N N N N N -32.962 5.630  2.067  6.690  -0.252 0.564  H13 D8E 51 
D8E H14 H14 H 0 1 N N N N N N -30.915 5.763  0.681  4.373  -0.698 1.267  H14 D8E 52 
D8E H15 H15 H 0 1 N N N N N N -23.324 1.878  -4.161 -4.120 -4.597 1.101  H15 D8E 53 
D8E H16 H16 H 0 1 N N N N N N -24.335 3.103  -3.321 -3.907 -3.134 0.106  H16 D8E 54 
D8E H17 H17 H 0 1 N N N N N N -25.523 0.380  -3.393 -4.038 -3.043 2.811  H17 D8E 55 
D8E H18 H18 H 0 1 N N N N N N -23.960 0.485  -2.515 -2.288 -3.310 2.622  H18 D8E 56 
D8E H19 H19 H 0 1 N N N N N N -24.858 2.166  -0.987 -2.526 -1.406 0.778  H19 D8E 57 
D8E H20 H20 H 0 1 N N N N N N -26.378 2.285  -1.938 -3.979 -0.984 1.715  H20 D8E 58 
D8E H21 H21 H 0 1 N N N N N N -27.797 2.943  1.344  -0.668 1.140  -0.094 H21 D8E 59 
D8E H22 H22 H 0 1 N N N N N N -27.897 0.501  0.696  -1.804 1.326  3.087  H22 D8E 60 
D8E H23 H23 H 0 1 N N N N N N -28.430 0.032  -2.220 -3.005 0.296  0.632  H23 D8E 61 
D8E H24 H24 H 0 1 N N N N N N -26.169 -0.456 -1.238 -2.694 -0.668 3.728  H24 D8E 62 
D8E H25 H25 H 0 1 N N N N N N -25.656 0.437  0.234  -1.243 -1.390 2.990  H25 D8E 63 
D8E H26 H26 H 0 1 N N N N N N -28.342 6.186  -1.979 0.381  -0.413 -1.941 H26 D8E 64 
D8E H27 H27 H 0 1 N N N N N N -26.207 9.597  -1.765 4.062  -1.389 -3.781 H27 D8E 65 
D8E H28 H28 H 0 1 N N N N N N -32.330 -1.975 -0.397 -3.551 4.925  -0.292 H28 D8E 66 
D8E H29 H29 H 0 1 N N N N N N -33.418 -3.481 -3.899 -5.986 4.428  -3.375 H29 D8E 67 
D8E H30 H30 H 0 1 N N N N N N -33.484 -4.099 -2.214 -5.979 5.534  -1.981 H30 D8E 68 
D8E H31 H31 H 0 1 N N N N N N -34.279 -2.544 -2.632 -4.580 5.478  -3.079 H31 D8E 69 
D8E H32 H32 H 0 1 N N N N N N -24.529 0.481  -5.838 -0.622 -5.723 0.345  H32 D8E 70 
D8E H33 H33 H 0 1 N N N N N N -26.184 0.996  -6.309 -1.404 -5.485 1.926  H33 D8E 71 
D8E H34 H34 H 0 1 N N N N N N -24.753 1.770  -7.068 -2.254 -6.371 0.637  H34 D8E 72 
# 
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 
D8E O19 C18 DOUB N N 1  
D8E C38 N20 SING N N 2  
D8E C18 N20 SING N N 3  
D8E C18 C17 SING N N 4  
D8E N20 C27 SING N N 5  
D8E C15 C17 SING N N 6  
D8E C15 C13 SING N N 7  
D8E C27 C28 SING N N 8  
D8E O34 N33 SING Y N 9  
D8E O34 C35 SING Y N 10 
D8E N33 C31 DOUB Y N 11 
D8E C28 C29 SING N N 12 
D8E C37 C35 SING N N 13 
D8E C14 C13 SING N N 14 
D8E C14 O16 SING N N 15 
D8E C13 N11 SING N N 16 
D8E C35 C36 DOUB Y N 17 
D8E N11 C10 SING N N 18 
D8E O5  C4  DOUB N N 19 
D8E C31 C36 SING Y N 20 
D8E C31 C9  SING N N 21 
D8E C29 C8  SING N N 22 
D8E N7  C9  SING N N 23 
D8E N7  C6  SING N N 24 
D8E C9  O32 DOUB N N 25 
D8E C8  C6  SING N N 26 
D8E C10 O12 DOUB N N 27 
D8E C10 C2  SING N N 28 
D8E C4  C6  SING N N 29 
D8E C4  N1  SING N N 30 
D8E C2  N1  SING N N 31 
D8E C2  C3  SING N N 32 
D8E C3  C21 SING N N 33 
D8E C26 C21 DOUB Y N 34 
D8E C26 C25 SING Y N 35 
D8E C21 C22 SING Y N 36 
D8E C25 C24 DOUB Y N 37 
D8E C22 C23 DOUB Y N 38 
D8E C24 C23 SING Y N 39 
D8E C24 F30 SING N N 40 
D8E C2  H1  SING N N 41 
D8E C3  H2  SING N N 42 
D8E C3  H3  SING N N 43 
D8E C13 H4  SING N N 44 
D8E C14 H5  SING N N 45 
D8E C14 H6  SING N N 46 
D8E C15 H7  SING N N 47 
D8E C15 H8  SING N N 48 
