data_A1EEF # _chem_comp.id A1EEF _chem_comp.name "(6~{S},9~{a}~{S})-6-(1~{H}-imidazol-5-ylmethyl)-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-~{N}-(phenylmethyl)-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 "C30 H30 N6 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-10-20 _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 522.598 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1EEF _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 9K2C _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 A1EEF C10 C1 C 0 1 Y N N N N N 100.514 43.347 28.846 -1.945 3.478 1.003 C10 A1EEF 1 A1EEF C17 C2 C 0 1 N N S N N N 99.365 40.540 26.569 -0.528 0.270 -0.613 C17 A1EEF 2 A1EEF C20 C3 C 0 1 N N N N N N 100.064 37.274 28.509 2.135 -0.885 1.824 C20 A1EEF 3 A1EEF C21 C4 C 0 1 Y N N N N N 98.644 36.893 28.954 3.579 -0.664 1.456 C21 A1EEF 4 A1EEF C22 C5 C 0 1 Y N N N N N 98.012 37.468 30.065 4.121 -1.283 0.317 C22 A1EEF 5 A1EEF C24 C6 C 0 1 Y N N N N N 97.991 38.997 31.966 3.898 -2.697 -1.599 C24 A1EEF 6 A1EEF C26 C7 C 0 1 Y N N N N N 96.054 37.637 31.534 6.023 -1.681 -1.153 C26 A1EEF 7 A1EEF C28 C8 C 0 1 Y N N N N N 96.057 36.104 29.638 6.263 -0.230 0.806 C28 A1EEF 8 A1EEF O01 O1 O 0 1 N N N N N N 96.876 41.795 25.925 -2.108 -1.483 -3.261 O01 A1EEF 9 A1EEF C02 C9 C 0 1 N N N N N N 97.572 41.535 24.955 -1.836 -1.102 -2.139 C02 A1EEF 10 A1EEF N03 N1 N 0 1 N N N N N N 98.862 40.824 25.184 -0.934 -0.116 -1.962 N03 A1EEF 11 A1EEF C04 C10 C 0 1 N N N N N N 99.819 40.507 24.133 -0.359 0.572 -3.124 C04 A1EEF 12 A1EEF C05 C11 C 0 1 N N N N N N 100.880 41.544 24.220 -0.642 2.071 -2.968 C05 A1EEF 13 A1EEF C06 C12 C 0 1 N N N N N N 101.531 41.566 25.614 -0.204 2.511 -1.599 C06 A1EEF 14 A1EEF N07 N2 N 0 1 N N N N N N 100.721 41.055 26.764 -0.189 1.692 -0.543 N07 A1EEF 15 A1EEF C08 C13 C 0 1 N N S N N N 101.150 40.973 28.068 0.184 2.227 0.781 C08 A1EEF 16 A1EEF C09 C14 C 0 1 N N N N N N 100.344 41.840 29.066 -1.075 2.419 1.629 C09 A1EEF 17 A1EEF N11 N3 N 0 1 Y N N N N N 100.823 43.910 27.640 -1.964 4.810 1.318 N11 A1EEF 18 A1EEF C12 C15 C 0 1 Y N N N N N 100.897 45.216 27.802 -2.884 5.397 0.522 C12 A1EEF 19 A1EEF N13 N4 N 0 1 Y N N N N N 100.644 45.497 29.072 -3.412 4.485 -0.248 N13 A1EEF 20 A1EEF C14 C16 C 0 1 Y N N N N N 100.410 44.367 29.728 -2.850 3.298 0.022 C14 A1EEF 21 A1EEF C18 C17 C 0 1 N N N N N N 99.291 39.053 26.920 