data_YKM
# 
_chem_comp.id                                    YKM 
_chem_comp.name                                  "(1R,2S)-2-((S)-2-((((S)-1-(4,4-difluorocyclohexyl)ethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H37 F2 N3 O8 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-03-11 
_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                        541.606 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YKM 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        7LZU 
_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 
YKM C01 C1  C 0 1 N N N N N N 8.068  25.392 26.425 -4.311 3.198  0.841  C01 YKM 1  
YKM C02 C2  C 0 1 N N S N N N 9.419  25.776 25.781 -4.361 1.675  0.979  C02 YKM 2  
YKM C04 C3  C 0 1 N N N N N N 10.667 23.884 26.518 -2.124 0.887  0.714  C04 YKM 3  
YKM C06 C4  C 0 1 N N S N N N 11.654 21.958 27.629 0.189  0.128  0.614  C06 YKM 4  
YKM C07 C5  C 0 1 N N N N N N 12.756 21.673 28.654 0.193  -1.205 1.365  C07 YKM 5  
YKM C08 C6  C 0 1 N N N N N N 14.148 22.222 28.204 -0.796 -1.137 2.531  C08 YKM 6  
YKM C09 C7  C 0 1 N N N N N N 15.264 21.893 29.236 -0.885 -2.507 3.205  C09 YKM 7  
YKM C10 C8  C 0 1 N N N N N N 14.546 21.713 26.799 -0.315 -0.099 3.547  C10 YKM 8  
YKM C11 C9  C 0 1 N N N N N N 10.300 21.447 28.119 1.250  0.105  -0.456 C11 YKM 9  
YKM C13 C10 C 0 1 N N S N N N 8.551  19.601 28.113 3.573  -0.100 -1.162 C13 YKM 10 
YKM C14 C11 C 0 1 N N N N N N 7.588  19.596 26.876 4.881  0.458  -0.597 C14 YKM 11 
YKM C15 C12 C 0 1 N N S N N N 7.220  21.000 26.374 4.686  1.927  -0.214 C15 YKM 12 
YKM C16 C13 C 0 1 N N N N N N 6.305  20.940 25.161 5.966  2.501  0.351  C16 YKM 13 
YKM C18 C14 C 0 1 N N N N N N 5.267  22.471 26.659 5.152  4.093  -1.133 C18 YKM 14 
YKM C19 C15 C 0 1 N N N N N N 6.380  21.756 27.424 4.410  2.782  -1.473 C19 YKM 15 
YKM C21 C16 C 0 1 N N R N N N 8.736  18.158 28.628 3.793  -1.539 -1.630 C21 YKM 16 
YKM C25 C17 C 0 1 N N N N N N 9.674  27.321 25.770 -5.733 1.167  0.531  C25 YKM 17 
YKM C26 C18 C 0 1 N N N N N N 8.611  28.082 24.985 -5.828 -0.338 0.785  C26 YKM 18 
YKM C27 C19 C 0 1 N N N N N N 8.832  29.581 25.128 -7.200 -0.846 0.338  C27 YKM 19 
YKM C28 C20 C 0 1 N N N N N N 10.249 29.992 24.632 -7.384 -0.569 -1.156 C28 YKM 20 
YKM C31 C21 C 0 1 N N N N N N 11.394 29.116 25.210 -7.289 0.937  -1.410 C31 YKM 21 
YKM C32 C22 C 0 1 N N N N N N 11.052 27.620 25.132 -5.917 1.445  -0.962 C32 YKM 22 
YKM F29 F1  F 0 1 N N N N N N 10.281 29.953 23.267 -6.384 -1.227 -1.879 F29 YKM 23 
YKM F30 F2  F 0 1 N N N N N N 10.495 31.340 24.796 -8.638 -1.033 -1.565 F30 YKM 24 
YKM N05 N1  N 0 1 N N N N N N 11.580 23.377 27.414 -1.123 0.338  -0.002 N05 YKM 25 
YKM N12 N2  N 0 1 N N N N N N 9.859  20.176 27.722 2.542  -0.077 -0.121 N12 YKM 26 
YKM N17 N3  N 0 1 N N N N N N 5.198  21.795 25.352 6.206  3.711  -0.184 N17 YKM 27 
YKM O03 O1  O 0 1 N N N N N N 10.402 25.231 26.587 -3.330 1.080  0.148  O03 YKM 28 
YKM O20 O2  O 0 1 N N N N N N 6.489  20.283 24.141 6.673  1.951  1.168  O20 YKM 29 
YKM O22 O3  O 0 1 N N N N N N 9.498  18.217 29.820 2.606  -2.021 -2.263 O22 YKM 30 
YKM O23 O4  O 0 1 N N N N N N 9.601  22.166 28.843 0.940  0.249  -1.620 O23 YKM 31 
YKM O24 O5  O 0 1 N N N N N N 10.096 23.184 25.684 -1.938 1.207  1.872  O24 YKM 32 
