data_A9F
# 
_chem_comp.id                                    A9F 
_chem_comp.name                                  "N-{[3-({[(1R,2S)-2-{[(2E)-2-cyano-4,4-dimethylpent-2-enoyl]amino}cyclopentyl]oxy}methyl)phenyl]methyl}-4-[(4-methylpiperazin-1-yl)methyl]benzamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C34 H45 N5 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-10-24 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        571.753 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A9F 
_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        6IJS 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_chem_comp.pdbx_pcm                              Y 
# 
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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
A9F CAV C1  C 0 1 N N N N N N 21.173 21.444 8.262  -7.833 1.612  1.721  CAV A9F 1  
A9F CAT C2  C 0 1 N N N N N N 21.055 21.394 9.763  -8.697 2.276  0.646  CAT A9F 2  
A9F NBN N1  N 0 1 N N N N N N 22.165 20.579 10.281 -7.852 3.133  -0.198 NBN A9F 3  
A9F CAA C3  C 0 1 N N N N N N 21.930 20.190 11.690 -8.659 3.847  -1.196 CAA A9F 4  
A9F CAU C4  C 0 1 N N N N N N 23.412 21.349 10.137 -6.790 2.349  -0.842 CAU A9F 5  
A9F CAW C5  C 0 1 N N N N N N 23.652 21.823 8.706  -5.926 1.685  0.233  CAW A9F 6  
A9F NBO N2  N 0 1 N N N N N N 22.481 21.925 7.770  -6.771 0.828  1.077  NBO A9F 7  
A9F CAZ C6  C 0 1 N N N N N N 22.858 21.221 6.515  -5.964 0.113  2.075  CAZ A9F 8  
A9F CBH C7  C 0 1 Y N N N N N 21.893 21.246 5.348  -5.052 -0.863 1.378  CBH A9F 9  
A9F CAM C8  C 0 1 Y N N N N N 21.203 22.382 5.025  -3.788 -0.463 0.982  CAM A9F 10 
A9F CAO C9  C 0 1 Y N N N N N 20.329 22.391 3.950  -2.948 -1.352 0.345  CAO A9F 11 
A9F CAL C10 C 0 1 Y N N N N N 21.697 20.127 4.560  -5.480 -2.158 1.143  CAL A9F 12 
A9F CAN C11 C 0 1 Y N N N N N 20.819 20.138 3.479  -4.649 -3.057 0.506  CAN A9F 13 
A9F CBJ C12 C 0 1 Y N N N N N 20.126 21.281 3.154  -3.375 -2.658 0.099  CBJ A9F 14 
A9F CBE C13 C 0 1 N N N N N N 19.141 21.462 2.038  -2.480 -3.616 -0.584 CBE A9F 15 
A9F OAF O1  O 0 1 N N N N N N 18.816 22.609 1.763  -2.853 -4.754 -0.792 OAF A9F 16 
A9F NBB N3  N 0 1 N N N N N N 18.609 20.557 1.257  -1.250 -3.227 -0.976 NBB A9F 17 
A9F CAX C14 C 0 1 N N N N N N 18.987 19.197 0.942  -0.363 -4.177 -1.652 CAX A9F 18 
A9F CBG C15 C 0 1 Y N N N N N 19.651 19.175 -0.441 0.941  -3.498 -1.982 CBG A9F 19 
A9F CAP C16 C 0 1 Y N N N N N 19.661 20.314 -1.255 1.984  -3.526 -1.075 CAP A9F 20 
A9F CAJ C17 C 0 1 Y N N N N N 20.287 18.038 -0.887 1.097  -2.852 -3.195 CAJ A9F 21 
A9F CAI C18 C 0 1 Y N N N N N 20.921 18.004 -2.119 2.293  -2.230 -3.498 CAI A9F 22 
