data_K5O
# 
_chem_comp.id                                    K5O 
_chem_comp.name                                  Ziftomenib 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C33 H42 F3 N9 O2 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-02 
_chem_comp.pdbx_modified_date                    2024-11-15 
_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                        717.871 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     K5O 
_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        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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_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 
K5O C1  C1  C 0 1 N N N N N N ? ? ? -7.685  -5.030 1.495  C1  K5O 1  
K5O N1  N1  N 0 1 N N N N N N ? ? ? -6.698  -4.240 0.756  N1  K5O 2  
K5O C2  C2  C 0 1 Y N N N N N ? ? ? -6.845  -2.866 0.655  C2  K5O 3  
K5O N2  N2  N 0 1 Y N N N N N ? ? ? -5.939  -2.169 -0.019 N2  K5O 4  
K5O C3  C3  C 0 1 Y N N N N N ? ? ? -6.039  -0.855 -0.141 C3  K5O 5  
K5O N3  N3  N 0 1 N N N N N N ? ? ? -5.087  -0.142 -0.848 N3  K5O 6  
K5O C4  C4  C 0 1 N N N N N N ? ? ? -3.958  -0.841 -1.467 C4  K5O 7  
K5O C5  C5  C 0 1 N N N N N N ? ? ? -3.431  -0.019 -2.646 C5  K5O 8  
K5O C6  C6  C 0 1 N N N N N N ? ? ? -2.215  -0.724 -3.250 C6  K5O 9  
K5O N4  N4  N 0 1 N N N N N N ? ? ? -1.172  -0.868 -2.226 N4  K5O 10 
K5O C7  C7  C 0 1 N N N N N N ? ? ? 0.062   -1.416 -2.805 C7  K5O 11 
K5O C8  C8  C 0 1 Y N N N N N ? ? ? 1.206   -1.193 -1.850 C8  K5O 12 
K5O C9  C9  C 0 1 Y N N N N N ? ? ? 1.681   -2.251 -1.085 C9  K5O 13 
K5O C10 C10 C 0 1 Y N N N N N ? ? ? 2.726   -2.069 -0.207 C10 K5O 14 
K5O C11 C11 C 0 1 Y N N N N N ? ? ? 3.314   -0.814 -0.081 C11 K5O 15 
K5O N5  N5  N 0 1 Y N N N N N ? ? ? 4.346   -0.331 0.690  N5  K5O 16 
K5O C12 C12 C 0 1 N N N N N N ? ? ? 5.134   -1.112 1.646  C12 K5O 17 
K5O C13 C13 C 0 1 N N S N N N ? ? ? 6.346   -1.717 0.935  C13 K5O 18 
K5O C14 C14 C 0 1 N N N N N N ? ? ? 7.100   -2.633 1.901  C14 K5O 19 
K5O N6  N6  N 0 1 N N N N N N ? ? ? 7.238   -0.641 0.484  N6  K5O 20 
K5O C15 C15 C 0 1 N N N N N N ? ? ? 8.285   -1.163 -0.405 C15 K5O 21 
K5O C16 C16 C 0 1 N N N N N N ? ? ? 9.079   0.008  -0.995 C16 K5O 22 
K5O N7  N7  N 0 1 N N N N N N ? ? ? 9.563   0.848  0.110  N7  K5O 23 
K5O C17 C17 C 0 1 N N N N N N ? ? ? 8.592   1.297  1.120  C17 K5O 24 
K5O C18 C18 C 0 1 N N N N N N ? ? ? 7.817   0.076  1.627  C18 K5O 25 
K5O S1  S1  S 0 1 N N N N N N ? ? ? 11.159  1.279  0.214  S1  K5O 26 
K5O C19 C19 C 0 1 N N N N N N ? ? ? 11.920  -0.043 1.196  C19 K5O 27 
K5O O1  O1  O 0 1 N N N N N N ? ? ? 11.622  1.233  -1.128 O1  K5O 28 
K5O O2  O2  O 0 1 N N N N N N ? ? ? 11.146  2.498  0.945  O2  K5O 29 
K5O C20 C20 C 0 1 Y N N N N N ? ? ? 4.517   1.011  0.413  C20 K5O 30 
K5O C21 C21 C 0 1 Y N N N N N ? ? ? 3.609   1.393  -0.524 C21 K5O 31 
K5O C22 C22 C 0 1 Y N N N N N ? ? ? 2.831   0.257  -0.858 C22 K5O 32 
K5O C23 C23 C 0 1 Y N N N N N ? ? ? 1.771   0.046  -1.748 C23 K5O 33 
K5O C24 C24 C 0 1 N N N N N N ? ? ? 1.252   1.184  -2.589 C24 K5O 34 
