data_A1EEK
# 
_chem_comp.id                                    A1EEK 
_chem_comp.name                                  "(6~{S},9~{a}~{S})-6-[(2~{S})-butan-2-yl]-8-[(4-methoxynaphthalen-1-yl)methyl]-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" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C28 H35 F3 N4 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-10-22 
_chem_comp.pdbx_modified_date                    2025-02-14 
_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                        548.597 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EEK 
_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        9K2D 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_chem_comp.pdbx_pcm                              ? 
# 
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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1EEK N1  N1  N 0 1 N N N N N N -19.902 72.995 41.283 -1.001 1.048  -2.057 N1  A1EEK 1  
A1EEK C7  C1  C 0 1 Y N N N N N -20.522 67.815 41.787 2.959  -1.189 1.286  C7  A1EEK 2  
A1EEK C8  C2  C 0 1 Y N N N N N -19.213 67.519 41.508 4.042  -0.746 1.983  C8  A1EEK 3  
A1EEK N2  N2  N 0 1 N N N N N N -19.355 74.709 39.887 -2.878 -0.032 -1.186 N2  A1EEK 4  
A1EEK C9  C3  C 0 1 Y N N N N N -18.844 66.882 40.337 5.335  -1.087 1.595  C9  A1EEK 5  
A1EEK O1  O1  O 0 1 N N N N N N -19.519 65.935 38.227 6.821  -2.202 0.136  O1  A1EEK 6  
A1EEK C1  C4  C 0 1 N N N N N N -24.127 72.847 40.988 -0.837 4.617  0.790  C1  A1EEK 7  
A1EEK C5  C5  C 0 1 N N N N N N -22.429 70.379 43.389 1.383  1.558  1.371  C5  A1EEK 8  
A1EEK C6  C6  C 0 1 N N N N N N -20.878 68.543 43.063 1.570  -0.805 1.724  C6  A1EEK 9  
A1EEK N3  N3  N 0 1 N N N N N N -21.806 72.597 42.656 0.347  2.454  -0.626 N3  A1EEK 10 
A1EEK C4  C7  C 0 1 N N S N N N -22.954 71.730 42.946 0.885  2.809  0.700  C4  A1EEK 11 
A1EEK C3  C8  C 0 1 N N N N N N -25.208 70.911 42.185 0.374  3.941  2.868  C3  A1EEK 12 
A1EEK O3  O2  O 0 1 N N N N N N -22.439 74.088 44.210 1.388  4.163  -1.520 O3  A1EEK 13 
A1EEK C2  C9  C 0 1 N N S N N N -23.892 71.538 41.738 -0.219 3.441  1.549  C2  A1EEK 14 
A1EEK C27 C10 C 0 1 N N N N N N -21.648 73.740 43.353 0.638  3.224  -1.679 C27 A1EEK 15 
A1EEK C26 C11 C 0 1 N N N N N N -20.437 74.585 43.067 0.077  2.979  -3.052 C26 A1EEK 16 
A1EEK C25 C12 C 0 1 N N N N N N -19.362 73.726 42.428 -0.208 1.481  -3.215 C25 A1EEK 17 
A1EEK C20 C13 C 0 1 N N N N N N -20.083 73.603 40.081 -2.198 0.457  -2.242 C20 A1EEK 18 
A1EEK C21 C14 C 0 1 N N N N N N -19.377 75.401 38.607 -4.125 -0.771 -1.397 C21 A1EEK 19 
A1EEK C22 C15 C 0 1 N N N N N N -18.137 75.122 37.790 -4.691 -1.213 -0.045 C22 A1EEK 20 
A1EEK C23 C16 C 0 1 N N N N N N -18.230 73.721 37.209 -5.994 -1.984 -0.266 C23 A1EEK 21 
A1EEK C24 C17 C 0 1 N N N N N N -17.138 73.413 36.272 -6.559 -2.426 1.086  C24 A1EEK 22 
