data_LXD
# 
_chem_comp.id                                    LXD 
_chem_comp.name                                  "(4~{S})-2-azanyl-4-[3-[6-[(2~{S})-2,4-dimethylpiperazin-1-yl]-4-(4-prop-2-enoylpiperazin-1-yl)pyridin-2-yl]-1,2,4-oxadiazol-5-yl]-4-methyl-6,7-dihydro-5~{H}-1-benzothiophene-3-carbonitrile" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C30 H37 N9 O2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-07-18 
_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                        587.739 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     LXD 
_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        8AFB 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
LXD C4  C1  C 0 1 Y N N N N N 11.694 -10.621 20.968 3.386  -0.111 0.009  C4  LXD 1  
LXD C5  C2  C 0 1 Y N N N N N 12.893 -11.108 20.456 2.410  0.785  -0.416 C5  LXD 2  
LXD C6  C3  C 0 1 Y N N N N N 14.075 -10.577 20.972 1.107  0.317  -0.586 C6  LXD 3  
LXD C8  C4  C 0 1 Y N N N N N 15.241 -8.913  22.421 -0.554 -1.528 -0.504 C8  LXD 4  
LXD C13 C5  C 0 1 N N S N N N 18.707 -8.158  22.082 -4.071 -1.332 -1.217 C13 LXD 5  
LXD C15 C6  C 0 1 N N N N N N 20.478 -6.302  22.089 -6.319 -2.329 -1.645 C15 LXD 6  
LXD C17 C7  C 0 1 Y N N N N N 20.435 -8.030  23.885 -5.971 -0.970 0.397  C17 LXD 7  
LXD C20 C8  C 0 1 Y N N N N N 20.172 -10.268 24.920 -4.916 0.815  1.799  C20 LXD 8  
LXD C22 C9  C 0 1 N N N N N N 18.377 -11.055 23.439 -2.800 0.874  0.536  C22 LXD 9  
LXD C26 C10 C 0 1 N N N N N N 11.681 -12.763 19.000 1.541  2.868  -1.101 C26 LXD 10 
LXD C1  C11 C 0 1 Y N N N N N 14.002 -9.568  21.940 0.829  -1.018 -0.326 C1  LXD 11 
LXD C12 C12 C 0 1 Y N N N N N 17.244 -8.308  22.422 -2.637 -1.649 -0.881 C12 LXD 12 
LXD C14 C13 C 0 1 N N N N N N 20.876 -6.641  23.522 -6.863 -2.014 -0.249 C14 LXD 13 
LXD C16 C14 C 0 1 N N N N N N 19.018 -6.657  21.832 -4.820 -2.627 -1.541 C16 LXD 14 
LXD C18 C15 C 0 1 Y N N N N N 19.474 -8.754  23.256 -4.739 -0.666 -0.025 C18 LXD 15 
LXD C19 C16 C 0 1 Y N N N N N 19.319 -10.056 23.842 -4.118 0.370  0.782  C19 LXD 16 
LXD C25 C17 C 0 1 N N N N N N 19.011 -8.988  20.819 -4.120 -0.393 -2.424 C25 LXD 17 
LXD C27 C18 C 0 1 N N N N N N 12.018 -14.002 18.177 1.963  4.275  -1.538 C27 LXD 18 
LXD C29 C19 C 0 1 N N N N N N 13.776 -12.571 17.220 3.845  4.142  0.140  C29 LXD 19 
LXD C3  C20 C 0 1 Y N N N N N 11.700 -9.650  21.979 3.033  -1.434 0.250  C3  LXD 20 
LXD C30 C21 C 0 1 N N N N N N 14.105 -12.482 18.705 3.349  2.740  0.511  C30 LXD 21 
LXD C32 C22 C 0 1 N N N N N N 9.240  -9.668  22.025 5.201  -2.257 -0.177 C32 LXD 22 
LXD C33 C23 C 0 1 N N N N N N 8.287  -9.914  23.192 6.271  -3.207 0.364  C33 LXD 23 
LXD C35 C24 C 0 1 N N N N N N 9.515  -8.315  24.608 4.540  -4.658 1.237  C35 LXD 24 
LXD C36 C25 C 0 1 N N S N N N 10.555 -8.047  23.466 3.470  -3.707 0.695  C36 LXD 25 
LXD C37 C26 C 0 1 N N N N N N 7.173  -8.880  25.137 6.762  -5.532 0.833  C37 LXD 26 
