data_YK3
# 
_chem_comp.id                                    YK3 
_chem_comp.name                                  "tert-butyl [(6S,10P)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H31 N5 O4 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-09 
_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                        529.675 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YK3 
_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        8G46 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
YK3 O3  O1  O 0 1 N N N N N N 129.974 113.680 93.657 -2.021 -2.712 -1.392 O3  YK3 1  
YK3 C16 C1  C 0 1 N N N N N N 130.813 114.295 93.042 -2.865 -2.242 -0.666 C16 YK3 2  
YK3 O2  O2  O 0 1 N N N N N N 131.538 115.339 93.477 -3.509 -3.029 0.210  O2  YK3 3  
YK3 C17 C2  C 0 1 N N N N N N 131.384 115.910 94.837 -3.141 -4.433 0.231  C17 YK3 4  
YK3 C20 C3  C 0 1 N N N N N N 129.959 116.412 94.974 -3.974 -5.164 1.285  C20 YK3 5  
YK3 C19 C4  C 0 1 N N N N N N 131.685 114.828 95.847 -3.403 -5.049 -1.145 C19 YK3 6  
YK3 C18 C5  C 0 1 N N N N N N 132.381 117.038 94.960 -1.655 -4.565 0.574  C18 YK3 7  
YK3 C15 C6  C 0 1 N N N N N N 131.119 113.997 91.602 -3.191 -0.773 -0.740 C15 YK3 8  
YK3 C14 C7  C 0 1 N N S N N N 130.680 115.230 90.816 -2.322 -0.112 -1.812 C14 YK3 9  
YK3 C22 C8  C 0 1 Y N N N N N 130.632 115.001 89.339 -2.725 1.331  -1.967 C22 YK3 10 
YK3 N3  N1  N 0 1 Y N N N N N 130.729 113.923 88.579 -3.176 1.924  -3.035 N3  YK3 11 
YK3 N4  N2  N 0 1 Y N N N N N 130.648 114.337 87.239 -3.397 3.168  -2.781 N4  YK3 12 
YK3 C23 C9  C 0 1 Y N N N N N 130.517 115.636 87.224 -3.100 3.429  -1.533 C23 YK3 13 
YK3 C24 C10 C 0 1 N N N N N N 130.394 116.514 86.036 -3.211 4.763  -0.842 C24 YK3 14 
YK3 N2  N3  N 0 1 Y N N N N N 130.491 116.088 88.522 -2.674 2.266  -0.983 N2  YK3 15 
YK3 C21 C11 C 0 1 Y N N N N N 130.400 117.389 89.045 -2.263 2.015  0.329  C21 YK3 16 
YK3 C4  C12 C 0 1 Y N N N N N 129.726 117.795 90.231 -1.289 1.100  0.670  C4  YK3 17 
YK3 C2  C13 C 0 1 Y N N N N N 129.918 119.197 90.542 -1.114 1.012  2.110  C2  YK3 18 
YK3 C3  C14 C 0 1 N N N N N N 129.305 119.873 91.729 -0.144 0.062  2.763  C3  YK3 19 
YK3 S1  S1  S 0 1 Y N N N N N 131.200 118.749 88.371 -2.888 2.788  1.715  S1  YK3 20 
YK3 C1  C15 C 0 1 Y N N N N N 130.684 119.842 89.616 -1.883 1.842  2.795  C1  YK3 21 
YK3 C   C16 C 0 1 N N N N N N 131.054 121.287 89.562 -1.895 1.957  4.297  C   YK3 22 
YK3 N1  N4  N 0 1 N N N N N N 129.396 115.668 91.365 -0.915 -0.176 -1.411 N1  YK3 23 
YK3 C5  C17 C 0 1 N N N N N N 128.980 116.845 91.069 -0.487 0.324  -0.296 C5  YK3 24 