0.701 -0.543 -0.197 C18 A1EEF 22 A1EEF N19 N5 N 0 1 N N N N N N 100.123 38.643 27.985 1.286 -0.000 1.022 N19 A1EEF 23 A1EEF C23 C18 C 0 1 Y N N N N N 98.636 38.439 30.860 3.339 -2.115 -0.502 C23 A1EEF 24 A1EEF C25 C19 C 0 1 Y N N N N N 96.702 38.597 32.309 5.236 -2.481 -1.923 C25 A1EEF 25 A1EEF C27 C20 C 0 1 Y N N N N N 96.717 37.064 30.399 5.482 -1.062 -0.013 C27 A1EEF 26 A1EEF C29 C21 C 0 1 Y N N N N N 96.686 35.537 28.537 5.703 0.357 1.899 C29 A1EEF 27 A1EEF C30 C22 C 0 1 Y N N N N N 97.975 35.927 28.200 4.365 0.141 2.223 C30 A1EEF 28 A1EEF C31 C23 C 0 1 N N N N N N 101.096 39.597 28.576 1.103 1.247 1.457 C31 A1EEF 29 A1EEF O32 O2 O 0 1 N N N N N N 101.833 39.259 29.489 1.705 1.608 2.446 O32 A1EEF 30 A1EEF O33 O3 O 0 1 N N N N N N 102.663 41.988 25.760 0.151 3.661 -1.446 O33 A1EEF 31 A1EEF N34 N6 N 0 1 N N N N N N 97.127 41.867 23.602 -2.437 -1.666 -1.072 N34 A1EEF 32 A1EEF C35 C24 C 0 1 N N N N N N 95.842 42.552 23.353 -3.496 -2.659 -1.268 C35 A1EEF 33 A1EEF C36 C25 C 0 1 Y N N N N N 94.642 41.609 23.095 -3.997 -3.130 0.073 C36 A1EEF 34 A1EEF C37 C26 C 0 1 Y N N N N N 93.833 41.816 21.976 -3.405 -4.216 0.690 C37 A1EEF 35 A1EEF C38 C27 C 0 1 Y N N N N N 92.742 40.989 21.747 -3.865 -4.648 1.920 C38 A1EEF 36 A1EEF C39 C28 C 0 1 Y N N N N N 92.455 39.956 22.630 -4.917 -3.994 2.533 C39 A1EEF 37 A1EEF C41 C29 C 0 1 Y N N N N N 93.261 39.758 23.751 -5.509 -2.907 1.917 C41 A1EEF 38 A1EEF C42 C30 C 0 1 Y N N N N N 94.350 40.587 23.986 -5.045 -2.472 0.689 C42 A1EEF 39 A1EEF H1 H1 H 0 1 N N N N N N 98.703 41.068 27.271 -1.348 0.060 0.074 H1 A1EEF 40 A1EEF H2 H2 H 0 1 N N N N N N 100.389 36.577 27.722 1.865 -1.923 1.629 H2 A1EEF 41 A1EEF H3 H3 H 0 1 N N N N N N 100.741 37.194 29.372 1.991 -0.665 2.882 H3 A1EEF 42 A1EEF H4 H4 H 0 1 N N N N N N 98.496 39.745 32.560 3.295 -3.337 -2.226 H4 A1EEF 43 A1EEF H5 H5 H 0 1 N N N N N N 95.052 37.324 31.788 7.058 -1.523 -1.416 H5 A1EEF 44 A1EEF H6 H6 H 0 1 N N N N N N 95.055 35.800 29.904 7.301 -0.053 0.567 H6 A1EEF 45 A1EEF H7 H7 H 0 1 N N N N N N 99.331 40.541 23.148 0.717 0.401 -3.159 H7 A1EEF 46 A1EEF H8 H8 H 0 1 N N N N N N 100.248 39.507 24.295 -0.823 0.202 -4.039 H8 A1EEF 47 A1EEF H9 H9 H 0 1 N N N N N N 101.653 41.329 23.467 -0.089 2.627 -3.725 H9 A1EEF 48 A1EEF H10 H10 H 0 1 N N N N N N 100.435 42.529 24.017 -1.710 2.255 -3.086 H10 A1EEF 49 A1EEF H11 H11 H 0 1 N N N N N N 102.195 41.311 28.124 