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 #