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 #