data_A1D8K # _chem_comp.id A1D8K _chem_comp.name "(2S)-N-[[4-[[3-(cyclohexylamino)propylamino]methyl]phenyl]methyl]-5-(diaminomethylideneamino)-2-(pyridin-2-ylmethylamino)pentanamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C29 H46 N8 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms HF51116 _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-06-04 _chem_comp.pdbx_modified_date 2025-02-21 _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 522.729 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1D8K _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 8ZPL _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 A1D8K C1 C1 C 0 1 N N N N N N 130.171 137.916 115.506 -14.040 0.512 -0.172 C1 A1D8K 1 A1D8K C10 C2 C 0 1 N N N N N N 122.443 141.168 120.226 -3.948 0.552 1.005 C10 A1D8K 2 A1D8K C11 C3 C 0 1 Y N N N N N 121.859 139.974 120.938 -2.627 0.159 0.396 C11 A1D8K 3 A1D8K C12 C4 C 0 1 Y N N N N N 122.610 139.244 121.842 -2.043 0.960 -0.567 C12 A1D8K 4 A1D8K C13 C5 C 0 1 Y N N N N N 122.073 138.147 122.485 -0.831 0.599 -1.125 C13 A1D8K 5 A1D8K C14 C6 C 0 1 Y N N N N N 120.771 137.756 122.239 -0.203 -0.564 -0.720 C14 A1D8K 6 A1D8K C15 C7 C 0 1 Y N N N N N 120.016 138.491 121.346 -0.787 -1.366 0.243 C15 A1D8K 7 A1D8K C16 C8 C 0 1 Y N N N N N 120.553 139.586 120.700 -1.996 -1.002 0.805 C16 A1D8K 8 A1D8K C17 C9 C 0 1 N N N N N N 120.169 136.571 122.934 1.118 -0.958 -1.329 C17 A1D8K 9 A1D8K C18 C10 C 0 1 N N N N N N 118.605 135.178 121.761 3.490 -0.605 -0.900 C18 A1D8K 10 A1D8K C19 C11 C 0 1 N N S N N N 117.700 135.283 120.555 4.614 -0.014 -0.088 C19 A1D8K 11 A1D8K C2 C12 C 0 1 N N N N N N 129.345 137.378 116.642 -13.608 -0.852 0.371 C2 A1D8K 12 A1D8K C20 C13 C 0 1 N N N N N N 116.259 135.097 120.963 4.899 1.410 -0.573 C20 A1D8K 13 A1D8K C21 C14 C 0 1 N N N N N N 115.479 134.287 119.949 5.952 2.054 0.330 C21 A1D8K 14 A1D8K C22 C15 C 0 1 N N N N N N 114.163 133.990 120.564 6.238 3.477 -0.154 C22 A1D8K 15 A1D8K C23 C16 C 0 1 N N N N N N 112.638 135.390 121.583 8.418 4.402 0.229 C23 A1D8K 16 A1D8K C24 C17 C 0 1 N N N N N N 118.760 134.601 118.420 5.790 -1.997 0.650 C24 A1D8K 17 A1D8K C25 C18 C 0 1 Y N N N N N 118.911 133.448 117.459 7.088 -2.754 0.539 C25 A1D8K 18 A1D8K C26 C19 C 0 1 Y N N N N N 117.822 132.742 116.994 8.107 -2.497 1.436 C26 A1D8K 19 A1D8K C27 C20 C 0 1 Y N N N N N 118.025 131.692 116.122 9.298 -3.199 1.325 C27 A1D8K 20 A1D8K C28 C21 C 0 1 Y N N N N N 119.301 131.374 115.745 9.420 -4.136 0.310 C28 A1D8K 21 A1D8K C29 C22 C 0 1 Y N N N N N 120.330 132.113 116.261 8.357 -4.338 -0.550 C29 A1D8K 22 A1D8K C3 C23 C 0 1 N N N N N N 128.226 138.349 116.993 -12.229 -1.210 -0.188 C3 A1D8K 23 A1D8K C4 C24 C 0 1 N N N N N N 127.440 138.723 115.762 -11.215 -0.147 0.238 C4 A1D8K 24 A1D8K C5 C25 C 0 1 N N N N N N 128.333 139.415 114.761 -11.647 1.217 -0.304 C5 A1D8K 25 A1D8K C6 C26 C 0 1 N N N N N N 129.783 139.342 