YK3 C6  C18 C 0 1 Y N N N N N 127.640 117.202 91.618 0.937  0.097  0.041  C6  YK3 25 
YK3 C13 C19 C 0 1 Y N N N N N 126.800 118.085 90.947 1.571  -1.080 -0.362 C13 YK3 26 
YK3 C12 C20 C 0 1 Y N N N N N 125.550 118.394 91.447 2.896  -1.288 -0.048 C12 YK3 27 
YK3 C9  C21 C 0 1 Y N N N N N 125.118 117.811 92.626 3.601  -0.328 0.670  C9  YK3 28 
YK3 C8  C22 C 0 1 Y N N N N N 125.943 116.928 93.300 2.971  0.845  1.073  C8  YK3 29 
YK3 C7  C23 C 0 1 Y N N N N N 127.194 116.628 92.801 1.648  1.061  0.757  C7  YK3 30 
YK3 N   N5  N 0 1 N N N N N N 123.841 118.059 93.201 4.941  -0.541 0.986  N   YK3 31 
YK3 S   S2  S 0 1 N N N N N N 123.031 119.464 93.405 6.101  -0.405 -0.188 S   YK3 32 
YK3 O   O3  O 0 1 N N N N N N 122.942 120.109 92.130 7.320  -0.669 0.492  O   YK3 33 
YK3 O1  O4  O 0 1 N N N N N N 121.823 119.130 94.094 5.645  -1.255 -1.231 O1  YK3 34 
YK3 C10 C24 C 0 1 N N N N N N 123.844 120.625 94.432 6.022  1.333  -0.702 C10 YK3 35 
YK3 C11 C25 C 0 1 N N N N N N 124.290 120.056 95.765 6.995  1.567  -1.859 C11 YK3 36 
YK3 H1  H1  H 0 1 N N N N N N 129.816 116.842 95.976 -5.032 -5.070 1.041  H1  YK3 37 
YK3 H2  H2  H 0 1 N N N N N N 129.767 117.183 94.213 -3.697 -6.218 1.300  H2  YK3 38 
YK3 H3  H3  H 0 1 N N N N N N 129.260 115.575 94.831 -3.787 -4.725 2.265  H3  YK3 39 
YK3 H4  H4  H 0 1 N N N N N N 131.576 115.234 96.864 -2.809 -4.529 -1.896 H4  YK3 40 
YK3 H5  H5  H 0 1 N N N N N N 130.984 113.992 95.709 -3.126 -6.104 -1.129 H5  YK3 41 
YK3 H6  H6  H 0 1 N N N N N N 132.715 114.470 95.704 -4.461 -4.955 -1.389 H6  YK3 42 
YK3 H7  H7  H 0 1 N N N N N N 132.300 117.492 95.959 -1.468 -4.126 1.554  H7  YK3 43 
YK3 H8  H8  H 0 1 N N N N N N 133.398 116.645 94.817 -1.378 -5.619 0.589  H8  YK3 44 
YK3 H9  H9  H 0 1 N N N N N N 132.170 117.798 94.194 -1.061 -4.044 -0.177 H9  YK3 45 
YK3 H10 H10 H 0 1 N N N N N N 130.559 113.111 91.268 -4.243 -0.646 -0.996 H10 YK3 46 
YK3 H11 H11 H 0 1 N N N N N N 132.197 113.822 91.468 -2.993 -0.308 0.225  H11 YK3 47 
YK3 H12 H12 H 0 1 N N N N N N 131.420 116.021 91.007 -2.455 -0.632 -2.761 H12 YK3 48 
YK3 H13 H13 H 0 1 N N N N N N 130.429 115.902 85.122 -4.203 4.862  -0.400 H13 YK3 49 
YK3 H14 H14 H 0 1 N N N N N N 129.438 117.056 86.078 -2.456 4.831  -0.059 H14 YK3 50 
YK3 H15 H15 H 0 1 N N N N N N 131.224 117.236 86.026 -3.056 5.562  -1.567 H15 YK3 51 
YK3 H16 H16 H 0 1 N N N N N N 128.313 120.263 91.458 0.795  0.580  2.960  H16 YK3 52 
YK3 H17 H17 H 0 1 N N N N N N 129.202 119.149 92.551 -0.564 -0.297 3.703  H17 YK3 53 
YK3 H18 H18 H 0 1 N N N N N N 129.950 120.704 92.051 0.039  -0.783 2.100  H18 YK3 54 
