data_K9D
# 
_chem_comp.id                                    K9D 
_chem_comp.name                                  "5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[2-[6-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-1,3-bis(oxidanylidene)benzo[de]isoquinolin-2-yl]ethyl]pentanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C33 H35 N5 O4 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-05-23 
_chem_comp.pdbx_modified_date                    2022-08-22 
_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                        597.727 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     K9D 
_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        7ZX9 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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.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 
K9D N1  N1  N 0 1 N N N 20.607 24.011 -14.249 -2.179  -1.534 0.593  N1  K9D 1  
K9D C7  C1  C 0 1 Y N N 25.514 27.607 -14.845 3.616   -0.657 0.844  C7  K9D 2  
K9D C8  C2  C 0 1 N N N 24.113 27.137 -14.840 2.266   -1.152 1.127  C8  K9D 3  
K9D N2  N2  N 0 1 N N N 16.477 29.525 -7.606  -11.979 1.524  -0.830 N2  K9D 4  
K9D C9  C3  C 0 1 N N N 22.420 25.607 -13.918 0.176   -2.183 0.473  C9  K9D 5  
K9D O1  O1  O 0 1 N N N 14.279 29.391 -8.244  -10.771 3.081  -1.910 O1  K9D 6  
K9D C1  C4  C 0 1 Y N N 26.151 25.754 -13.361 3.310   -1.350 -1.477 C1  K9D 7  
K9D C5  C5  C 0 1 Y N N 27.851 27.334 -14.156 5.412   -0.305 -0.784 C5  K9D 8  
K9D C6  C6  C 0 1 Y N N 26.501 26.896 -14.122 4.119   -0.769 -0.474 C6  K9D 9  
K9D N3  N3  N 0 1 N N N 16.013 29.197 -9.721  -10.005 2.194  0.007  N3  K9D 10 
K9D C4  C7  C 0 1 Y N N 28.795 26.594 -13.401 5.883   -0.429 -2.099 C4  K9D 11 
K9D C3  C8  C 0 1 Y N N 28.410 25.552 -12.610 5.083   -0.997 -3.066 C3  K9D 12 
K9D O3  O2  O 0 1 N N N 23.235 27.683 -15.484 1.814   -1.065 2.254  O3  K9D 13 
K9D C2  C9  C 0 1 Y N N 27.095 25.115 -12.589 3.807   -1.456 -2.769 C2  K9D 14 
K9D N4  N4  N 0 1 N N N 29.530 28.956 -14.972 7.469   0.735  -0.035 N4  K9D 15 
K9D C21 C10 C 0 1 Y N N 25.851 28.740 -15.544 4.416   -0.090 1.832  C21 K9D 16 
K9D C22 C11 C 0 1 Y N N 27.162 29.193 -15.569 5.685   0.366  1.528  C22 K9D 17 
K9D C23 C12 C 0 1 Y N N 28.173 28.513 -14.908 6.197   0.272  0.242  C23 K9D 18 
K9D C32 C13 C 0 1 N N N 30.080 29.957 -14.054 7.583   2.173  0.261  C32 K9D 19 
K9D C31 C14 C 0 1 N N N 30.956 30.945 -14.802 8.858   2.704  -0.394 C31 K9D 20 
K9D C30 C15 C 0 1 Y N N 31.883 30.277 -15.794 10.028  1.826  -0.029 C30 K9D 21 
K9D C29 C16 C 0 1 Y N N 32.958 30.996 -16.317 11.309  2.320  -0.219 C29 K9D 22 
K9D C28 C17 C 0 1 Y N N 33.766 30.449 -17.301 12.409  1.547  0.100  C28 K9D 23 
K9D C27 C18 C 0 1 Y N N 33.520 29.180 -17.770 12.231  0.275  0.610  C27 K9D 24 
K9D C26 C19 C 0 1 Y N N 32.468 28.441 -17.254 10.955  -0.216 0.801  C26 K9D 25 
