data_D4E
# 
_chem_comp.id                                    D4E 
_chem_comp.name                                  "(6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C28 H35 F3 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-04-06 
_chem_comp.pdbx_modified_date                    2022-11-11 
_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                        532.598 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D4E 
_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        7XBZ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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.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 
D4E C10 C1  C 0 1 N N N 86.069 47.725 42.987 0.361  3.182  2.975  C10 D4E 1  
D4E C2  C2  C 0 1 N N N 85.827 46.939 47.406 -2.574 1.959  -1.525 C2  D4E 2  
D4E C4  C3  C 0 1 N N N 83.312 46.677 47.667 -1.263 3.974  -1.943 C4  D4E 3  
D4E C6  C4  C 0 1 N N N 82.994 48.414 45.769 0.273  4.364  -0.056 C6  D4E 4  
D4E C9  C5  C 0 1 N N S 84.727 48.454 42.842 1.041  2.041  2.215  C9  D4E 5  
D4E N3  N1  N 0 1 N N N 84.596 46.596 46.968 -1.419 2.634  -1.365 N3  D4E 6  
D4E O1  O1  O 0 1 N N N 86.725 47.139 46.562 -3.454 2.418  -2.228 O1  D4E 7  
D4E F42 F1  F 0 1 N N N 90.012 44.531 50.530 -4.271 -4.067 -0.060 F42 D4E 8  
D4E C38 C6  C 0 1 N N N 90.394 45.558 49.839 -5.273 -3.250 0.474  C38 D4E 9  
D4E F40 F2  F 0 1 N N N 90.413 45.216 48.549 -6.506 -3.905 0.384  F40 D4E 10 
D4E F41 F3  F 0 1 N N N 91.577 45.981 50.270 -4.987 -2.976 1.815  F41 D4E 11 
D4E C37 C7  C 0 1 N N N 89.382 46.611 50.140 -5.334 -1.938 -0.312 C37 D4E 12 
D4E C36 C8  C 0 1 N N N 88.265 46.402 49.188 -3.986 -1.222 -0.214 C36 D4E 13 
D4E C35 C9  C 0 1 N N N 87.322 47.584 49.247 -4.046 0.090  -1.000 C35 D4E 14 
D4E N34 N2  N 0 1 N N N 86.045 47.148 48.729 -2.755 0.776  -0.906 N34 D4E 15 
D4E C17 C10 C 0 1 N N S 84.435 46.382 45.520 -0.319 2.032  -0.615 C17 D4E 16 
D4E N7  N3  N 0 1 N N N 83.677 47.540 44.963 0.493  3.050  0.055  N7  D4E 17 
D4E O33 O2  O 0 1 N N N 82.502 49.455 45.313 1.036  5.128  0.498  O33 D4E 18 
D4E C5  C11 C 0 1 N N N 82.799 48.082 47.273 -0.899 4.937  -0.806 C5  D4E 19 
D4E C18 C12 C 0 1 N N N 83.708 45.103 45.107 0.592  1.260  -1.574 C18 D4E 20 
D4E N19 N4  N 0 1 N N N 83.493 45.181 43.617 1.829  0.875  -0.909 N19 D4E 21 
D4E C31 C13 C 0 1 N N N 83.409 46.314 42.845 2.319  1.473  0.179  C31 D4E 22 
D4E O32 O3  O 0 1 N N N 83.175 46.327 41.646 3.399  1.114  0.599  O32 D4E 23 
D4E C8  C14 C 0 1 N N S 83.560 47.667 43.490 1.606  2.572  0.896  C8  D4E 24 