LXD C38 C27 C 0 1 N N N N N N 10.336 -6.710  22.766 3.083  -4.130 -0.724 C38 LXD 27 
LXD C39 C28 C 0 1 N N N N N N 12.565 -14.248 15.789 2.403  6.122  0.014  C39 LXD 28 
LXD C40 C29 C 0 1 N N N N N N 13.327 -13.793 14.596 1.210  6.810  -0.502 C40 LXD 29 
LXD C42 C30 C 0 1 N N N N N N 12.763 -12.952 13.688 0.952  8.062  -0.133 C42 LXD 30 
LXD N10 N1  N 0 1 Y N N N N N 15.310 -8.151  23.482 -0.950 -2.765 -0.354 N10 LXD 31 
LXD N2  N2  N 0 1 Y N N N N N 12.844 -9.102  22.437 1.787  -1.844 0.078  N2  LXD 32 
LXD N23 N3  N 0 1 N N N N N N 17.653 -11.894 23.164 -1.755 1.274  0.341  N23 LXD 33 
LXD N24 N4  N 0 1 N N N N N N 20.300 -11.372 25.677 -4.557 1.795  2.708  N24 LXD 34 
LXD N28 N5  N 0 1 N N N N N N 12.779 -13.625 16.976 2.724  4.895  -0.443 N28 LXD 35 
LXD N31 N6  N 0 1 N N N N N N 10.535 -9.176  22.516 4.003  -2.337 0.670  N31 LXD 36 
LXD N34 N7  N 0 1 N N N N N N 8.175  -8.694  24.048 5.738  -4.577 0.389  N34 LXD 37 
LXD N7  N8  N 0 1 N N N N N N 12.911 -12.123 19.480 2.727  2.118  -0.666 N7  LXD 38 
LXD N9  N9  N 0 1 Y N N N N N 16.430 -9.041  21.754 -1.641 -0.799 -0.846 N9  LXD 39 
LXD O11 O1  O 0 1 Y N N N N N 16.688 -7.731  23.492 -2.141 -2.851 -0.572 O11 LXD 40 
LXD O41 O2  O 0 1 N N N N N N 11.714 -15.133 15.681 3.099  6.660  0.854  O41 LXD 41 
LXD S21 S1  S 0 1 Y N N N N N 21.185 -8.890  25.182 -6.409 -0.002 1.795  S21 LXD 42 
LXD H1  H1  H 0 1 N N N N N N 10.755 -10.993 20.585 4.406  0.216  0.147  H1  LXD 43 
LXD H2  H2  H 0 1 N N N N N N 15.033 -10.939 20.630 0.324  0.985  -0.914 H2  LXD 44 
LXD H3  H3  H 0 1 N N N N N N 21.114 -6.870  21.394 -6.837 -3.199 -2.049 H3  LXD 45 
LXD H4  H4  H 0 1 N N N N N N 20.622 -5.225  21.921 -6.477 -1.473 -2.300 H4  LXD 46 
LXD H5  H5  H 0 1 N N N N N N 11.122 -12.052 18.374 0.833  2.940  -0.276 H5  LXD 47 
LXD H6  H6  H 0 1 N N N N N N 11.064 -13.056 19.862 1.072  2.352  -1.939 H6  LXD 48 
LXD H7  H7  H 0 1 N N N N N N 21.970 -6.574  23.618 -7.878 -1.626 -0.331 H7  LXD 49 
LXD H8  H8  H 0 1 N N N N N N 20.403 -5.922  24.207 -6.863 -2.920 0.357  H8  LXD 50 
LXD H9  H9  H 0 1 N N N N N N 18.778 -6.419  20.785 -4.462 -3.028 -2.489 H9  LXD 51 
LXD H10 H10 H 0 1 N N N N N N 18.387 -6.052  22.500 -4.648 -3.355 -0.748 H10 LXD 52 
LXD H11 H11 H 0 1 N N N N N N 18.786 -10.047 21.013 -3.646 -0.875 -3.279 H11 LXD 53 
LXD H12 H12 H 0 1 N N N N N N 18.390 -8.628  19.985 -5.159 -0.165 -2.665 H12 LXD 54 
LXD H13 H13 H 0 1 N N N N N N 20.074 -8.881  20.557 -3.592 0.530  -2.188 H13 LXD 55 
LXD H14 H14 H 0 1 N N N N N N 11.086 -14.501 17.874 2.589  4.210  -2.428 H14 LXD 56 
LXD H15 H15 H 0 1 N N N N N N 12.621 -14.690 18.788 1.078  4.871  -1.756 H15 LXD 57 
LXD H16 H16 H 0 1 N N N N N N 14.693 -12.803 16.659 4.203  4.652  1.035  H16 LXD 58 
LXD H17 H17 H 0 1 N N N N N N 13.373 -11.606 16.880 4.654  4.064  -0.586 H17 LXD 59 
LXD H18 H18 H 0 1 N N N N N N 14.481 -13.456 19.051 4.191  2.132  0.842  H18 LXD 60 
LXD H19 H19 H 0 1 N N N N N N 14.879 -11.715 18.858 2.615  2.814  1.314  H19 LXD 61 