A1EEK F2  F1  F 0 1 N N N N N N -17.306 72.247 35.682 -7.751 -3.131 0.885  F2  A1EEK 23 
A1EEK F1  F2  F 0 1 N N N N N N -17.026 74.303 35.310 -5.632 -3.251 1.732  F1  A1EEK 24 
A1EEK F   F3  F 0 1 N N N N N N -15.962 73.367 36.864 -6.812 -1.300 1.876  F   A1EEK 25 
A1EEK O2  O3  O 0 1 N N N N N N -20.854 73.154 39.251 -2.664 0.365  -3.361 O2  A1EEK 26 
A1EEK C   C18 C 0 1 N N N N N N -24.813 73.891 41.798 -2.022 5.171  1.583  C   A1EEK 27 
A1EEK C19 C19 C 0 1 N N S N N N -20.907 72.010 41.654 -0.486 1.252  -0.706 C19 A1EEK 28 
A1EEK C18 C20 C 0 1 N N N N N N -20.211 70.807 42.347 0.363  0.046  -0.294 C18 A1EEK 29 
A1EEK N   N4  N 0 1 N N N N N N -21.270 69.936 42.856 1.102  0.332  0.928  N   A1EEK 30 
A1EEK O   O4  O 0 1 N N N N N N -23.059 69.735 44.194 2.074  1.670  2.362  O   A1EEK 31 
A1EEK C17 C21 C 0 1 Y N N N N N -21.538 67.445 40.857 3.143  -1.999 0.153  C17 A1EEK 32 
A1EEK C16 C22 C 0 1 Y N N N N N -22.916 67.682 41.090 2.048  -2.469 -0.593 C16 A1EEK 33 
A1EEK C15 C23 C 0 1 Y N N N N N -23.859 67.310 40.177 2.264  -3.252 -1.685 C15 A1EEK 34 
A1EEK C14 C24 C 0 1 Y N N N N N -23.491 66.694 38.996 3.556  -3.596 -2.077 C14 A1EEK 35 
A1EEK C13 C25 C 0 1 Y N N N N N -22.179 66.444 38.724 4.640  -3.160 -1.378 C13 A1EEK 36 
A1EEK C12 C26 C 0 1 Y N N N N N -21.162 66.801 39.645 4.457  -2.350 -0.246 C12 A1EEK 37 
A1EEK C10 C27 C 0 1 Y N N N N N -19.787 66.534 39.418 5.554  -1.878 0.502  C10 A1EEK 38 
A1EEK C11 C28 C 0 1 N N N N N N -18.155 65.735 37.879 7.882  -1.686 0.943  C11 A1EEK 39 
A1EEK H1  H1  H 0 1 N N N N N N -18.449 67.790 42.222 3.896  -0.120 2.851  H1  A1EEK 40 
A1EEK H2  H2  H 0 1 N N N N N N -18.789 75.064 40.631 -2.541 0.105  -0.287 H2  A1EEK 41 
A1EEK H3  H3  H 0 1 N N N N N N -17.804 66.660 40.151 6.176  -0.722 2.166  H3  A1EEK 42 
A1EEK H4  H4  H 0 1 N N N N N N -23.152 73.242 40.667 -0.089 5.399  0.661  H4  A1EEK 43 
A1EEK H5  H5  H 0 1 N N N N N N -24.745 72.633 40.103 -1.180 4.278  -0.188 H5  A1EEK 44 
A1EEK H6  H6  H 0 1 N N N N N N -21.715 68.014 43.542 0.897  -1.650 1.580  H6  A1EEK 45 
A1EEK H7  H7  H 0 1 N N N N N N -20.003 68.524 43.729 1.584  -0.528 2.779  H7  A1EEK 46 
A1EEK H8  H8  H 0 1 N N N N N N -23.538 72.166 43.770 1.708  3.514  0.584  H8  A1EEK 47 
A1EEK H9  H9  H 0 1 N N N N N N -25.004 69.972 42.721 1.096  4.732  2.665  H9  A1EEK 48 
A1EEK H10 H10 H 0 1 N N N N N N -25.737 71.607 42.853 -0.423 4.331  3.501  H10 A1EEK 49 
A1EEK H11 H11 H 0 1 N N N N N N -25.832 70.702 41.304 0.873  3.116  3.378  H11 A1EEK 50 
A1EEK H12 H12 H 0 1 N N N N N N -23.403 70.837 41.045 -0.989 2.698  1.756  H12 A1EEK 51 
A1EEK H13 H13 H 0 1 N N N N N N -20.056 75.010 44.007 -0.848 3.543  -3.174 H13 A1EEK 52 
A1EEK H14 H14 H 0 1 N N N N N N -20.712 75.400 42.381 0.800  3.297  -3.804 H14 A1EEK 53 
A1EEK H15 H15 H 0 1 N N N N N N -18.984 73.007 43.170 0.730  0.928  -3.248 H15 A1EEK 54 