D4E C46 C15 C 0 1 N N N 84.820 49.910 43.333 2.179  1.470  3.064  C46 D4E 25 
D4E C11 C16 C 0 1 N N N 86.889 47.752 41.729 -0.311 2.628  4.233  C11 D4E 26 
D4E C20 C17 C 0 1 N N R 83.263 43.858 42.952 2.588  -0.244 -1.472 C20 D4E 27 
D4E C51 C18 C 0 1 N N N 81.784 43.460 43.210 1.946  -0.683 -2.790 C51 D4E 28 
D4E C21 C19 C 0 1 Y N N 84.407 42.876 43.242 2.579  -1.396 -0.501 C21 D4E 29 
D4E C30 C20 C 0 1 Y N N 84.286 41.908 44.250 1.562  -1.529 0.394  C30 D4E 30 
D4E C29 C21 C 0 1 Y N N 85.284 40.990 44.541 1.537  -2.588 1.300  C29 D4E 31 
D4E C28 C22 C 0 1 Y N N 86.433 41.060 43.822 2.528  -3.521 1.315  C28 D4E 32 
D4E C27 C23 C 0 1 Y N N 86.586 41.995 42.803 3.594  -3.418 0.405  C27 D4E 33 
D4E C22 C24 C 0 1 Y N N 85.594 42.918 42.498 3.617  -2.344 -0.519 C22 D4E 34 
D4E C26 C25 C 0 1 Y N N 87.793 42.002 42.057 4.635  -4.361 0.391  C26 D4E 35 
D4E C25 C26 C 0 1 Y N N 88.007 42.921 40.989 5.651  -4.230 -0.505 C25 D4E 36 
D4E C24 C27 C 0 1 Y N N 86.998 43.841 40.648 5.676  -3.171 -1.410 C24 D4E 37 
D4E C23 C28 C 0 1 Y N N 85.820 43.823 41.411 4.683  -2.241 -1.429 C23 D4E 38 
D4E H1  H1  H 0 1 N N N 85.871 46.676 43.255 1.107  3.925  3.258  H1  D4E 39 
D4E H2  H2  H 0 1 N N N 86.645 48.206 43.791 -0.390 3.647  2.336  H2  D4E 40 
D4E H3  H3  H 0 1 N N N 82.623 45.892 47.323 -0.468 3.965  -2.688 H3  D4E 41 
D4E H4  H4  H 0 1 N N N 83.447 46.595 48.756 -2.199 4.287  -2.406 H4  D4E 42 
D4E H5  H5  H 0 1 N N N 84.510 48.501 41.765 0.313  1.257  2.009  H5  D4E 43 
D4E H6  H6  H 0 1 N N N 89.820 47.610 50.000 -5.557 -2.151 -1.358 H6  D4E 44 
D4E H7  H7  H 0 1 N N N 89.024 46.510 51.175 -6.115 -1.301 0.103  H7  D4E 45 
D4E H8  H8  H 0 1 N N N 87.720 45.485 49.458 -3.763 -1.009 0.831  H8  D4E 46 
D4E H9  H9  H 0 1 N N N 88.666 46.304 48.168 -3.205 -1.859 -0.629 H9  D4E 47 
D4E H10 H10 H 0 1 N N N 87.714 48.408 48.633 -4.269 -0.123 -2.045 H10 D4E 48 
D4E H11 H11 H 0 1 N N N 87.209 47.923 50.287 -4.827 0.726  -0.584 H11 D4E 49 
D4E H12 H12 H 0 1 N N N 85.293 46.994 49.370 -2.031 0.378  -0.398 H12 D4E 50 
D4E H13 H13 H 0 1 N N N 85.432 46.367 45.056 -0.723 1.346  0.129  H13 D4E 51 
D4E H14 H14 H 0 1 N N N 83.343 48.831 47.868 -0.620 5.896  -1.242 H14 D4E 52 
D4E H15 H15 H 0 1 N N N 81.725 48.138 47.505 -1.738 5.075  -0.123 H15 D4E 53 
D4E H16 H16 H 0 1 N N N 82.740 45.034 45.625 0.075  0.363  -1.917 H16 D4E 54 
D4E H17 H17 H 0 1 N N N 84.320 44.223 45.355 0.827  1.889  -2.432 H17 D4E 55 
D4E H18 H18 H 0 1 N N N 82.641 48.233 43.279 2.300  3.387  1.098  H18 D4E 56 
D4E H19 H19 H 0 1 N N N 83.843 50.401 43.215 1.770  1.049  3.983  H19 D4E 57 