K5O C25 C25 C 0 1 N N N N N N ? ? ? 5.495   1.865  1.018  C25 K5O 35 
K5O N8  N8  N 0 1 N N N N N N ? ? ? 6.270   2.543  1.497  N8  K5O 36 
K5O C26 C26 C 0 1 N N N N N N ? ? ? -1.639  -1.694 -1.105 C26 K5O 37 
K5O C27 C27 C 0 1 N N N N N N ? ? ? -2.839  -1.018 -0.437 C27 K5O 38 
K5O C28 C28 C 0 1 Y N N N N N ? ? ? -7.136  -0.187 0.462  C28 K5O 39 
K5O C29 C29 C 0 1 Y N N N N N ? ? ? -7.483  1.222  0.483  C29 K5O 40 
K5O C30 C30 C 0 1 Y N N N N N ? ? ? -8.587  1.510  1.143  C30 K5O 41 
K5O C31 C31 C 0 1 N N N N N N ? ? ? -9.144  2.902  1.299  C31 K5O 42 
K5O C32 C32 C 0 1 N N N N N N ? ? ? -10.101 3.201  0.144  C32 K5O 43 
K5O F1  F1  F 0 1 N N N N N N ? ? ? -10.618 4.493  0.289  F1  K5O 44 
K5O F2  F2  F 0 1 N N N N N N ? ? ? -9.410  3.109  -1.069 F2  K5O 45 
K5O F3  F3  F 0 1 N N N N N N ? ? ? -11.149 2.275  0.155  F3  K5O 46 
K5O S2  S2  S 0 1 Y N N N N N ? ? ? -9.325  0.069  1.816  S2  K5O 47 
K5O C33 C33 C 0 1 Y N N N N N ? ? ? -8.063  -0.964 1.161  C33 K5O 48 
K5O N9  N9  N 0 1 Y N N N N N ? ? ? -7.885  -2.290 1.228  N9  K5O 49 
K5O H1  H1  H 0 1 N N N N N N ? ? ? -7.719  -4.692 2.531  H1  K5O 50 
K5O H2  H2  H 0 1 N N N N N N ? ? ? -8.667  -4.903 1.039  H2  K5O 51 
K5O H3  H3  H 0 1 N N N N N N ? ? ? -7.404  -6.083 1.465  H3  K5O 52 
K5O H4  H4  H 0 1 N N N N N N ? ? ? -5.941  -4.678 0.337  H4  K5O 53 
K5O H5  H5  H 0 1 N N N N N N ? ? ? -5.167  0.821  -0.933 H5  K5O 54 
K5O H6  H6  H 0 1 N N N N N N ? ? ? -4.285  -1.819 -1.821 H6  K5O 55 
K5O H7  H7  H 0 1 N N N N N N ? ? ? -4.211  0.074  -3.402 H7  K5O 56 
K5O H8  H8  H 0 1 N N N N N N ? ? ? -3.142  0.973  -2.298 H8  K5O 57 
K5O H9  H9  H 0 1 N N N N N N ? ? ? -2.509  -1.710 -3.611 H9  K5O 58 
K5O H10 H10 H 0 1 N N N N N N ? ? ? -1.828  -0.134 -4.081 H10 K5O 59 
K5O H12 H12 H 0 1 N N N N N N ? ? ? -0.062  -2.484 -2.980 H12 K5O 60 
K5O H13 H13 H 0 1 N N N N N N ? ? ? 0.274   -0.915 -3.749 H13 K5O 61 
K5O H14 H14 H 0 1 N N N N N N ? ? ? 1.225   -3.226 -1.181 H14 K5O 62 
K5O H15 H15 H 0 1 N N N N N N ? ? ? 3.087   -2.898 0.384  H15 K5O 63 
K5O H16 H16 H 0 1 N N N N N N ? ? ? 5.474   -0.462 2.453  H16 K5O 64 
K5O H17 H17 H 0 1 N N N N N N ? ? ? 4.518   -1.910 2.059  H17 K5O 65 
K5O H18 H18 H 0 1 N N N N N N ? ? ? 6.010   -2.296 0.074  H18 K5O 66 
K5O H19 H19 H 0 1 N N N N N N ? ? ? 6.438   -3.432 2.236  H19 K5O 67 
K5O H20 H20 H 0 1 N N N N N N ? ? ? 7.963   -3.065 1.395  H20 K5O 68 
K5O H21 H21 H 0 1 N N N N N N ? ? ? 7.436   -2.055 2.762  H21 K5O 69 
K5O H23 H23 H 0 1 N N N N N N ? ? ? 8.955   -1.808 0.163  H23 K5O 70 
K5O H24 H24 H 0 1 N N N N N N ? ? ? 7.826   -1.735 -1.211 H24 K5O 71 
K5O H25 H25 H 0 1 N N N N N N ? ? ? 9.927   -0.375 -1.563 H25 K5O 72 
K5O H26 H26 H 0 1 N N N N N N ? ? ? 8.434   0.594  -1.650 H26 K5O 73 
K5O H27 H27 H 0 1 N N N N N N ? ? ? 9.119   1.768  1.950  H27 K5O 74 
K5O H28 H28 H 0 1 N N N N N N ? ? ? 7.900   2.010  0.671  H28 K5O 75 
K5O H29 H29 H 0 1 N N N N N N ? ? ? 7.020   0.403  2.294  H29 K5O 76 
K5O H30 H30 H 0 1 N N N N N N ? ? ? 8.495   -0.586 2.166  H30 K5O 77 
K5O H31 H31 H 0 1 N N N N N N ? ? ? 11.789  -0.997 0.685  H31 K5O 78 