YK3 H19 H19 H 0 1 N N N N N N 131.656 121.478 88.661 -2.618 2.714  4.598  H19 YK3 55 
YK3 H20 H20 H 0 1 N N N N N N 130.140 121.898 89.529 -2.171 0.997  4.733  H20 YK3 56 
YK3 H21 H21 H 0 1 N N N N N N 131.638 121.549 90.456 -0.903 2.243  4.647  H21 YK3 57 
YK3 H22 H22 H 0 1 N N N N N N 127.130 118.535 90.022 1.024  -1.826 -0.920 H22 YK3 58 
YK3 H23 H23 H 0 1 N N N N N N 124.912 119.088 90.920 3.387  -2.198 -0.360 H23 YK3 59 
YK3 H24 H24 H 0 1 N N N N N N 125.607 116.472 94.220 3.520  1.589  1.631  H24 YK3 60 
YK3 H25 H25 H 0 1 N N N N N N 127.832 115.940 93.336 1.160  1.974  1.066  H25 YK3 61 
YK3 H26 H26 H 0 1 N N N N N N 123.217 117.495 92.660 5.194  -0.770 1.894  H26 YK3 62 
YK3 H27 H27 H 0 1 N N N N N N 124.732 120.997 93.899 5.008  1.570  -1.026 H27 YK3 63 
YK3 H28 H28 H 0 1 N N N N N N 123.155 121.460 94.625 6.294  1.973  0.137  H28 YK3 64 
YK3 H29 H29 H 0 1 N N N N N N 124.790 120.841 96.351 8.008  1.330  -1.535 H29 YK3 65 
YK3 H30 H30 H 0 1 N N N N N N 123.413 119.688 96.318 6.722  0.927  -2.698 H30 YK3 66 
YK3 H31 H31 H 0 1 N N N N N N 124.990 119.225 95.593 6.947  2.611  -2.168 H31 YK3 67 
# 
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 
YK3 C24 C23 SING N N 1  
YK3 C23 N4  DOUB Y N 2  
YK3 C23 N2  SING Y N 3  
YK3 N4  N3  SING Y N 4  
YK3 S1  C21 SING Y N 5  
YK3 S1  C1  SING Y N 6  
YK3 N2  C21 SING N N 7  
YK3 N2  C22 SING Y N 8  
YK3 N3  C22 DOUB Y N 9  
YK3 C21 C4  DOUB Y N 10 
YK3 C22 C14 SING N N 11 
YK3 C   C1  SING N N 12 
YK3 C1  C2  DOUB Y N 13 
YK3 C4  C2  SING Y N 14 
YK3 C4  C5  SING N N 15 
YK3 C2  C3  SING N N 16 
YK3 C14 N1  SING N N 17 
YK3 C14 C15 SING N N 18 
YK3 C13 C12 DOUB Y N 19 
YK3 C13 C6  SING Y N 20 
YK3 C5  N1  DOUB N N 21 
YK3 C5  C6  SING N N 22 
YK3 C12 C9  SING Y N 23 
YK3 C15 C16 SING N N 24 
YK3 C6  C7  DOUB Y N 25 
YK3 O   S   DOUB N N 26 
YK3 C9  N   SING N N 27 
YK3 C9  C8  DOUB Y N 28 
YK3 C7  C8  SING Y N 29 
YK3 C16 O2  SING N N 30 
YK3 C16 O3  DOUB N N 31 
YK3 N   S   SING N N 32 
YK3 S   O1  DOUB N N 33 
YK3 S   C10 SING N N 34 
YK3 O2  C17 SING N N 35 
YK3 C10 C11 SING N N 36 
YK3 C17 C18 SING N N 37 
YK3 C17 C20 SING N N 38 
YK3 C17 C19 SING N N 39 
YK3 C20 H1  SING N N 40 
YK3 C20 H2  SING N N 41 
YK3 C20 H3  SING N N 42 
YK3 C19 H4  SING N N 43 
YK3 C19 H5  SING N N 44 
YK3 C19 H6  SING N N 45 
YK3 C18 H7  SING N N 46 
YK3 C18 H8  SING N N 47 
YK3 C18 H9  SING N N 48 
YK3 C15 H10 SING N N 49 
YK3 C15 H11 SING N N 50 
YK3 C14 H12 SING N N 51 
YK3 C24 H13 SING N N 52 
YK3 C24 H14 SING N N 53 
YK3 C24 H15 SING N N 54 
YK3 C3  H16 SING N N 55 
YK3 C3  H17 SING N N 56 
YK3 C3  H18 SING N N 57 
YK3 C   H19 SING N N 58 
