data_X08
# 
_chem_comp.id                                    X08 
_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-[(5-methylpyridin-2-yl)methylamino]ethyl]pentanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H29 N5 O2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-26 
_chem_comp.pdbx_modified_date                    2023-09-08 
_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                        391.531 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     X08 
_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        8P5Z 
_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 
X08 C02  C1  C 0 1 N N N -8.595  16.590 36.716 -6.504  -1.275 0.317  C02  X08 1  
X08 C03  C2  C 0 1 Y N N -9.792  15.615 36.971 -7.775  -0.471 0.224  C03  X08 2  
X08 C04  C3  C 0 1 Y N N -9.543  14.370 37.543 -8.493  -0.461 -0.957 C04  X08 3  
X08 C05  C4  C 0 1 Y N N -10.596 13.475 37.788 -9.661  0.282  -1.032 C05  X08 4  
X08 C06  C5  C 0 1 Y N N -11.870 13.872 37.427 -10.066 0.990  0.089  C06  X08 5  
X08 C07  C6  C 0 1 Y N N -12.072 15.127 36.851 -9.296  0.932  1.236  C07  X08 6  
X08 C09  C7  C 0 1 N N N -13.027 12.904 37.678 -11.328 1.813  0.058  C09  X08 7  
X08 C10  C8  C 0 1 N N N -8.147  18.663 35.422 -4.094  -1.158 0.113  C10  X08 8  
X08 C11  C9  C 0 1 N N N -6.960  19.068 36.326 -2.922  -0.223 -0.189 C11  X08 9  
X08 C13  C10 C 0 1 N N N -6.226  21.394 35.847 -0.493  -0.349 -0.338 C13  X08 10 
X08 C15  C11 C 0 1 N N N -5.199  22.361 35.262 0.799   -1.120 -0.255 C15  X08 11 
X08 C16  C12 C 0 1 N N N -5.753  23.737 34.872 1.972   -0.184 -0.557 C16  X08 12 
X08 C17  C13 C 0 1 N N N -6.526  23.624 33.530 3.283   -0.967 -0.473 C17  X08 13 
X08 C18  C14 C 0 1 N N N -7.184  24.977 33.178 4.456   -0.032 -0.775 C18  X08 14 
X08 C19  C15 C 0 1 N N S -7.923  24.852 31.771 5.768   -0.814 -0.690 C19  X08 15 
X08 C20  C16 C 0 1 N N S -8.676  26.067 31.548 6.966   0.086  -1.050 C20  X08 16 
X08 C22  C17 C 0 1 N N N -7.992  28.097 30.600 7.526   1.936  0.180  C22  X08 17 
X08 C25  C18 C 0 1 N N R -9.001  26.048 29.921 8.203   -0.220 -0.197 C25  X08 18 
X08 C26  C19 C 0 1 N N N -7.981  24.830 29.375 7.955   -1.360 0.809  C26  X08 19 
X08 N01  N1  N 0 1 N N N -9.125  17.875 36.197 -5.354  -0.407 0.032  N01  X08 20 
X08 N08  N2  N 0 1 Y N N -11.038 15.953 36.635 -8.193  0.211  1.273  N08  X08 21 
X08 N12  N3  N 0 1 N N N -5.989  19.968 35.682 -1.666  -0.972 -0.108 N12  X08 22 
X08 N21  N4  N 0 1 N N N -8.001  27.245 31.844 6.639   1.482  -0.716 N21  X08 23 
X08 N24  N5  N 0 1 N N N -8.605  27.239 29.461 8.452   1.034  0.532  N24  X08 24 
X08 O14  O1  O 0 1 N N N -7.204  21.758 36.415 -0.478  0.832  -0.613 O14  X08 25 
X08 O23  O2  O 0 1 N N N -7.503  29.217 30.499 7.493   3.064  0.633  O23  X08 26 
X08 S27  S1  S 0 1 N N N -6.867  24.649 30.403 6.126   -1.300 1.047  S27  X08 27 