A9F CAK C19 C 0 1 Y N N N N N 20.929 19.117 -2.920 3.334  -2.253 -2.588 CAK A9F 23 
A9F CBI C20 C 0 1 Y N N N N N 20.299 20.282 -2.483 3.180  -2.903 -1.378 CBI A9F 24 
A9F CAY C21 C 0 1 N N N N N N 20.271 21.509 -3.374 4.315  -2.928 -0.387 CAY A9F 25 
A9F OBD O2  O 0 1 N N N N N N 21.599 21.933 -3.736 4.216  -1.796 0.480  OBD A9F 26 
A9F CBM C22 C 0 1 N N R N N N 21.549 23.005 -4.688 5.250  -1.725 1.463  CBM A9F 27 
A9F CAS C23 C 0 1 N N N N N N 22.827 23.256 -5.485 4.789  -2.409 2.766  CAS A9F 28 
A9F CAQ C24 C 0 1 N N N N N N 22.734 24.688 -5.967 5.393  -1.533 3.891  CAQ A9F 29 
A9F CAR C25 C 0 1 N N N N N N 21.670 25.333 -5.103 5.246  -0.099 3.323  CAR A9F 30 
A9F CBL C26 C 0 1 N N S N N N 21.314 24.329 -4.027 5.541  -0.256 1.817  CBL A9F 31 
A9F NBC N4  N 0 1 N N N N N N 22.147 24.452 -2.858 4.670  0.629  1.040  NBC A9F 32 
A9F CBF C27 C 0 1 N N N N N N 21.716 24.111 -1.630 5.050  1.897  0.788  CBF A9F 33 
A9F OAG O3  O 0 1 N N N N N N 20.624 23.612 -1.407 6.116  2.306  1.206  OAG A9F 34 
A9F CBK C28 C 0 1 N N N N N N 22.606 24.406 -0.450 4.172  2.790  0.004  CBK A9F 35 
A9F CAH C29 C 0 1 N N N N N N 23.711 25.324 -0.742 2.917  2.308  -0.488 CAH A9F 36 
A9F NAE N5  N 0 1 N N N N N N 24.646 26.004 -0.770 1.921  1.925  -0.879 NAE A9F 37 
A9F CBA C30 C 0 1 N N N N N N 23.249 23.139 0.119  4.552  4.057  -0.248 CBA A9F 38 
A9F CBP C31 C 0 1 N N N N N N 23.755 23.365 1.572  3.723  4.925  -1.159 CBP A9F 39 
A9F CAC C32 C 0 1 N N N N N N 22.677 24.051 2.409  3.568  4.237  -2.516 CAC A9F 40 
A9F CAD C33 C 0 1 N N N N N N 25.025 24.222 1.701  2.343  5.145  -0.537 CAD A9F 41 
A9F CAB C34 C 0 1 N N N N N N 24.007 21.977 2.179  4.418  6.275  -1.348 CAB A9F 42 
A9F H1  H1  H 0 1 N N N N N N 20.392 22.116 7.877  -7.386 2.380  2.353  H1  A9F 43 
A9F H2  H2  H 0 1 N N N N N N 21.009 20.429 7.870  -8.453 0.954  2.330  H2  A9F 44 
A9F H3  H3  H 0 1 N N N N N N 21.115 22.412 10.176 -9.166 1.508  0.031  H3  A9F 45 
A9F H4  H4  H 0 1 N N N N N N 20.094 20.939 10.047 -9.468 2.882  1.122  H4  A9F 46 
A9F H6  H6  H 0 1 N N N N N N 22.774 19.583 12.049 -9.394 4.472  -0.689 H6  A9F 47 
A9F H7  H7  H 0 1 N N N N N N 21.839 21.094 12.310 -8.009 4.474  -1.807 H7  A9F 48 
A9F H8  H8  H 0 1 N N N N N N 21.002 19.604 11.758 -9.171 3.126  -1.833 H8  A9F 49 
A9F H9  H9  H 0 1 N N N N N N 24.255 20.712 10.443 -7.237 1.581  -1.474 H9  A9F 50 
A9F H10 H10 H 0 1 N N N N N N 23.360 22.229 10.795 -6.171 3.007  -1.452 H10 A9F 51 
A9F H11 H11 H 0 1 N N N N N N 24.370 21.125 8.251  -5.155 1.079  -0.243 H11 A9F 52 
A9F H12 H12 H 0 1 N N N N N N 24.104 22.824 8.769  -5.457 2.453  0.848  H12 A9F 53 
A9F H14 H14 H 0 1 N N N N N N 23.025 20.165 6.774  -5.367 0.830  2.640  H14 A9F 54 