K5O H32 H32 H 0 1 N N N N N N ? ? ? 12.984  0.161  1.316  H32 K5O 79 
K5O H33 H33 H 0 1 N N N N N N ? ? ? 11.446  -0.087 2.176  H33 K5O 80 
K5O H34 H34 H 0 1 N N N N N N ? ? ? 3.500   2.384  -0.939 H34 K5O 81 
K5O H35 H35 H 0 1 N N N N N N ? ? ? 1.730   1.158  -3.569 H35 K5O 82 
K5O H36 H36 H 0 1 N N N N N N ? ? ? 0.173   1.085  -2.708 H36 K5O 83 
K5O H37 H37 H 0 1 N N N N N N ? ? ? 1.479   2.130  -2.099 H37 K5O 84 
K5O H38 H38 H 0 1 N N N N N N ? ? ? -1.936  -2.675 -1.476 H38 K5O 85 
K5O H39 H39 H 0 1 N N N N N N ? ? ? -0.835  -1.808 -0.378 H39 K5O 86 
K5O H40 H40 H 0 1 N N N N N N ? ? ? -2.539  -0.042 -0.054 H40 K5O 87 
K5O H41 H41 H 0 1 N N N N N N ? ? ? -3.195  -1.638 0.385  H41 K5O 88 
K5O H42 H42 H 0 1 N N N N N N ? ? ? -6.883  1.976  -0.005 H42 K5O 89 
K5O H43 H43 H 0 1 N N N N N N ? ? ? -9.682  2.974  2.245  H43 K5O 90 
K5O H44 H44 H 0 1 N N N N N N ? ? ? -8.327  3.624  1.291  H44 K5O 91 
# 
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 
K5O O2  S1  DOUB N N 1  
K5O O1  S1  DOUB N N 2  
K5O C19 S1  SING N N 3  
K5O S1  N7  SING N N 4  
K5O N7  C17 SING N N 5  
K5O N7  C16 SING N N 6  
K5O C17 C18 SING N N 7  
K5O C24 C23 SING N N 8  
K5O C1  N1  SING N N 9  
K5O C16 C15 SING N N 10 
K5O C18 N6  SING N N 11 
K5O C21 C22 SING Y N 12 
K5O C21 C20 DOUB Y N 13 
K5O C23 C22 DOUB Y N 14 
K5O C23 C8  SING Y N 15 
K5O N1  C2  SING N N 16 
K5O C7  C8  SING N N 17 
K5O C7  N4  SING N N 18 
K5O C22 C11 SING Y N 19 
K5O C15 N6  SING N N 20 
K5O C26 N4  SING N N 21 
K5O C26 C27 SING N N 22 
K5O N8  C25 TRIP N N 23 
K5O C8  C9  DOUB Y N 24 
K5O C25 C20 SING N N 25 
K5O C20 N5  SING Y N 26 
K5O N6  C13 SING N N 27 
K5O N4  C6  SING N N 28 
K5O C2  N2  DOUB Y N 29 
K5O C2  N9  SING Y N 30 
K5O C11 N5  SING Y N 31 
K5O C11 C10 DOUB Y N 32 
K5O C27 C4  SING N N 33 
K5O N2  C3  SING Y N 34 
K5O N5  C12 SING N N 35 
K5O C9  C10 SING Y N 36 
K5O C6  C5  SING N N 37 
K5O C4  C5  SING N N 38 
K5O C4  N3  SING N N 39 
K5O C13 C12 SING N N 40 
K5O C13 C14 SING N N 41 
K5O N9  C33 DOUB Y N 42 
K5O C3  N3  SING N N 43 
K5O C3  C28 DOUB Y N 44 
K5O C33 C28 SING Y N 45 
K5O C33 S2  SING Y N 46 
K5O C28 C29 SING Y N 47 
K5O S2  C30 SING Y N 48 
K5O C29 C30 DOUB Y N 49 
K5O C30 C31 SING N N 50 
K5O F1  C32 SING N N 51 
K5O F2  C32 SING N N 52 
K5O C31 C32 SING N N 53 
K5O C32 F3  SING N N 54 
K5O C1  H1  SING N N 55 
K5O C1  H2  SING N N 56 
K5O C1  H3  SING N N 57 
K5O N1  H4  SING N N 58 
K5O N3  H5  SING N N 59 
K5O C4  H6  SING N N 60 
K5O C5  H7  SING N N 61 
K5O C5  H8  SING N N 62 
K5O C6  H9  SING N N 63 
K5O C6  H10 SING N N 64 
K5O C7  H12 SING N N 65 
K5O C7  H13 SING N N 66 
K5O C9  H14 SING N N 67 
K5O C10 H15 SING N N 68 
K5O C12 H16 SING N N 69 
K5O C12 H17 SING N N 70 
K5O C13 H18 SING N N 71 
K5O C14 H19 SING N N 72 
K5O C14 H20 SING N N 73 
K5O C14 H21 SING N N 74 
K5O C15 H23 SING N N 75 
K5O C15 H24 SING N N 76 
K5O C16 H25 SING N N 77 
K5O C16 H26 SING N N 78 
K5O C17 H27 SING N N 79 
K5O C17 H28 SING N N 80 
K5O C18 H29 SING N N 81 
K5O C18 H30 SING N N 82 
K5O C19 H31 SING N N 83 
K5O C19 H32 SING N N 84 
K5O C19 H33 SING N N 85 
K5O C21 H34 SING N N 86 