X08 H021 H1  H 0 0 N N N -7.909  16.148 35.978 -6.408  -1.688 1.321  H021 X08 28 
X08 H022 H2  H 0 0 N N N -8.055  16.767 37.658 -6.535  -2.088 -0.409 H022 X08 29 
X08 H041 H3  H 0 0 N N N -8.532  14.091 37.800 -8.147  -1.024 -1.811 H041 X08 30 
X08 H051 H4  H 0 0 N N N -10.417 12.511 38.242 -10.242 0.309  -1.942 H051 X08 31 
X08 H071 H5  H 0 0 N N N -13.070 15.436 36.577 -9.605  1.481  2.114  H071 X08 32 
X08 H092 H6  H 0 0 N N N -13.166 12.261 36.796 -12.171 1.197  0.370  H092 X08 33 
X08 H093 H7  H 0 0 N N N -12.799 12.280 38.554 -11.226 2.660  0.736  H093 X08 34 
X08 H091 H8  H 0 0 N N N -13.949 13.475 37.864 -11.499 2.177  -0.955 H091 X08 35 
X08 H101 H9  H 0 0 N N N -7.775  18.058 34.582 -4.108  -1.970 -0.614 H101 X08 36 
X08 H102 H10 H 0 0 N N N -8.635  19.569 35.034 -3.981  -1.570 1.116  H102 X08 37 
X08 H111 H11 H 0 0 N N N -7.362  19.574 37.216 -3.035  0.189  -1.192 H111 X08 38 
X08 H112 H12 H 0 0 N N N -6.432  18.153 36.632 -2.908  0.589  0.538  H112 X08 39 
X08 H152 H13 H 0 0 N N N -4.769  21.898 34.361 0.912   -1.532 0.748  H152 X08 40 
X08 H151 H14 H 0 0 N N N -4.407  22.512 36.010 0.785   -1.932 -0.982 H151 X08 41 
X08 H161 H15 H 0 0 N N N -4.921  24.448 34.757 1.858   0.228  -1.560 H161 X08 42 
X08 H162 H16 H 0 0 N N N -6.434  24.094 35.658 1.985   0.627  0.170  H162 X08 43 
X08 H172 H17 H 0 0 N N N -7.306  22.854 33.624 3.397   -1.379 0.530  H172 X08 44 
X08 H171 H18 H 0 0 N N N -5.826  23.341 32.730 3.270   -1.779 -1.200 H171 X08 45 
X08 H182 H19 H 0 0 N N N -6.411  25.757 33.119 4.343   0.380  -1.778 H182 X08 46 
X08 H181 H20 H 0 0 N N N -7.916  25.243 33.955 4.470   0.780  -0.048 H181 X08 47 
X08 H191 H21 H 0 0 N N N -8.591  23.978 31.798 5.735   -1.691 -1.337 H191 X08 48 
X08 H201 H22 H 0 0 N N N -9.639  26.019 32.078 7.200   -0.003 -2.110 H201 X08 49 
X08 H251 H23 H 0 0 N N N -10.052 25.782 29.736 9.052   -0.459 -0.837 H251 X08 50 
X08 H262 H24 H 0 0 N N N -8.545  23.892 29.267 8.264   -2.319 0.391  H262 X08 51 
X08 H261 H25 H 0 0 N N N -7.550  25.112 28.403 8.470   -1.164 1.750  H261 X08 52 
X08 H011 H26 H 0 0 N N N -9.427  18.427 36.974 -5.340  0.390  0.650  H011 X08 53 
X08 H121 H28 H 0 0 N N N -5.210  19.619 35.161 -1.678  -1.917 0.111  H121 X08 54 
X08 H211 H29 H 0 0 N N N -7.594  27.485 32.725 5.902   1.991  -1.086 H211 X08 55 
X08 H241 H30 H 0 0 N N N -8.692  27.537 28.510 9.171   1.183  1.166  H241 X08 56 
# 
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 
X08 C26 C25  SING N N 1  
X08 C26 S27  SING N N 2  
X08 N24 C25  SING N N 3  
X08 N24 C22  SING N N 4  
X08 C25 C20  SING N N 5  
X08 S27 C19  SING N N 6  
X08 O23 C22  DOUB N N 7  
X08 C22 N21  SING N N 8  
X08 C20 C19  SING N N 9  
X08 C20 N21  SING N N 10 
X08 C19 C18  SING N N 11 
X08 C18 C17  SING N N 12 
X08 C17 C16  SING N N 13 
X08 C16 C15  SING N N 14 
X08 C15 C13  SING N N 15 
X08 C10 N01  SING N N 16 
X08 C10 C11  SING N N 17 