LXD H20 H20 H 0 1 N N N N N N 8.800  -8.919  21.350 5.583  -1.236 -0.170 H20 LXD 62 
LXD H21 H21 H 0 1 N N N N N N 9.394  -10.610 21.478 4.944  -2.541 -1.198 H21 LXD 63 
LXD H22 H22 H 0 1 N N N N N N 7.293  -10.171 22.798 7.150  -3.170 -0.279 H22 LXD 64 
LXD H23 H23 H 0 1 N N N N N N 8.668  -10.748 23.800 6.547  -2.906 1.375  H23 LXD 65 
LXD H24 H24 H 0 1 N N N N N N 9.883  -9.135  25.242 4.797  -4.373 2.257  H24 LXD 66 
LXD H25 H25 H 0 1 N N N N N N 9.405  -7.403  25.214 4.157  -5.678 1.229  H25 LXD 67 
LXD H26 H26 H 0 1 N N N N N N 11.549 -8.015  23.937 2.591  -3.744 1.338  H26 LXD 68 
LXD H27 H27 H 0 1 N N N N N N 7.117  -7.965  25.745 7.044  -5.310 1.863  H27 LXD 69 
LXD H28 H28 H 0 1 N N N N N N 6.187  -9.088  24.696 6.364  -6.545 0.775  H28 LXD 70 
LXD H29 H29 H 0 1 N N N N N N 7.476  -9.725  25.773 7.639  -5.449 0.191  H29 LXD 71 
LXD H30 H30 H 0 1 N N N N N N 10.358 -5.899  23.509 2.766  -5.173 -0.718 H30 LXD 72 
LXD H31 H31 H 0 1 N N N N N N 11.132 -6.550  22.024 2.264  -3.504 -1.079 H31 LXD 73 
LXD H32 H32 H 0 1 N N N N N N 9.359  -6.717  22.260 3.941  -4.014 -1.385 H32 LXD 74 
LXD H33 H33 H 0 1 N N N N N N 14.341 -14.135 14.449 0.544  6.300  -1.182 H33 LXD 75 
LXD H34 H34 H 0 1 N N N N N N 13.329 -12.630 12.826 1.618  8.572  0.546  H34 LXD 76 
LXD H35 H35 H 0 1 N N N N N N 11.750 -12.606 13.829 0.076  8.567  -0.512 H35 LXD 77 
LXD H36 H36 H 0 1 N N N N N N 21.028 -11.234 26.348 -5.177 2.060  3.405  H36 LXD 78 
LXD H37 H37 H 0 1 N N N N N N 19.439 -11.552 26.152 -3.686 2.218  2.647  H37 LXD 79 
# 
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 
LXD C42 C40 DOUB N N 1  
LXD C40 C39 SING N N 2  
LXD O41 C39 DOUB N N 3  
LXD C39 N28 SING N N 4  
LXD N28 C29 SING N N 5  
LXD N28 C27 SING N N 6  
LXD C29 C30 SING N N 7  
LXD C27 C26 SING N N 8  
LXD C30 N7  SING N N 9  
LXD C26 N7  SING N N 10 
LXD N7  C5  SING N N 11 
LXD C5  C4  DOUB Y N 12 
LXD C5  C6  SING Y N 13 
LXD C25 C13 SING N N 14 
LXD C4  C3  SING Y N 15 
LXD C6  C1  DOUB Y N 16 
LXD N9  C8  SING Y N 17 
LXD N9  C12 DOUB Y N 18 
LXD C16 C13 SING N N 19 
LXD C16 C15 SING N N 20 
LXD C1  C8  SING N N 21 
LXD C1  N2  SING Y N 22 
LXD C3  N2  DOUB Y N 23 
LXD C3  N31 SING N N 24 
LXD C32 N31 SING N N 25 
LXD C32 C33 SING N N 26 
LXD C13 C12 SING N N 27 
LXD C13 C18 SING N N 28 
LXD C15 C14 SING N N 29 
LXD C8  N10 DOUB Y N 30 
LXD C12 O11 SING Y N 31 
LXD N31 C36 SING N N 32 
LXD C38 C36 SING N N 33 
LXD N23 C22 TRIP N N 34 
LXD C33 N34 SING N N 35 
LXD C18 C19 SING Y N 36 
LXD C18 C17 DOUB Y N 37 
LXD C22 C19 SING N N 38 
LXD C36 C35 SING N N 39 
LXD N10 O11 SING Y N 40 
LXD C14 C17 SING N N 41 
LXD C19 C20 DOUB Y N 42 
LXD C17 S21 SING Y N 43 
LXD N34 C35 SING N N 44 
LXD N34 C37 SING N N 45 
LXD C20 S21 SING Y N 46 
LXD C20 N24 SING N N 47 
LXD C4  H1  SING N N 48 
LXD C6  H2  SING N N 49 
LXD C15 H3  SING N N 50 
LXD C15 H4  SING N N 51 
LXD C26 H5  SING N N 52 
LXD C26 H6  SING N N 53 