A9F H15 H15 H 0 1 N N N N N N 23.801 21.666 6.165  -6.623 -0.426 2.755  H15 A9F 55 
A9F H16 H16 H 0 1 N N N N N N 21.340 23.278 5.612  -3.459 0.548  1.172  H16 A9F 56 
A9F H17 H17 H 0 1 N N N N N N 19.787 23.298 3.727  -1.962 -1.038 0.035  H17 A9F 57 
A9F H18 H18 H 0 1 N N N N N N 22.239 19.221 4.789  -6.465 -2.465 1.459  H18 A9F 58 
A9F H19 H19 H 0 1 N N N N N N 20.681 19.242 2.891  -4.984 -4.067 0.324  H19 A9F 59 
A9F H20 H20 H 0 1 N N N N N N 17.782 20.865 0.787  -0.953 -2.319 -0.809 H20 A9F 60 
A9F H21 H21 H 0 1 N N N N N N 18.092 18.558 0.932  -0.175 -5.028 -0.998 H21 A9F 61 
A9F H22 H22 H 0 1 N N N N N N 19.695 18.826 1.698  -0.835 -4.523 -2.572 H22 A9F 62 
A9F H23 H23 H 0 1 N N N N N N 19.171 21.218 -0.925 1.863  -4.034 -0.130 H23 A9F 63 
A9F H24 H24 H 0 1 N N N N N N 20.292 17.155 -0.265 0.284  -2.834 -3.905 H24 A9F 64 
A9F H25 H25 H 0 1 N N N N N N 21.410 17.099 -2.449 2.415  -1.726 -4.445 H25 A9F 65 
A9F H26 H26 H 0 1 N N N N N N 21.419 19.092 -3.882 4.269  -1.767 -2.825 H26 A9F 66 
A9F H27 H27 H 0 1 N N N N N N 19.769 22.328 -2.838 4.261  -3.843 0.203  H27 A9F 67 
A9F H28 H28 H 0 1 N N N N N N 19.710 21.272 -4.290 5.265  -2.895 -0.921 H28 A9F 68 
A9F H29 H29 H 0 1 N N N N N N 20.732 22.821 -5.401 6.155  -2.205 1.089  H29 A9F 69 
A9F H30 H30 H 0 1 N N N N N N 22.888 22.567 -6.340 3.700  -2.414 2.830  H30 A9F 70 
A9F H31 H31 H 0 1 N N N N N N 23.711 23.124 -4.844 5.177  -3.426 2.822  H31 A9F 71 
A9F H32 H32 H 0 1 N N N N N N 23.698 25.201 -5.838 4.825  -1.643 4.814  H32 A9F 72 
A9F H33 H33 H 0 1 N N N N N N 22.441 24.719 -7.027 6.443  -1.778 4.050  H33 A9F 73 
A9F H34 H34 H 0 1 N N N N N N 22.060 26.255 -4.647 4.231  0.269  3.476  H34 A9F 74 
A9F H35 H35 H 0 1 N N N N N N 20.783 25.570 -5.708 5.970  0.571  3.786  H35 A9F 75 
A9F H36 H36 H 0 1 N N N N N N 20.252 24.432 -3.761 6.587  -0.023 1.615  H36 A9F 76 
A9F H37 H37 H 0 1 N N N N N N 23.078 24.803 -2.963 3.820  0.302  0.706  H37 A9F 77 
A9F H39 H39 H 0 1 N N N N N N 23.340 22.207 -0.420 5.451  4.451  0.203  H39 A9F 78 
A9F H41 H41 H 0 1 N N N N N N 23.049 24.204 3.433  3.072  3.276  -2.382 H41 A9F 79 
A9F H42 H42 H 0 1 N N N N N N 22.428 25.024 1.960  2.968  4.865  -3.175 H42 A9F 80 
A9F H43 H43 H 0 1 N N N N N N 21.777 23.419 2.437  4.551  4.081  -2.959 H43 A9F 81 
A9F H44 H44 H 0 1 N N N N N N 25.296 24.320 2.763  2.447  5.712  0.388  H44 A9F 82 
A9F H45 H45 H 0 1 N N N N N N 25.849 23.740 1.155  1.714  5.700  -1.234 H45 A9F 83 
A9F H46 H46 H 0 1 N N N N N N 24.839 25.220 1.277  1.883  4.181  -0.322 H46 A9F 84 
A9F H47 H47 H 0 1 N N N N N N 24.368 22.088 3.212  5.402  6.119  -1.791 H47 A9F 85 