D8E C17 H9  SING N N 49 
D8E C17 H10 SING N N 50 
D8E C22 H11 SING N N 51 
D8E C23 H12 SING N N 52 
D8E C25 H13 SING N N 53 
D8E C26 H14 SING N N 54 
D8E C27 H15 SING N N 55 
D8E C27 H16 SING N N 56 
D8E C28 H17 SING N N 57 
D8E C28 H18 SING N N 58 
D8E C29 H19 SING N N 59 
D8E C29 H20 SING N N 60 
D8E N1  H21 SING N N 61 
D8E C6  H22 SING N N 62 
D8E N7  H23 SING N N 63 
D8E C8  H24 SING N N 64 
D8E C8  H25 SING N N 65 
D8E N11 H26 SING N N 66 
D8E O16 H27 SING N N 67 
D8E C36 H28 SING N N 68 
D8E C37 H29 SING N N 69 
D8E C37 H30 SING N N 70 
D8E C37 H31 SING N N 71 
D8E C38 H32 SING N N 72 
D8E C38 H33 SING N N 73 
D8E C38 H34 SING N N 74 
# 
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 
D8E InChI            InChI                1.03  "InChI=1S/C26H34FN5O6/c1-16-13-22(31-38-16)26(37)29-20-5-3-4-12-32(2)23(34)11-10-19(15-33)28-25(36)21(30-24(20)35)14-17-6-8-18(27)9-7-17/h6-9,13,19-21,33H,3-5,10-12,14-15H2,1-2H3,(H,28,36)(H,29,37)(H,30,35)/t19-,20-,21-/m0/s1" 
D8E InChIKey         InChI                1.03  NMKVYCKPYPCEGS-ACRUOGEOSA-N                                                                                                                                                                                                        
D8E SMILES_CANONICAL CACTVS               3.385 "CN1CCCC[C@H](NC(=O)c2cc(C)on2)C(=O)N[C@@H](Cc3ccc(F)cc3)C(=O)N[C@H](CO)CCC1=O"                                                                                                                                                    
D8E SMILES           CACTVS               3.385 "CN1CCCC[CH](NC(=O)c2cc(C)on2)C(=O)N[CH](Cc3ccc(F)cc3)C(=O)N[CH](CO)CCC1=O"                                                                                                                                                        
D8E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1cc(no1)C(=O)N[C@H]2CCCCN(C(=O)CC[C@H](NC(=O)[C@@H](NC2=O)Cc3ccc(cc3)F)CO)C"                                                                                                                                                    
D8E SMILES           "OpenEye OEToolkits" 2.0.6 "Cc1cc(no1)C(=O)NC2CCCCN(C(=O)CCC(NC(=O)C(NC2=O)Cc3ccc(cc3)F)CO)C"                                                                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           D8E 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.6 
_pdbx_chem_comp_identifier.identifier        "~{N}-[(2~{S},5~{S},14~{S})-2-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-9-methyl-3,8,15-tris(oxidanylidene)-1,4,9-triazacyclopentadec-14-yl]-5-methyl-1,2-oxazole-3-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
D8E "Create component" 2018-01-09 RCSB 
D8E "Initial release"  2018-02-21 RCSB 
D8E "Modify synonyms"  2021-03-01 PDBE 
D8E "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      D8E 
_pdbx_chem_comp_synonyms.name         "LIPID FRAGMENT" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            D8E 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C14 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