115.213 -13.026 1.575 0.255 C6 A1D8K 26 A1D8K C7 C27 C 0 1 N N N N N N 125.932 139.484 117.545 -8.823 0.102 0.517 C7 A1D8K 27 A1D8K C8 C28 C 0 1 N N N N N N 125.560 140.840 118.109 -7.462 -0.277 -0.071 C8 A1D8K 28 A1D8K C9 C29 C 0 1 N N N N N N 124.088 140.989 118.422 -6.349 0.340 0.778 C9 A1D8K 29 A1D8K N1 N1 N 0 1 N N N N N N 126.304 139.559 116.135 -9.891 -0.491 -0.298 N1 A1D8K 30 A1D8K N2 N2 N 0 1 N N N N N N 123.841 140.993 119.866 -5.043 -0.024 0.213 N2 A1D8K 31 A1D8K N3 N3 N 0 1 N N N N N N 118.853 136.288 122.440 2.210 -0.384 -0.540 N3 A1D8K 32 A1D8K N4 N4 N 0 1 N N N N N N 113.871 134.998 121.569 7.246 4.094 0.711 N4 A1D8K 33 A1D8K N5 N5 N 0 1 N N N N N N 111.659 134.761 120.934 9.393 4.902 1.059 N5 A1D8K 34 A1D8K N6 N6 N 0 1 N N N N N N 112.337 136.467 122.290 8.678 4.226 -1.109 N6 A1D8K 35 A1D8K N7 N7 N 0 1 N N N N N N 117.966 134.236 119.591 5.820 -0.837 -0.250 N7 A1D8K 36 A1D8K N8 N8 N 0 1 Y N N N N N 120.159 133.136 117.106 7.237 -3.656 -0.411 N8 A1D8K 37 A1D8K O1 O1 O 0 1 N N N N N N 119.097 134.104 122.066 3.737 -1.280 -1.877 O1 A1D8K 38 A1D8K H1 H1 H 0 1 N N N N N N 130.001 137.301 114.610 -14.088 0.471 -1.260 H1 A1D8K 39 A1D8K H2 H2 H 0 1 N N N N N N 131.236 137.878 115.780 -15.022 0.766 0.226 H2 A1D8K 40 A1D8K H3 H3 H 0 1 N N N N N N 122.359 142.044 120.886 -4.003 0.178 2.027 H3 A1D8K 41 A1D8K H4 H4 H 0 1 N N N N N N 121.865 141.344 119.307 -4.036 1.639 1.010 H4 A1D8K 42 A1D8K H5 H5 H 0 1 N N N N N N 123.629 139.536 122.047 -2.534 1.868 -0.883 H5 A1D8K 43 A1D8K H6 H6 H 0 1 N N N N N N 122.676 137.589 123.187 -0.376 1.225 -1.878 H6 A1D8K 44 A1D8K H7 H7 H 0 1 N N N N N N 118.993 138.205 121.151 -0.296 -2.274 0.559 H7 A1D8K 45 A1D8K H8 H8 H 0 1 N N N N N N 119.948 140.145 120.002 -2.450 -1.625 1.561 H8 A1D8K 46 A1D8K H9 H9 H 0 1 N N N N N N 120.811 135.693 122.766 1.206 -2.045 -1.335 H9 A1D8K 47 A1D8K H10 H10 H 0 1 N N N N N N 120.109 136.781 124.012 1.172 -0.584 -2.352 H10 A1D8K 48 A1D8K H11 H11 H 0 1 N N N N N N 117.824 136.272 120.089 4.329 0.011 0.963 H11 A1D8K 49 A1D8K H12 H12 H 0 1 N N N N N N 128.908 136.413 116.346 -13.560 -0.812 1.459 H12 A1D8K 50 A1D8K H13 H13 H 0 1 N N N N N N 129.989 137.234 117.522 -14.331 -1.610 0.067 H13 A1D8K 51 A1D8K H14 H14 H 0 1 N N N N N N 115.789 136.086 121.064 5.269 1.377 -1.597 H14 A1D8K 52 A1D8K H15 H15 H 0 1 N N N N N N 116.229 134.576 121.931 3.981 1.996 -0.536 H15 A1D8K 53 A1D8K H16 H16 H 0 1 N N N N N N 116.011 133.352 119.721 5.582 2.086 1.355 H16 A1D8K 54 A1D8K H17 H17 H 0 1 N N N N N N 115.343 134.867 119.024 6.870 1.467 0.294 H17 A1D8K 55 A1D8K H18 H18 H 0 1 N N N N N N 113.382 134.005 119.789 6.608 3.445 -1.178 H18 A1D8K 56 A1D8K H19 H19 H 0 1 N N N N N N 114.192 132.997 121.036 5.320 4.064 -0.117 H19 A1D8K 57 A1D8K H20 H20 H 0 1 N N N N N N 119.759 134.919 118.753 4.963 -2.651 0.372 H20 A1D8K 58 A1D8K H21 H21 H 0 1 N N N N N N 118.264 135.434 117.900 5.654 -1.657 1.677 H21 A1D8K 59 A1D8K H22 H22 H 0 1 N N N N N N 116.823 133.007 117.308 7.977 -1.760 2.215 H22 A1D8K 60 A1D8K H23 H23 H 0 1 N N N N N N 117.186 131.128 115.742 10.112 -3.019 2.012 H23 A1D8K 61 A1D8K H24 H24 H 0 1 N N N N N N 119.491 130.562 115.059 10.333 -4.700 0.194 H24 A1D8K 62 A1D8K H25 H25 H 0 1 N N N N N N 121.338 131.856 115.970 8.444 -5.066 -1.344 H25 A1D8K 63 A1D8K H26 H26 H 0 1 N N N N N N 128.662 139.258 117.433 -11.922 -2.182 0.198 H26 A1D8K 64 A1D8K H27 H27 H 0 1 N N N N N N 127.552 137.875 117.722 -12.278 -1.250 -1.276 H27 A1D8K 65 A1D8K H28 H28 H 0 1 N N N N N N 127.063 137.798 115.302 -11.167 -0.107 1.326 H28 A1D8K 66 A1D8K H29 H29 H 0 1 N N N N N N 128.032 140.469 114.674 -10.924 1.974 -0.001 H29 A1D8K 67 A1D8K H30 H30 H 0 1 N N N N N N 128.232 138.923 113.783 -11.695 1.176 -1.392 H30 A1D8K 68 A1D8K H31 H31 H 0 1 N N N N N N 130.431 139.738 114.417 -13.333 2.546 -0.132 H31 A1D8K 69 A1D8K H32 H32 H 0 1 N N N N N N 129.910 139.946 116.123 -12.977 1.615 1.343 H32 A1D8K 70 A1D8K H33 H33 H 0 1 N N N N N N 125.070 138.808 117.649 -8.894 -0.274 1.538 H33 A1D8K 71 A1D8K H34 H34 H 0 1 N N N N N N 126.783 139.084 118.116 -8.927 1.187 0.521 H34 A1D8K 72 A1D8K H35 H35 H 0 1 N N N N N N 126.129 140.997 119.037 -7.357 -1.362 -0.075 H35 A1D8K 73 A1D8K H36 H36 H 0 1 N N N N N N 125.838 141.609 117.373 -7.391 0.098 -1.092 H36 A1D8K 74 A1D8K H37 H37 H 0 1 N N N N N N 123.727 141.936 117.995 -6.454 1.425 0.782 H37 A1D8K 75 A1D8K H38 H38 H 0 1 N N N N N N 123.540 140.150 117.968 -6.421 -0.036 1.799 H38 A1D8K 76 A1D8K H39 H39 H 0 1 N N N N N N 126.533 140.509 115.923 -9.779 -1.491 -0.371 H39 A1D8K 77 A1D8K H41 H41 H 0 1 N N N N N N 124.156 140.121 120.241 -4.948 -1.026 0.139 H41 A1D8K 78 A1D8K H43 H43 H 0 1 N N N N N N 118.112 136.938 122.610 2.012 0.156 0.241 H43 A1D8K 79 A1D8K H45 H45 H 0 1 N N N N N N 110.722 135.105 120.988 10.265 5.131 0.701 H45 A1D8K 80 A1D8K H46 H46 H 0 1 N N N N N N 113.053 136.951 122.792 8.019 3.801 -1.680 H46 A1D8K 81 A1D8K H47 H47 H 0 1 N N N N N N 111.393 136.797 122.322 9.522 4.526 -1.483 H47 A1D8K 82 A1D8K H48 H48 H 0 1 N N N N N N 117.084 133.896 119.264 6.654 -0.288 -0.104 H48 A1D8K 83 A1D8K H40 H40 H 0 1 N N N N N N 111.862 133.945 120.393 9.209 5.026 2.003 H40 A1D8K 84 # 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 A1D8K C5 C6 SING N N 1 A1D8K C5 C4 SING N N 2 A1D8K C6 C1 SING N N 3 A1D8K C1 C2 SING N N 4 A1D8K C28 C27 DOUB Y N 5 A1D8K C28 C29 SING Y N 6 A1D8K C4 N1 SING N N 7 A1D8K C4 C3 SING N N 8 A1D8K C27 C26 SING Y N 9 A1D8K N1 C7 SING N N 10 A1D8K C29 N8 DOUB Y N 11 A1D8K C2 C3 SING N N 12 A1D8K C26 C25 DOUB Y N 13 A1D8K N8 C25 SING Y N 14 A1D8K C25 C24 SING N N 15 A1D8K C7 C8 SING N N 16 A1D8K C8 C9 SING N N 17 A1D8K C24 N7 SING N N 18 A1D8K C9 N2 SING N N 19 A1D8K N7 C19 SING N N 20 A1D8K N2 C10 SING N N 21 A1D8K C21 C22 SING N N 22 A1D8K C21 C20 SING N N 23 A1D8K C10 C11 