K9D C25 C20 C 0 1 Y N N 31.641 28.972 -16.263 9.850   0.559  0.483  C25 K9D 26 
K9D C24 C21 C 0 1 N N N 30.497 28.140 -15.726 8.478   -0.018 0.717  C24 K9D 27 
K9D N   N5  N 0 1 N N N 23.829 25.997 -14.083 1.521   -1.701 0.149  N   K9D 28 
K9D C   C22 C 0 1 N N N 24.765 25.261 -13.363 1.966   -1.822 -1.116 C   K9D 29 
K9D O   O3  O 0 1 N N N 24.433 24.238 -12.823 1.253   -2.325 -1.963 O   K9D 30 
K9D C10 C23 C 0 1 N N N 21.958 24.372 -14.666 -0.834  -1.052 0.269  C10 K9D 31 
K9D C11 C24 C 0 1 N N N 19.546 24.787 -14.444 -3.237  -0.707 0.480  C11 K9D 32 
K9D O2  O4  O 0 1 N N N 19.589 25.850 -15.069 -3.075  0.439  0.116  O2  K9D 33 
K9D C12 C25 C 0 1 N N N 18.254 24.292 -13.855 -4.621  -1.205 0.807  C12 K9D 34 
K9D C13 C26 C 0 1 N N N 17.489 25.400 -13.153 -5.632  -0.075 0.598  C13 K9D 35 
K9D C14 C27 C 0 1 N N N 18.284 26.051 -12.027 -7.038  -0.581 0.930  C14 K9D 36 
K9D C15 C28 C 0 1 N N N 17.529 27.202 -11.386 -8.048  0.549  0.721  C15 K9D 37 
K9D C16 C29 C 0 1 N N S 18.121 27.842 -10.147 -9.454  0.043  1.053  C16 K9D 38 
K9D C19 C30 C 0 1 N N S 17.459 29.159 -9.714  -10.480 1.190  0.973  C19 K9D 39 
K9D C18 C31 C 0 1 N N R 17.795 29.400 -8.206  -11.826 0.731  0.400  C18 K9D 40 
K9D C17 C32 C 0 1 N N N 18.595 28.193 -7.695  -11.830 -0.768 0.040  C17 K9D 41 
K9D S   S1  S 0 1 N N N 17.969 26.810 -8.655  -10.047 -1.122 -0.240 S   K9D 42 
K9D C20 C33 C 0 1 N N N 15.479 29.399 -8.504  -10.908 2.317  -0.975 C20 K9D 43 
K9D H10 H1  H 0 1 N N N 20.472 23.132 -13.792 -2.309  -2.450 0.884  H10 K9D 44 
K9D H21 H2  H 0 1 N N N 16.326 29.687 -6.631  -12.731 1.477  -1.440 H21 K9D 45 
K9D H7  H3  H 0 1 N N N 21.800 26.451 -14.255 -0.078  -3.018 -0.180 H7  K9D 46 
K9D H6  H4  H 0 1 N N N 22.247 25.430 -12.846 0.148   -2.512 1.511  H6  K9D 47 
K9D H22 H5  H 0 1 N N N 15.465 29.084 -10.550 -9.172  2.686  0.071  H22 K9D 48 
K9D H5  H6  H 0 1 N N N 29.840 26.861 -13.453 6.872   -0.079 -2.355 H5  K9D 49 
K9D H4  H7  H 0 1 N N N 29.143 25.059 -11.989 5.456   -1.087 -4.075 H4  K9D 50 
K9D H3  H8  H 0 1 N N N 26.812 24.277 -11.970 3.200   -1.898 -3.545 H3  K9D 51 
K9D H23 H9  H 0 1 N N N 25.087 29.284 -16.080 4.042   -0.004 2.842  H23 K9D 52 
K9D H24 H10 H 0 1 N N N 27.400 30.094 -16.115 6.291   0.804  2.308  H24 K9D 53 
K9D H34 H11 H 0 1 N N N 29.253 30.500 -13.573 6.718   2.699  -0.143 H34 K9D 54 
K9D H33 H12 H 0 1 N N N 30.682 29.450 -13.285 7.632   2.322  1.339  H33 K9D 55 
K9D H32 H13 H 0 1 N N N 31.564 31.498 -14.071 8.734   2.708  -1.477 H32 K9D 56 
K9D H31 H14 H 0 1 N N N 30.307 31.647 -15.346 9.047   3.720  -0.048 H31 K9D 57 
K9D H30 H15 H 0 1 N N N 33.163 31.991 -15.951 11.449  3.314  -0.618 H30 K9D 58 
K9D H29 H16 H 0 1 N N N 34.591 31.021 -17.700 13.405  1.936  -0.050 H29 K9D 59 
K9D H28 H17 H 0 1 N N N 34.148 28.759 -18.541 13.088  -0.333 0.859  H28 K9D 60 
K9D H27 H18 H 0 1 N N N 32.286 27.442 -17.623 10.817  -1.211 1.199  H27 K9D 61 