YK3 C   H20 SING N N 59 
YK3 C   H21 SING N N 60 
YK3 C13 H22 SING N N 61 
YK3 C12 H23 SING N N 62 
YK3 C8  H24 SING N N 63 
YK3 C7  H25 SING N N 64 
YK3 N   H26 SING N N 65 
YK3 C10 H27 SING N N 66 
YK3 C10 H28 SING N N 67 
YK3 C11 H29 SING N N 68 
YK3 C11 H30 SING N N 69 
YK3 C11 H31 SING N N 70 
# 
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 
YK3 SMILES           ACDLabs              12.01 "CCS(=O)(=O)Nc1ccc(cc1)C1=NC(CC(=O)OC(C)(C)C)c2nnc(C)n2c2sc(C)c(C)c21"                                                                                                       
YK3 InChI            InChI                1.06  "InChI=1S/C25H31N5O4S2/c1-8-36(32,33)29-18-11-9-17(10-12-18)22-21-14(2)15(3)35-24(21)30-16(4)27-28-23(30)19(26-22)13-20(31)34-25(5,6)7/h9-12,19,29H,8,13H2,1-7H3/t19-/m0/s1" 
YK3 InChIKey         InChI                1.06  XORZMCOMRGZMHU-IBGZPJMESA-N                                                                                                                                                  
YK3 SMILES_CANONICAL CACTVS               3.385 "CC[S](=O)(=O)Nc1ccc(cc1)C2=N[C@@H](CC(=O)OC(C)(C)C)c3nnc(C)n3c4sc(C)c(C)c24"                                                                                                
YK3 SMILES           CACTVS               3.385 "CC[S](=O)(=O)Nc1ccc(cc1)C2=N[CH](CC(=O)OC(C)(C)C)c3nnc(C)n3c4sc(C)c(C)c24"                                                                                                  
YK3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCS(=O)(=O)Nc1ccc(cc1)C2=N[C@H](c3nnc(n3-c4c2c(c(s4)C)C)C)CC(=O)OC(C)(C)C"                                                                                                  
YK3 SMILES           "OpenEye OEToolkits" 2.0.7 "CCS(=O)(=O)Nc1ccc(cc1)C2=NC(c3nnc(n3-c4c2c(c(s4)C)C)C)CC(=O)OC(C)(C)C"                                                                                                      
# 
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 
YK3 "SYSTEMATIC NAME" ACDLabs              12.01 "tert-butyl [(6S,10P)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate"                               
YK3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{tert}-butyl 2-[(9~{S})-7-[4-(ethylsulfonylamino)phenyl]-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YK3 "Create component" 2023-02-09 RCSB 
YK3 "Initial release"  2023-03-08 RCSB 
YK3 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YK3 
_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               C11 
_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      ? 
# 