0.694 3.182 0.659 H11 A1EEF 50 A1EEF H12 H12 H 0 1 N N N N N N 99.278 41.591 28.960 -0.792 2.729 2.635 H12 A1EEF 51 A1EEF H13 H13 H 0 1 N N N N N N 100.678 41.598 30.086 -1.626 1.480 1.680 H13 A1EEF 52 A1EEF H14 H14 H 0 1 N N N N N N 100.968 43.416 26.782 -1.418 5.251 1.988 H14 A1EEF 53 A1EEF H15 H15 H 0 1 N N N N N N 101.125 45.936 27.030 -3.139 6.446 0.523 H15 A1EEF 54 A1EEF H17 H17 H 0 1 N N N N N N 100.178 44.278 30.779 -3.085 2.360 -0.460 H17 A1EEF 55 A1EEF H18 H18 H 0 1 N N N N N N 98.251 38.819 27.192 0.406 -1.578 -0.024 H18 A1EEF 56 A1EEF H19 H19 H 0 1 N N N N N N 99.575 38.478 26.026 1.441 -0.510 -0.996 H19 A1EEF 57 A1EEF H20 H20 H 0 1 N N N N N N 99.636 38.762 30.612 2.301 -2.292 -0.264 H20 A1EEF 58 A1EEF H21 H21 H 0 1 N N N N N N 96.209 39.027 33.168 5.655 -2.955 -2.798 H21 A1EEF 59 A1EEF H22 H22 H 0 1 N N N N N N 96.173 34.794 27.944 6.306 0.996 2.527 H22 A1EEF 60 A1EEF H23 H23 H 0 1 N N N N N N 98.464 35.479 27.348 3.945 0.618 3.096 H23 A1EEF 61 A1EEF H24 H24 H 0 1 N N N N N N 97.708 41.624 22.825 -2.167 -1.415 -0.175 H24 A1EEF 62 A1EEF H25 H25 H 0 1 N N N N N N 95.964 43.199 22.472 -4.318 -2.208 -1.825 H25 A1EEF 63 A1EEF H26 H26 H 0 1 N N N N N N 95.608 43.170 24.232 -3.101 -3.507 -1.826 H26 A1EEF 64 A1EEF H27 H27 H 0 1 N N N N N N 94.056 42.619 21.289 -2.583 -4.727 0.211 H27 A1EEF 65 A1EEF H28 H28 H 0 1 N N N N N N 92.116 41.149 20.882 -3.402 -5.497 2.401 H28 A1EEF 66 A1EEF H29 H29 H 0 1 N N N N N N 91.610 39.308 22.449 -5.276 -4.332 3.494 H29 A1EEF 67 A1EEF H30 H30 H 0 1 N N N N N N 93.037 38.956 24.439 -6.331 -2.396 2.396 H30 A1EEF 68 A1EEF H31 H31 H 0 1 N N N N N N 94.967 40.436 24.859 -5.505 -1.621 0.209 H31 A1EEF 69 # 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 A1EEF C38 C37 DOUB Y N 1 A1EEF C38 C39 SING Y N 2 A1EEF C37 C36 SING Y N 3 A1EEF C39 C41 DOUB Y N 4 A1EEF C36 C35 SING N N 5 A1EEF C36 C42 DOUB Y N 6 A1EEF C35 N34 SING N N 7 A1EEF N34 C02 SING N N 8 A1EEF C41 C42 SING Y N 9 A1EEF C04 C05 SING N N 10 A1EEF C04 N03 SING N N 11 A1EEF C05 C06 SING N N 12 A1EEF C02 N03 SING N N 13 A1EEF C02 O01 DOUB N N 14 A1EEF N03 C17 SING N N 15 A1EEF C06 O33 DOUB N N 16 A1EEF C06 N07 SING N N 17 A1EEF C17 N07 SING N N 18 A1EEF C17 C18 SING N N 19 A1EEF N07 C08 SING N N 20 A1EEF C18 N19 SING N N 21 A1EEF N11 C12 SING Y N 22 A1EEF N11 C10 SING Y N 23 A1EEF C12 N13 DOUB Y N 24 A1EEF N19 C20 SING N N 25 A1EEF N19 C31 