K9D H25 H19 H 0 1 N N N 29.978 27.663 -16.570 8.244   0.027  1.780  H25 K9D 62 
K9D H26 H20 H 0 1 N N N 30.903 27.365 -15.060 8.465   -1.059 0.393  H26 K9D 63 
K9D H9  H21 H 0 1 N N N 22.641 23.538 -14.449 -0.807  -0.723 -0.770 H9  K9D 64 
K9D H8  H22 H 0 1 N N N 21.963 24.578 -15.747 -0.581  -0.217 0.922  H8  K9D 65 
K9D H11 H23 H 0 1 N N N 17.628 23.885 -14.663 -4.871  -2.041 0.154  H11 K9D 66 
K9D H12 H24 H 0 1 N N N 18.476 23.498 -13.127 -4.653  -1.533 1.846  H12 K9D 67 
K9D H13 H25 H 0 1 N N N 17.232 26.172 -13.893 -5.383  0.761  1.252  H13 K9D 68 
K9D H14 H26 H 0 1 N N N 16.566 24.976 -12.731 -5.600  0.253  -0.440 H14 K9D 69 
K9D H15 H27 H 0 1 N N N 18.495 25.293 -11.258 -7.287  -1.417 0.277  H15 K9D 70 
K9D H16 H28 H 0 1 N N N 19.231 26.432 -12.436 -7.069  -0.910 1.969  H16 K9D 71 
K9D H17 H29 H 0 1 N N N 17.430 27.991 -12.146 -7.799  1.385  1.375  H17 K9D 72 
K9D H18 H30 H 0 1 N N N 16.531 26.827 -11.115 -8.016  0.877  -0.317 H18 K9D 73 
K9D H   H31 H 0 1 N N N 19.198 28.008 -10.297 -9.472  -0.424 2.038  H   K9D 74 
K9D H2  H32 H 0 1 N N N 17.871 29.987 -10.309 -10.617 1.646  1.954  H2  K9D 75 
K9D H1  H33 H 0 1 N N N 18.381 30.324 -8.094  -12.632 0.958  1.098  H1  K9D 76 
K9D H19 H34 H 0 1 N N N 18.418 28.034 -6.621  -12.217 -1.363 0.868  H19 K9D 77 
K9D H20 H35 H 0 1 N N N 19.671 28.335 -7.872  -12.410 -0.947 -0.865 H20 K9D 78 
# 
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 
K9D C27 C28 DOUB Y N 1  
K9D C27 C26 SING Y N 2  
K9D C28 C29 SING Y N 3  
K9D C26 C25 DOUB Y N 4  
K9D C29 C30 DOUB Y N 5  
K9D C25 C30 SING Y N 6  
K9D C25 C24 SING N N 7  
K9D C30 C31 SING N N 8  
K9D C24 N4  SING N N 9  
K9D C22 C21 DOUB Y N 10 
K9D C22 C23 SING Y N 11 
K9D C21 C7  SING Y N 12 
K9D O3  C8  DOUB N N 13 
K9D O2  C11 DOUB N N 14 
K9D N4  C23 SING N N 15 
K9D N4  C32 SING N N 16 
K9D C23 C5  DOUB Y N 17 
K9D C7  C8  SING N N 18 
K9D C7  C6  DOUB Y N 19 
K9D C8  N   SING N N 20 
K9D C31 C32 SING N N 21 
K9D C10 N1  SING N N 22 
K9D C10 C9  SING N N 23 
K9D C11 N1  SING N N 24 
K9D C11 C12 SING N N 25 
K9D C5  C6  SING Y N 26 
K9D C5  C4  SING Y N 27 
K9D C6  C1  SING Y N 28 
K9D N   C9  SING N N 29 
K9D N   C   SING N N 30 
K9D C12 C13 SING N N 31 
K9D C4  C3  DOUB Y N 32 
K9D C   C1  SING N N 33 
K9D C   O   DOUB N N 34 
K9D C1  C2  DOUB Y N 35 
K9D C13 C14 SING N N 36 
K9D C3  C2  SING Y N 37 
K9D C14 C15 SING N N 38 
K9D C15 C16 SING N N 39 
K9D C16 C19 SING N N 40 
K9D C16 S   SING N N 41 
K9D N3  C19 SING N N 42 
K9D N3  C20 SING N N 43 
K9D C19 C18 SING N N 44 
K9D S   C17 SING N N 45 
K9D C20 O1  DOUB N N 46 
K9D C20 N2  SING N N 47 
K9D C18 C17 SING N N 48 
K9D C18 N2  SING N N 49 
K9D N1  H10 SING N N 50 
K9D N2  H21 SING N N 51 
K9D C9  H7  SING N N 52 
K9D C9  H6  SING N N 53 
K9D N3  H22 SING N N 54 
K9D C4  H5  SING N N 55 
K9D C3  H4  SING N N 56 
K9D C2  H3  SING N N 57 
K9D C21 H23 SING N N 58 
K9D C22 H24 SING N N 59 