K5O C24 H35 SING N N 87 
K5O C24 H36 SING N N 88 
K5O C24 H37 SING N N 89 
K5O C26 H38 SING N N 90 
K5O C26 H39 SING N N 91 
K5O C27 H40 SING N N 92 
K5O C27 H41 SING N N 93 
K5O C29 H42 SING N N 94 
K5O C31 H43 SING N N 95 
K5O C31 H44 SING N N 96 
# 
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 
K5O SMILES           ACDLabs              12.01 "CS(=O)(=O)N1CCN(CC1)C(C)Cn1c2ccc(CN3CCC(CC3)Nc3nc(nc4sc(cc34)CC(F)(F)F)NC)c(C)c2cc1C#N"                                                                                                                                                                   
K5O InChI            InChI                1.06  "InChI=1S/C33H42F3N9O2S2/c1-21(43-11-13-44(14-12-43)49(4,46)47)19-45-25(18-37)15-27-22(2)23(5-6-29(27)45)20-42-9-7-24(8-10-42)39-30-28-16-26(17-33(34,35)36)48-31(28)41-32(38-3)40-30/h5-6,15-16,21,24H,7-14,17,19-20H2,1-4H3,(H2,38,39,40,41)/t21-/m0/s1" 
K5O InChIKey         InChI                1.06  BGGALFIXXQOTPY-NRFANRHFSA-N                                                                                                                                                                                                                                
K5O SMILES_CANONICAL CACTVS               3.385 "CNc1nc(NC2CCN(CC2)Cc3ccc4n(C[C@H](C)N5CCN(CC5)[S](C)(=O)=O)c(cc4c3C)C#N)c6cc(CC(F)(F)F)sc6n1"                                                                                                                                                             
K5O SMILES           CACTVS               3.385 "CNc1nc(NC2CCN(CC2)Cc3ccc4n(C[CH](C)N5CCN(CC5)[S](C)(=O)=O)c(cc4c3C)C#N)c6cc(CC(F)(F)F)sc6n1"                                                                                                                                                              
K5O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(ccc2c1cc(n2C[C@H](C)N3CCN(CC3)S(=O)(=O)C)C#N)CN4CCC(CC4)Nc5c6cc(sc6nc(n5)NC)CC(F)(F)F"                                                                                                                                                               
K5O SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(ccc2c1cc(n2CC(C)N3CCN(CC3)S(=O)(=O)C)C#N)CN4CCC(CC4)Nc5c6cc(sc6nc(n5)NC)CC(F)(F)F"                                                                                                                                                                   
# 
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 
K5O "SYSTEMATIC NAME" ACDLabs              12.01 "1-{(2S)-2-[4-(methanesulfonyl)piperazin-1-yl]propyl}-4-methyl-5-[(4-{[2-(methylamino)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile"   
K5O "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "4-methyl-5-[[4-[[2-(methylamino)-6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]piperidin-1-yl]methyl]-1-[(2~{S})-2-(4-methylsulfonylpiperazin-1-yl)propyl]indole-2-carbonitrile" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
K5O "Create component" 2023-06-02 RCSB 
K5O "Modify name"      2023-12-12 RCSB 
K5O "Initial release"  2024-11-20 RCSB 
# 