A9F H48 H48 H 0 1 N N N N N N 23.070 21.401 2.178  3.819  6.903  -2.007 H48 A9F 86 
A9F H49 H49 H 0 1 N N N N N N 24.763 21.447 1.581  4.529  6.766  -0.381 H49 A9F 87 
# 
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 
A9F CAQ CAS SING N N 1  
A9F CAQ CAR SING N N 2  
A9F CAS CBM SING N N 3  
A9F CAR CBL SING N N 4  
A9F CBM CBL SING N N 5  
A9F CBM OBD SING N N 6  
A9F CBL NBC SING N N 7  
A9F OBD CAY SING N N 8  
A9F CAY CBI SING N N 9  
A9F CAK CBI DOUB Y N 10 
A9F CAK CAI SING Y N 11 
A9F NBC CBF SING N N 12 
A9F CBI CAP SING Y N 13 
A9F CAI CAJ DOUB Y N 14 
A9F CBF OAG DOUB N N 15 
A9F CBF CBK SING N N 16 
A9F CAP CBG DOUB Y N 17 
A9F CAJ CBG SING Y N 18 
A9F NAE CAH TRIP N N 19 
A9F CAH CBK SING N N 20 
A9F CBK CBA DOUB N E 21 
A9F CBG CAX SING N N 22 
A9F CBA CBP SING N N 23 
A9F CAX NBB SING N N 24 
A9F NBB CBE SING N N 25 
A9F CBP CAD SING N N 26 
A9F CBP CAB SING N N 27 
A9F CBP CAC SING N N 28 
A9F OAF CBE DOUB N N 29 
A9F CBE CBJ SING N N 30 
A9F CBJ CAN DOUB Y N 31 
A9F CBJ CAO SING Y N 32 
A9F CAN CAL SING Y N 33 
A9F CAO CAM DOUB Y N 34 
A9F CAL CBH DOUB Y N 35 
A9F CAM CBH SING Y N 36 
A9F CBH CAZ SING N N 37 
A9F CAZ NBO SING N N 38 
A9F NBO CAV SING N N 39 
A9F NBO CAW SING N N 40 
A9F CAV CAT SING N N 41 
A9F CAW CAU SING N N 42 
A9F CAT NBN SING N N 43 
A9F CAU NBN SING N N 44 
A9F NBN CAA SING N N 45 
A9F CAV H1  SING N N 46 
A9F CAV H2  SING N N 47 
A9F CAT H3  SING N N 48 
A9F CAT H4  SING N N 49 
A9F CAA H6  SING N N 50 
A9F CAA H7  SING N N 51 
A9F CAA H8  SING N N 52 
A9F CAU H9  SING N N 53 
A9F CAU H10 SING N N 54 
A9F CAW H11 SING N N 55 
A9F CAW H12 SING N N 56 
A9F CAZ H14 SING N N 57 
A9F CAZ H15 SING N N 58 
A9F CAM H16 SING N N 59 
A9F CAO H17 SING N N 60 
A9F CAL H18 SING N N 61 
A9F CAN H19 SING N N 62 
A9F NBB H20 SING N N 63 
A9F CAX H21 SING N N 64 
A9F CAX H22 SING N N 65 
A9F CAP H23 SING N N 66 
A9F CAJ H24 SING N N 67 
A9F CAI H25 SING N N 68 
A9F CAK H26 SING N N 69 
A9F CAY H27 SING N N 70 
A9F CAY H28 SING N N 71 
A9F CBM H29 SING N N 72 
A9F CAS H30 SING N N 73 
A9F CAS H31 SING N N 74 
A9F CAQ H32 SING N N 75 
A9F CAQ H33 SING N N 76 
A9F CAR H34 SING N N 77 
A9F CAR H35 SING N N 78 
A9F CBL H36 SING N N 79 
A9F NBC H37 SING N N 80 
A9F CBA H39 SING N N 81 
A9F CAC H41 SING N N 82 
A9F CAC H42 SING N N 83 
A9F CAC H43 SING N N 84 
A9F CAD H44 SING N N 85 
A9F CAD H45 SING N N 86 
A9F CAD H46 SING N N 87 
A9F CAB H47 SING N N 88 
A9F CAB H48 SING N N 89 
A9F CAB H49 SING N N 90 
# 
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 
A9F SMILES           ACDLabs              12.01 "C1CN(C)CCN1Cc2ccc(cc2)C(=O)NCc3cc(ccc3)COC4C(CCC4)NC(=O)\C(=C\C(C)(C)C)C#N"                                                                                                                                                                   