K9D C32 H34 SING N N 60 
K9D C32 H33 SING N N 61 
K9D C31 H32 SING N N 62 
K9D C31 H31 SING N N 63 
K9D C29 H30 SING N N 64 
K9D C28 H29 SING N N 65 
K9D C27 H28 SING N N 66 
K9D C26 H27 SING N N 67 
K9D C24 H25 SING N N 68 
K9D C24 H26 SING N N 69 
K9D C10 H9  SING N N 70 
K9D C10 H8  SING N N 71 
K9D C12 H11 SING N N 72 
K9D C12 H12 SING N N 73 
K9D C13 H13 SING N N 74 
K9D C13 H14 SING N N 75 
K9D C14 H15 SING N N 76 
K9D C14 H16 SING N N 77 
K9D C15 H17 SING N N 78 
K9D C15 H18 SING N N 79 
K9D C16 H   SING N N 80 
K9D C19 H2  SING N N 81 
K9D C18 H1  SING N N 82 
K9D C17 H19 SING N N 83 
K9D C17 H20 SING N N 84 
# 
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 
K9D InChI            InChI                1.06  "InChI=1S/C33H35N5O4S/c39-28(11-4-3-10-27-30-25(19-43-27)35-33(42)36-30)34-15-17-38-31(40)23-9-5-8-22-26(13-12-24(29(22)23)32(38)41)37-16-14-20-6-1-2-7-21(20)18-37/h1-2,5-9,12-13,25,27,30H,3-4,10-11,14-19H2,(H,34,39)(H2,35,36,42)/t25-,27-,30-/m0/s1" 
K9D InChIKey         InChI                1.06  OIYWBNMJMDVZAF-XXJPWZBZSA-N                                                                                                                                                                                                                               
K9D SMILES_CANONICAL CACTVS               3.385 "O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NCCN3C(=O)c4cccc5c(ccc(C3=O)c45)N6CCc7ccccc7C6"                                                                                                                                                                   
K9D SMILES           CACTVS               3.385 "O=C(CCCC[CH]1SC[CH]2NC(=O)N[CH]12)NCCN3C(=O)c4cccc5c(ccc(C3=O)c45)N6CCc7ccccc7C6"                                                                                                                                                                        
K9D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)CCN(C2)c3ccc4c5c3cccc5C(=O)N(C4=O)CCNC(=O)CCCC[C@H]6[C@@H]7[C@H](CS6)NC(=O)N7"                                                                                                                                                                
K9D SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)CCN(C2)c3ccc4c5c3cccc5C(=O)N(C4=O)CCNC(=O)CCCCC6C7C(CS6)NC(=O)N7"                                                                                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           K9D 
_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        "5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[2-[6-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-1,3-bis(oxidanylidene)benzo[de]isoquinolin-2-yl]ethyl]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 
K9D "Create component"  2022-05-23 PDBE 
K9D "Initial release"   2022-06-15 RCSB 
K9D "Modify descriptor" 2022-08-22 RCSB 
# 