D4E H20 H20 H 0 1 N N N 85.109 49.921 44.394 2.694  0.690  2.504  H20 D4E 58 
D4E H21 H21 H 0 1 N N N 85.575 50.449 42.741 2.882  2.265  3.311  H21 D4E 59 
D4E H22 H22 H 0 1 N N N 87.835 47.216 41.896 -1.057 1.886  3.949  H22 D4E 60 
D4E H23 H23 H 0 1 N N N 86.330 47.265 40.916 0.440  2.164  4.871  H23 D4E 61 
D4E H24 H24 H 0 1 N N N 87.103 48.795 41.453 -0.795 3.441  4.773  H24 D4E 62 
D4E H25 H25 H 0 1 N N N 83.320 44.057 41.872 3.616  0.069  -1.655 H25 D4E 63 
D4E H26 H26 H 0 1 N N N 81.126 44.299 42.939 0.918  -0.996 -2.607 H26 D4E 64 
D4E H27 H27 H 0 1 N N N 81.529 42.582 42.599 1.953  0.151  -3.492 H27 D4E 65 
D4E H28 H28 H 0 1 N N N 81.650 43.218 44.275 2.511  -1.515 -3.210 H28 D4E 66 
D4E H29 H29 H 0 1 N N N 83.373 41.876 44.826 0.764  -0.802 0.403  H29 D4E 67 
D4E H30 H30 H 0 1 N N N 85.152 40.246 45.312 0.719  -2.669 2.000  H30 D4E 68 
D4E H31 H31 H 0 1 N N N 87.241 40.379 44.044 2.495  -4.336 2.023  H31 D4E 69 
D4E H32 H32 H 0 1 N N N 88.569 41.293 42.305 4.628  -5.187 1.087  H32 D4E 70 
D4E H33 H33 H 0 1 N N N 88.939 42.912 40.444 6.450  -4.956 -0.513 H33 D4E 71 
D4E H34 H34 H 0 1 N N N 87.125 44.535 39.830 6.495  -3.089 -2.110 H34 D4E 72 
D4E H35 H35 H 0 1 N N N 85.042 44.530 41.165 4.716  -1.425 -2.136 H35 D4E 73 
# 
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 
D4E C24 C25 DOUB Y N 1  
D4E C24 C23 SING Y N 2  
D4E C25 C26 SING Y N 3  
D4E C23 C22 DOUB Y N 4  
D4E O32 C31 DOUB N N 5  
D4E C11 C10 SING N N 6  
D4E C26 C27 DOUB Y N 7  
D4E C22 C27 SING Y N 8  
D4E C22 C21 SING Y N 9  
D4E C27 C28 SING Y N 10 
D4E C9  C10 SING N N 11 
D4E C9  C46 SING N N 12 
D4E C9  C8  SING N N 13 
D4E C31 C8  SING N N 14 
D4E C31 N19 SING N N 15 
D4E C20 C51 SING N N 16 
D4E C20 C21 SING N N 17 
D4E C20 N19 SING N N 18 
D4E C21 C30 DOUB Y N 19 
D4E C8  N7  SING N N 20 
D4E N19 C18 SING N N 21 
D4E C28 C29 DOUB Y N 22 
D4E C30 C29 SING Y N 23 
D4E N7  C17 SING N N 24 
D4E N7  C6  SING N N 25 
D4E C18 C17 SING N N 26 
D4E O33 C6  DOUB N N 27 
D4E C17 N3  SING N N 28 
D4E C6  C5  SING N N 29 
D4E O1  C2  DOUB N N 30 
D4E N3  C2  SING N N 31 
D4E N3  C4  SING N N 32 
D4E C5  C4  SING N N 33 
D4E C2  N34 SING N N 34 
D4E F40 C38 SING N N 35 
D4E N34 C35 SING N N 36 
D4E C36 C35 SING N N 37 
D4E C36 C37 SING N N 38 
D4E C38 C37 SING N N 39 
D4E C38 F41 SING N N 40 
D4E C38 F42 SING N N 41 
D4E C10 H1  SING N N 42 
D4E C10 H2  SING N N 43 
D4E C4  H3  SING N N 44 
D4E C4  H4  SING N N 45 
D4E C9  H5  SING N N 46 
D4E C37 H6  SING N N 47 
D4E C37 H7  SING N N 48 
D4E C36 H8  SING N N 49 
D4E C36 H9  SING N N 50 
D4E C35 H10 SING N N 51 
D4E C35 H11 SING N N 52 