A9F InChI            InChI                1.03  "InChI=1S/C34H45N5O3/c1-34(2,3)20-29(21-35)33(41)37-30-9-6-10-31(30)42-24-27-8-5-7-26(19-27)22-36-32(40)28-13-11-25(12-14-28)23-39-17-15-38(4)16-18-39/h5,7-8,11-14,19-20,30-31H,6,9-10,15-18,22-24H2,1-4H3,(H,36,40)(H,37,41)/t30-,31+/m0/s1" 
A9F InChIKey         InChI                1.03  BUZJOXNDWIIWSG-IOWSJCHKSA-N                                                                                                                                                                                                                    
A9F SMILES_CANONICAL CACTVS               3.385 "CN1CCN(CC1)Cc2ccc(cc2)C(=O)NCc3cccc(CO[C@@H]4CCC[C@@H]4NC(=O)\C(=C\C(C)(C)C)C#N)c3"                                                                                                                                                           
A9F SMILES           CACTVS               3.385 "CN1CCN(CC1)Cc2ccc(cc2)C(=O)NCc3cccc(CO[CH]4CCC[CH]4NC(=O)C(=CC(C)(C)C)C#N)c3"                                                                                                                                                                 
A9F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC(C)(C)/C=C(\C#N)/C(=O)N[C@H]1CCC[C@H]1OCc2cccc(c2)CNC(=O)c3ccc(cc3)CN4CCN(CC4)C"                                                                                                                                                            
A9F SMILES           "OpenEye OEToolkits" 2.0.6 "CC(C)(C)C=C(C#N)C(=O)NC1CCCC1OCc2cccc(c2)CNC(=O)c3ccc(cc3)CN4CCN(CC4)C"                                                                                                                                                                       
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
A9F "SYSTEMATIC NAME" ACDLabs              12.01 "N-{[3-({[(1R,2S)-2-{[(2E)-2-cyano-4,4-dimethylpent-2-enoyl]amino}cyclopentyl]oxy}methyl)phenyl]methyl}-4-[(4-methylpiperazin-1-yl)methyl]benzamide"           
A9F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "~{N}-[[3-[[(1~{R},2~{S})-2-[[(~{E})-2-cyano-4,4-dimethyl-pent-2-enoyl]amino]cyclopentyl]oxymethyl]phenyl]methyl]-4-[(4-methylpiperazin-1-yl)methyl]benzamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A9F "Create component" 2018-10-24 PDBJ 
A9F "Initial release"  2019-10-16 RCSB 
A9F "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A9F 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               CBA 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