SING N N 26 A1EEF C08 C31 SING N N 27 A1EEF C08 C09 SING N N 28 A1EEF C30 C29 DOUB Y N 29 A1EEF C30 C21 SING Y N 30 A1EEF C20 C21 SING N N 31 A1EEF C29 C28 SING Y N 32 A1EEF C31 O32 DOUB N N 33 A1EEF C10 C09 SING N N 34 A1EEF C10 C14 DOUB Y N 35 A1EEF C21 C22 DOUB Y N 36 A1EEF N13 C14 SING Y N 37 A1EEF C28 C27 DOUB Y N 38 A1EEF C22 C27 SING Y N 39 A1EEF C22 C23 SING Y N 40 A1EEF C27 C26 SING Y N 41 A1EEF C23 C24 DOUB Y N 42 A1EEF C26 C25 DOUB Y N 43 A1EEF C24 C25 SING Y N 44 A1EEF C17 H1 SING N N 45 A1EEF C20 H2 SING N N 46 A1EEF C20 H3 SING N N 47 A1EEF C24 H4 SING N N 48 A1EEF C26 H5 SING N N 49 A1EEF C28 H6 SING N N 50 A1EEF C04 H7 SING N N 51 A1EEF C04 H8 SING N N 52 A1EEF C05 H9 SING N N 53 A1EEF C05 H10 SING N N 54 A1EEF C08 H11 SING N N 55 A1EEF C09 H12 SING N N 56 A1EEF C09 H13 SING N N 57 A1EEF N11 H14 SING N N 58 A1EEF C12 H15 SING N N 59 A1EEF C14 H17 SING N N 60 A1EEF C18 H18 SING N N 61 A1EEF C18 H19 SING N N 62 A1EEF C23 H20 SING N N 63 A1EEF C25 H21 SING N N 64 A1EEF C29 H22 SING N N 65 A1EEF C30 H23 SING N N 66 A1EEF N34 H24 SING N N 67 A1EEF C35 H25 SING N N 68 A1EEF C35 H26 SING N N 69 A1EEF C37 H27 SING N N 70 A1EEF C38 H28 SING N N 71 A1EEF C39 H29 SING N N 72 A1EEF C41 H30 SING N N 73 A1EEF C42 H31 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 A1EEF InChI InChI 1.06 "InChI=1S/C30H30N6O3/c37-28-13-14-35(30(39)32-16-21-7-2-1-3-8-21)27-19-34(18-23-11-6-10-22-9-4-5-12-25(22)23)29(38)26(36(27)28)15-24-17-31-20-33-24/h1-12,17,20,26-27H,13-16,18-19H2,(H,31,33)(H,32,39)/t26-,27+/m0/s1" A1EEF InChIKey InChI 1.06 ZXICHRIOFQGVQP-RRPNLBNLSA-N A1EEF SMILES_CANONICAL CACTVS 3.385 "O=C1CCN([C@H]2CN(Cc3cccc4ccccc34)C(=O)[C@H](Cc5[nH]cnc5)N12)C(=O)NCc6ccccc6" A1EEF SMILES CACTVS 3.385 "O=C1CCN([CH]2CN(Cc3cccc4ccccc34)C(=O)[CH](Cc5[nH]cnc5)N12)C(=O)NCc6ccccc6" A1EEF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)N2CCC(=O)N3[C@@H]2CN(C(=O)[C@@H]3Cc4cnc[nH]4)Cc5cccc6c5cccc6" A1EEF SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)N2CCC(=O)N3C2CN(C(=O)C3Cc4cnc[nH]4)Cc5cccc6c5cccc6" # _pdbx_chem_comp_identifier.comp_id A1EEF _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-(1~{H}-imidazol-5-ylmethyl)-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-~{N}-(phenylmethyl)-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 A1EEF "Create component" 2024-10-20 PDBC A1EEF "Initial release" 2025-02-19 RCSB #