D4E N34 H12 SING N N 53 
D4E C17 H13 SING N N 54 
D4E C5  H14 SING N N 55 
D4E C5  H15 SING N N 56 
D4E C18 H16 SING N N 57 
D4E C18 H17 SING N N 58 
D4E C8  H18 SING N N 59 
D4E C46 H19 SING N N 60 
D4E C46 H20 SING N N 61 
D4E C46 H21 SING N N 62 
D4E C11 H22 SING N N 63 
D4E C11 H23 SING N N 64 
D4E C11 H24 SING N N 65 
D4E C20 H25 SING N N 66 
D4E C51 H26 SING N N 67 
D4E C51 H27 SING N N 68 
D4E C51 H28 SING N N 69 
D4E C30 H29 SING N N 70 
D4E C29 H30 SING N N 71 
D4E C28 H31 SING N N 72 
D4E C26 H32 SING N N 73 
D4E C25 H33 SING N N 74 
D4E C24 H34 SING N N 75 
D4E C23 H35 SING N N 76 
# 
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 
D4E InChI            InChI                1.03  "InChI=1S/C28H35F3N4O3/c1-4-18(2)25-26(37)34(19(3)21-12-7-10-20-9-5-6-11-22(20)21)17-23-33(16-13-24(36)35(23)25)27(38)32-15-8-14-28(29,30)31/h5-7,9-12,18-19,23,25H,4,8,13-17H2,1-3H3,(H,32,38)/t18-,19+,23+,25-/m0/s1" 
D4E InChIKey         InChI                1.03  BAZGDIOJCKGDHH-RHDWJPPYSA-N                                                                                                                                                                                             
D4E SMILES_CANONICAL CACTVS               3.385 "CC[C@H](C)[C@@H]1N2[C@H](CN([C@H](C)c3cccc4ccccc34)C1=O)N(CCC2=O)C(=O)NCCCC(F)(F)F"                                                                                                                                    
D4E SMILES           CACTVS               3.385 "CC[CH](C)[CH]1N2[CH](CN([CH](C)c3cccc4ccccc34)C1=O)N(CCC2=O)C(=O)NCCCC(F)(F)F"                                                                                                                                         
D4E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC[C@H](C)[C@H]1C(=O)N(C[C@H]2N1C(=O)CCN2C(=O)NCCCC(F)(F)F)[C@H](C)c3cccc4c3cccc4"                                                                                                                                     
D4E SMILES           "OpenEye OEToolkits" 2.0.7 "CCC(C)C1C(=O)N(CC2N1C(=O)CCN2C(=O)NCCCC(F)(F)F)C(C)c3cccc4c3cccc4"                                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           D4E 
_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        "(6~{S},9~{a}~{S})-6-[(2~{S})-butan-2-yl]-8-[(1~{R})-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-~{N}-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-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 
D4E "Create component" 2022-04-06 PDBJ 
D4E "Initial release"  2022-11-16 RCSB 
# 