SING N N 24 A1D8K C19 C20 SING N N 25 A1D8K C19 C18 SING N N 26 A1D8K C22 N4 SING N N 27 A1D8K C16 C11 DOUB Y N 28 A1D8K C16 C15 SING Y N 29 A1D8K N5 C23 SING N N 30 A1D8K C11 C12 SING Y N 31 A1D8K C15 C14 DOUB Y N 32 A1D8K N4 C23 DOUB N N 33 A1D8K C23 N6 SING N N 34 A1D8K C18 O1 DOUB N N 35 A1D8K C18 N3 SING N N 36 A1D8K C12 C13 DOUB Y N 37 A1D8K C14 C13 SING Y N 38 A1D8K C14 C17 SING N N 39 A1D8K N3 C17 SING N N 40 A1D8K C1 H1 SING N N 41 A1D8K C1 H2 SING N N 42 A1D8K C10 H3 SING N N 43 A1D8K C10 H4 SING N N 44 A1D8K C12 H5 SING N N 45 A1D8K C13 H6 SING N N 46 A1D8K C15 H7 SING N N 47 A1D8K C16 H8 SING N N 48 A1D8K C17 H9 SING N N 49 A1D8K C17 H10 SING N N 50 A1D8K C19 H11 SING N N 51 A1D8K C2 H12 SING N N 52 A1D8K C2 H13 SING N N 53 A1D8K C20 H14 SING N N 54 A1D8K C20 H15 SING N N 55 A1D8K C21 H16 SING N N 56 A1D8K C21 H17 SING N N 57 A1D8K C22 H18 SING N N 58 A1D8K C22 H19 SING N N 59 A1D8K C24 H20 SING N N 60 A1D8K C24 H21 SING N N 61 A1D8K C26 H22 SING N N 62 A1D8K C27 H23 SING N N 63 A1D8K C28 H24 SING N N 64 A1D8K C29 H25 SING N N 65 A1D8K C3 H26 SING N N 66 A1D8K C3 H27 SING N N 67 A1D8K C4 H28 SING N N 68 A1D8K C5 H29 SING N N 69 A1D8K C5 H30 SING N N 70 A1D8K C6 H31 SING N N 71 A1D8K C6 H32 SING N N 72 A1D8K C7 H33 SING N N 73 A1D8K C7 H34 SING N N 74 A1D8K C8 H35 SING N N 75 A1D8K C8 H36 SING N N 76 A1D8K C9 H37 SING N N 77 A1D8K C9 H38 SING N N 78 A1D8K N1 H39 SING N N 79 A1D8K N2 H41 SING N N 80 A1D8K N3 H43 SING N N 81 A1D8K N5 H45 SING N N 82 A1D8K N6 H46 SING N N 83 A1D8K N6 H47 SING N N 84 A1D8K N7 H48 SING N N 85 A1D8K N5 H40 SING N N 86 # 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 A1D8K InChI InChI 1.06 "InChI=1S/C29H46N8O/c30-29(31)35-18-6-11-27(36-22-26-10-4-5-17-34-26)28(38)37-21-24-14-12-23(13-15-24)20-32-16-7-19-33-25-8-2-1-3-9-25/h4-5,10,12-15,17,25,27,32-33,36H,1-3,6-9,11,16,18-22H2,(H,37,38)(H4,30,31,35)/t27-/m0/s1" A1D8K InChIKey InChI 1.06 AMGQQWNQWHMPHG-MHZLTWQESA-N A1D8K SMILES_CANONICAL CACTVS 3.385 "NC(N)=NCCC[C@H](NCc1ccccn1)C(=O)NCc2ccc(CNCCCNC3CCCCC3)cc2" A1D8K SMILES CACTVS 3.385 "NC(N)=NCCC[CH](NCc1ccccn1)C(=O)NCc2ccc(CNCCCNC3CCCCC3)cc2" A1D8K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccnc(c1)CN[C@@H](CCCN=C(N)N)C(=O)NCc2ccc(cc2)CNCCCNC3CCCCC3" A1D8K SMILES "OpenEye OEToolkits" 2.0.7 "c1ccnc(c1)CNC(CCCN=C(N)N)C(=O)NCc2ccc(cc2)CNCCCNC3CCCCC3" # _pdbx_chem_comp_identifier.comp_id A1D8K _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 "(2~{S})-5-[bis(azanyl)methylideneamino]-~{N}-[[4-[[3-(cyclohexylamino)propylamino]methyl]phenyl]methyl]-2-(pyridin-2-ylmethylamino)pentanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1D8K "Create component" 2024-06-04 PDBC A1D8K "Initial release" 2025-02-26 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1D8K _pdbx_chem_comp_synonyms.name HF51116 _pdbx_chem_comp_synonyms.provenance PUBCHEM _pdbx_chem_comp_synonyms.type ? #