A1EEK H16 H16 H 0 1 N N N N N N -18.538 74.371 42.089 -0.771 1.310  -4.133 H16 A1EEK 55 
A1EEK H17 H17 H 0 1 N N N N N N -19.445 76.484 38.790 -4.847 -0.128 -1.900 H17 A1EEK 56 
A1EEK H18 H18 H 0 1 N N N N N N -20.258 75.069 38.039 -3.928 -1.649 -2.013 H18 A1EEK 57 
A1EEK H19 H19 H 0 1 N N N N N N -17.248 75.196 38.433 -3.969 -1.855 0.458  H19 A1EEK 58 
A1EEK H20 H20 H 0 1 N N N N N N -18.061 75.855 36.974 -4.888 -0.335 0.570  H20 A1EEK 59 
A1EEK H21 H21 H 0 1 N N N N N N -19.187 73.626 36.675 -6.716 -1.342 -0.769 H21 A1EEK 60 
A1EEK H22 H22 H 0 1 N N N N N N -18.197 72.996 38.036 -5.797 -2.862 -0.881 H22 A1EEK 61 
A1EEK H23 H23 H 0 1 N N N N N N -24.945 74.799 41.191 -2.462 6.008  1.042  H23 A1EEK 62 
A1EEK H24 H24 H 0 1 N N N N N N -25.797 73.518 42.119 -2.770 4.389  1.712  H24 A1EEK 63 
A1EEK H25 H25 H 0 1 N N N N N N -24.204 74.127 42.683 -1.679 5.510  2.560  H25 A1EEK 64 
A1EEK H26 H26 H 0 1 N N N N N N -21.468 71.662 40.775 -1.322 1.357  -0.014 H26 A1EEK 65 
A1EEK H27 H27 H 0 1 N N N N N N -19.589 70.262 41.622 -0.288 -0.812 -0.128 H27 A1EEK 66 
A1EEK H28 H28 H 0 1 N N N N N N -19.582 71.161 43.177 1.066  -0.188 -1.094 H28 A1EEK 67 
A1EEK H29 H29 H 0 1 N N N N N N -23.224 68.165 42.005 1.041  -2.210 -0.301 H29 A1EEK 68 
A1EEK H30 H30 H 0 1 N N N N N N -24.903 67.499 40.379 1.421  -3.612 -2.257 H30 A1EEK 69 
A1EEK H31 H31 H 0 1 N N N N N N -24.250 66.408 38.282 3.700  -4.219 -2.947 H31 A1EEK 70 
A1EEK H32 H32 H 0 1 N N N N N N -21.910 65.967 37.793 5.636  -3.435 -1.693 H32 A1EEK 71 
A1EEK H33 H33 H 0 1 N N N N N N -18.095 65.244 36.897 7.845  -0.597 0.938  H33 A1EEK 72 
A1EEK H34 H34 H 0 1 N N N N N N -17.642 66.707 37.835 7.770  -2.049 1.965  H34 A1EEK 73 
A1EEK H35 H35 H 0 1 N N N N N N -17.673 65.100 38.636 8.839  -2.020 0.542  H35 A1EEK 74 
# 
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 
A1EEK F1  C24 SING N N 1  
A1EEK F2  C24 SING N N 2  
A1EEK C24 F   SING N N 3  
A1EEK C24 C23 SING N N 4  
A1EEK C23 C22 SING N N 5  
A1EEK C22 C21 SING N N 6  
A1EEK C11 O1  SING N N 7  
A1EEK O1  C10 SING N N 8  
A1EEK C21 N2  SING N N 9  
A1EEK C13 C14 DOUB Y N 10 
A1EEK C13 C12 SING Y N 11 
A1EEK C14 C15 SING Y N 12 
A1EEK O2  C20 DOUB N N 13 
A1EEK C10 C12 DOUB Y N 14 
A1EEK C10 C9  SING Y N 15 
A1EEK C12 C17 SING Y N 16 
A1EEK N2  C20 SING N N 17 
A1EEK C20 N1  SING N N 18 
A1EEK C15 C16 DOUB Y N 19 
A1EEK C9  C8  DOUB Y N 20 
A1EEK C17 C16 SING Y N 21 
A1EEK C17 C7  DOUB Y N 22 
A1EEK C1  C2  SING N N 23 
A1EEK C1  C   SING N N 24 
A1EEK N1  C19 SING N N 25 
A1EEK N1  C25 SING N N 26 
A1EEK C8  C7  SING Y N 27 
A1EEK C19 C18 SING N N 28 
A1EEK C19 N3  SING N N 29 
A1EEK C2  C3  SING N N 30 
A1EEK C2  C4  SING N N 31 
A1EEK C7  C6  SING N N 32 
A1EEK C18 N   SING N N 33 
A1EEK C25 C26 SING N N 34 
A1EEK N3  C4  SING N N 35 
A1EEK N3  C27 SING N N 36 
A1EEK N   C6  SING N N 37 
A1EEK N   C5  SING N N 38 
A1EEK C4  C5  SING N N 39 