X08 N12 C13  SING N N 18 
X08 N12 C11  SING N N 19 
X08 C13 O14  DOUB N N 20 
X08 N01 C02  SING N N 21 
X08 N08 C07  DOUB Y N 22 
X08 N08 C03  SING Y N 23 
X08 C02 C03  SING N N 24 
X08 C07 C06  SING Y N 25 
X08 C03 C04  DOUB Y N 26 
X08 C06 C09  SING N N 27 
X08 C06 C05  DOUB Y N 28 
X08 C04 C05  SING Y N 29 
X08 C02 H021 SING N N 30 
X08 C02 H022 SING N N 31 
X08 C04 H041 SING N N 32 
X08 C05 H051 SING N N 33 
X08 C07 H071 SING N N 34 
X08 C09 H092 SING N N 35 
X08 C09 H093 SING N N 36 
X08 C09 H091 SING N N 37 
X08 C10 H101 SING N N 38 
X08 C10 H102 SING N N 39 
X08 C11 H111 SING N N 40 
X08 C11 H112 SING N N 41 
X08 C15 H152 SING N N 42 
X08 C15 H151 SING N N 43 
X08 C16 H161 SING N N 44 
X08 C16 H162 SING N N 45 
X08 C17 H172 SING N N 46 
X08 C17 H171 SING N N 47 
X08 C18 H182 SING N N 48 
X08 C18 H181 SING N N 49 
X08 C19 H191 SING N N 50 
X08 C20 H201 SING N N 51 
X08 C25 H251 SING N N 52 
X08 C26 H262 SING N N 53 
X08 C26 H261 SING N N 54 
X08 N01 H011 SING N N 55 
X08 N12 H121 SING N N 56 
X08 N21 H211 SING N N 57 
X08 N24 H241 SING N N 58 
# 
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 
X08 InChI            InChI                1.06  "InChI=1S/C19H29N5O2S/c1-13-6-7-14(22-10-13)11-20-8-9-21-17(25)5-3-2-4-16-18-15(12-27-16)23-19(26)24-18/h6-7,10,15-16,18,20H,2-5,8-9,11-12H2,1H3,(H,21,25)(H2,23,24,26)/t15-,16-,18-/m0/s1" 
X08 InChIKey         InChI                1.06  OQHGPOCPZMPZKJ-BQFCYCMXSA-N                                                                                                                                                                 
X08 SMILES_CANONICAL CACTVS               3.385 "Cc1ccc(CNCCNC(=O)CCCC[C@@H]2SC[C@@H]3NC(=O)N[C@H]23)nc1"                                                                                                                                   
X08 SMILES           CACTVS               3.385 "Cc1ccc(CNCCNC(=O)CCCC[CH]2SC[CH]3NC(=O)N[CH]23)nc1"                                                                                                                                        
X08 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1ccc(nc1)CNCCNC(=O)CCCC[C@H]2[C@@H]3[C@H](CS2)NC(=O)N3"                                                                                                                                  
X08 SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1ccc(nc1)CNCCNC(=O)CCCCC2C3C(CS2)NC(=O)N3"                                                                                                                                               
# 
_pdbx_chem_comp_identifier.comp_id           X08 
_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-[(5-methylpyridin-2-yl)methylamino]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 
X08 "Create component" 2023-05-26 PDBE 
X08 "Initial release"  2023-09-13 RCSB 
# 