LXD C14 H7  SING N N 54 
LXD C14 H8  SING N N 55 
LXD C16 H9  SING N N 56 
LXD C16 H10 SING N N 57 
LXD C25 H11 SING N N 58 
LXD C25 H12 SING N N 59 
LXD C25 H13 SING N N 60 
LXD C27 H14 SING N N 61 
LXD C27 H15 SING N N 62 
LXD C29 H16 SING N N 63 
LXD C29 H17 SING N N 64 
LXD C30 H18 SING N N 65 
LXD C30 H19 SING N N 66 
LXD C32 H20 SING N N 67 
LXD C32 H21 SING N N 68 
LXD C33 H22 SING N N 69 
LXD C33 H23 SING N N 70 
LXD C35 H24 SING N N 71 
LXD C35 H25 SING N N 72 
LXD C36 H26 SING N N 73 
LXD C37 H27 SING N N 74 
LXD C37 H28 SING N N 75 
LXD C37 H29 SING N N 76 
LXD C38 H30 SING N N 77 
LXD C38 H31 SING N N 78 
LXD C38 H32 SING N N 79 
LXD C40 H33 SING N N 80 
LXD C42 H34 SING N N 81 
LXD C42 H35 SING N N 82 
LXD N24 H36 SING N N 83 
LXD N24 H37 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 
LXD InChI            InChI                1.06  "InChI=1S/C30H37N9O2S/c1-5-25(40)38-12-10-37(11-13-38)20-15-22(33-24(16-20)39-14-9-36(4)18-19(39)2)28-34-29(41-35-28)30(3)8-6-7-23-26(30)21(17-31)27(32)42-23/h5,15-16,19H,1,6-14,18,32H2,2-4H3/t19-,30-/m0/s1" 
LXD InChIKey         InChI                1.06  CKAMBYUZKWQCKJ-ADSBAMQRSA-N                                                                                                                                                                                     
LXD SMILES_CANONICAL CACTVS               3.385 "C[C@H]1CN(C)CCN1c2cc(cc(n2)c3noc(n3)[C@@]4(C)CCCc5sc(N)c(C#N)c45)N6CCN(CC6)C(=O)C=C"                                                                                                                           
LXD SMILES           CACTVS               3.385 "C[CH]1CN(C)CCN1c2cc(cc(n2)c3noc(n3)[C]4(C)CCCc5sc(N)c(C#N)c45)N6CCN(CC6)C(=O)C=C"                                                                                                                              
LXD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]1CN(CCN1c2cc(cc(n2)c3nc(on3)[C@]4(CCCc5c4c(c(s5)N)C#N)C)N6CCN(CC6)C(=O)C=C)C"                                                                                                                            
LXD SMILES           "OpenEye OEToolkits" 2.0.7 "CC1CN(CCN1c2cc(cc(n2)c3nc(on3)C4(CCCc5c4c(c(s5)N)C#N)C)N6CCN(CC6)C(=O)C=C)C"                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           LXD 
_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        "(4~{S})-2-azanyl-4-[3-[6-[(2~{S})-2,4-dimethylpiperazin-1-yl]-4-(4-prop-2-enoylpiperazin-1-yl)pyridin-2-yl]-1,2,4-oxadiazol-5-yl]-4-methyl-6,7-dihydro-5~{H}-1-benzothiophene-3-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 
LXD "Create component"  2022-07-18 PDBE 
LXD "Modify descriptor" 2022-08-22 RCSB 
LXD "Initial release"   2022-11-09 RCSB 
LXD "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            LXD 
_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               C42 
_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      ? 
# 