A1EEK C26 C27 SING N N 40 
A1EEK C27 O3  DOUB N N 41 
A1EEK C5  O   DOUB N N 42 
A1EEK C8  H1  SING N N 43 
A1EEK N2  H2  SING N N 44 
A1EEK C9  H3  SING N N 45 
A1EEK C1  H4  SING N N 46 
A1EEK C1  H5  SING N N 47 
A1EEK C6  H6  SING N N 48 
A1EEK C6  H7  SING N N 49 
A1EEK C4  H8  SING N N 50 
A1EEK C3  H9  SING N N 51 
A1EEK C3  H10 SING N N 52 
A1EEK C3  H11 SING N N 53 
A1EEK C2  H12 SING N N 54 
A1EEK C26 H13 SING N N 55 
A1EEK C26 H14 SING N N 56 
A1EEK C25 H15 SING N N 57 
A1EEK C25 H16 SING N N 58 
A1EEK C21 H17 SING N N 59 
A1EEK C21 H18 SING N N 60 
A1EEK C22 H19 SING N N 61 
A1EEK C22 H20 SING N N 62 
A1EEK C23 H21 SING N N 63 
A1EEK C23 H22 SING N N 64 
A1EEK C   H23 SING N N 65 
A1EEK C   H24 SING N N 66 
A1EEK C   H25 SING N N 67 
A1EEK C19 H26 SING N N 68 
A1EEK C18 H27 SING N N 69 
A1EEK C18 H28 SING N N 70 
A1EEK C16 H29 SING N N 71 
A1EEK C15 H30 SING N N 72 
A1EEK C14 H31 SING N N 73 
A1EEK C13 H32 SING N N 74 
A1EEK C11 H33 SING N N 75 
A1EEK C11 H34 SING N N 76 
A1EEK C11 H35 SING N N 77 
# 
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 
A1EEK InChI            InChI                1.06  "InChI=1S/C28H35F3N4O4/c1-4-18(2)25-26(37)33(16-19-10-11-22(39-3)21-9-6-5-8-20(19)21)17-23-34(15-12-24(36)35(23)25)27(38)32-14-7-13-28(29,30)31/h5-6,8-11,18,23,25H,4,7,12-17H2,1-3H3,(H,32,38)/t18-,23+,25-/m0/s1" 
A1EEK InChIKey         InChI                1.06  ZCPTWZWAPHZUMM-UODBTFMRSA-N                                                                                                                                                                                         
A1EEK SMILES_CANONICAL CACTVS               3.385 "CC[C@H](C)[C@@H]1N2[C@H](CN(Cc3ccc(OC)c4ccccc34)C1=O)N(CCC2=O)C(=O)NCCCC(F)(F)F"                                                                                                                                   
A1EEK SMILES           CACTVS               3.385 "CC[CH](C)[CH]1N2[CH](CN(Cc3ccc(OC)c4ccccc34)C1=O)N(CCC2=O)C(=O)NCCCC(F)(F)F"                                                                                                                                       
A1EEK 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)Cc3ccc(c4c3cccc4)OC"                                                                                                                                    
A1EEK SMILES           "OpenEye OEToolkits" 2.0.7 "CCC(C)C1C(=O)N(CC2N1C(=O)CCN2C(=O)NCCCC(F)(F)F)Cc3ccc(c4c3cccc4)OC"                                                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           A1EEK 
_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-[(4-methoxynaphthalen-1-yl)methyl]-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 
A1EEK "Create component" 2024-10-22 PDBC 
A1EEK "Modify synonyms"  2024-11-01 PDBC 
A1EEK "Initial release"  2025-02-19 RCSB 
# 
