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         ? 
# 