YKM H1  H1  H 0 1 N N N N N N 7.948  24.299 26.403 -5.085 3.645  1.465  H1  YKM 33 
YKM H2  H2  H 0 1 N N N N N N 8.046  25.742 27.468 -3.334 3.560  1.160  H2  YKM 34 
YKM H3  H3  H 0 1 N N N N N N 7.247  25.862 25.863 -4.479 3.474  -0.200 H3  YKM 35 
YKM H4  H4  H 0 1 N N N N N N 9.464  25.389 24.752 -4.193 1.399  2.020  H4  YKM 36 
YKM H5  H5  H 0 1 N N N N N N 11.906 21.447 26.688 0.396  0.939  1.313  H5  YKM 37 
YKM H6  H6  H 0 1 N N N N N N 12.482 22.147 29.608 -0.101 -2.005 0.686  H6  YKM 38 
YKM H7  H7  H 0 1 N N N N N N 12.834 20.585 28.794 1.194  -1.403 1.749  H7  YKM 39 
YKM H8  H8  H 0 1 N N N N N N 14.065 23.317 28.148 -1.779 -0.851 2.157  H8  YKM 40 
YKM H9  H9  H 0 1 N N N N N N 14.966 22.261 30.229 0.098  -2.793 3.578  H9  YKM 41 
YKM H10 H10 H 0 1 N N N N N N 15.414 20.804 29.279 -1.590 -2.458 4.035  H10 YKM 42 
YKM H11 H11 H 0 1 N N N N N N 16.201 22.381 28.930 -1.228 -3.247 2.481  H11 YKM 43 
YKM H12 H12 H 0 1 N N N N N N 15.529 22.123 26.525 -0.252 0.878  3.067  H12 YKM 44 
YKM H13 H13 H 0 1 N N N N N N 14.597 20.614 26.808 -1.020 -0.050 4.377  H13 YKM 45 
YKM H14 H14 H 0 1 N N N N N N 13.795 22.039 26.065 0.668  -0.385 3.921  H14 YKM 46 
YKM H15 H15 H 0 1 N N N N N N 8.099  20.210 28.909 3.251  0.512  -2.005 H15 YKM 47 
YKM H16 H16 H 0 1 N N N N N N 6.662  19.075 27.159 5.168  -0.112 0.287  H16 YKM 48 
YKM H17 H17 H 0 1 N N N N N N 8.079  19.052 26.056 5.665  0.380  -1.350 H17 YKM 49 
YKM H18 H18 H 0 1 N N N N N N 8.131  21.569 26.138 3.871  2.029  0.502  H18 YKM 50 
YKM H19 H19 H 0 1 N N N N N N 5.511  23.536 26.530 5.593  4.521  -2.033 H19 YKM 51 
YKM H20 H20 H 0 1 N N N N N N 4.310  22.376 27.193 4.468  4.805  -0.672 H20 YKM 52 
YKM H21 H21 H 0 1 N N N N N N 5.949  21.048 28.147 4.832  2.314  -2.362 H21 YKM 53 
YKM H22 H22 H 0 1 N N N N N N 7.006  22.488 27.956 3.341  2.960  -1.597 H22 YKM 54 
YKM S1  S1  S 0 1 N Y N N N N 9.232  17.558 27.894 4.184  -2.587 -0.201 S1  YKM 55 
YKM H24 H24 H 0 1 N N N N N N 7.731  17.795 28.891 4.620  -1.569 -2.339 H24 YKM 56 
YKM H25 H25 H 0 1 N N N N N N 9.680  27.682 26.809 -6.512 1.681  1.095  H25 YKM 57 
YKM H26 H26 H 0 1 N N N N N N 7.615  27.822 25.373 -5.049 -0.852 0.221  H26 YKM 58 
YKM H27 H27 H 0 1 N N N N N N 8.674  27.804 23.923 -5.696 -0.536 1.849  H27 YKM 59 
YKM H28 H28 H 0 1 N N N N N N 8.728  29.859 26.187 -7.267 -1.919 0.519  H28 YKM 60 
YKM H29 H29 H 0 1 N N N N N N 8.075  30.113 24.533 -7.979 -0.333 0.901  H29 YKM 61 
YKM H30 H30 H 0 1 N N N N N N 12.313 29.303 24.635 -7.421 1.135  -2.474 H30 YKM 62 
YKM H31 H31 H 0 1 N N N N N N 11.558 29.391 26.262 -8.068 1.450  -0.846 H31 YKM 63 
YKM H32 H32 H 0 1 N N N N N N 11.032 27.312 24.076 -5.850 2.518  -1.143 H32 YKM 64 
YKM H33 H33 H 0 1 N N N N N N 11.825 27.048 25.666 -5.138 0.932  -1.526 H33 YKM 65 
YKM H34 H34 H 0 1 N N N N N N 12.189 23.993 27.913 -1.271 0.083  -0.926 H34 YKM 66 
YKM H35 H35 H 0 1 N N N N N N 10.461 19.627 27.142 2.790  -0.192 0.810  H35 YKM 67 
YKM H36 H36 H 0 1 N N N N N N 4.463  21.925 24.687 6.976  4.261  0.029  H36 YKM 68 
YKM H37 H37 H 0 1 N N N N N N 9.626  17.339 30.158 1.827  -2.024 -1.689 H37 YKM 69 
YKM O1  O6  O 0 1 N Y N N N N ?      ?      ?      5.459  -2.250 0.330  O1  YKM 70 
YKM O2  O7  O 0 1 N Y N N N N ?      ?      ?      3.050  -2.721 0.644  O2  YKM 71 
YKM O3  O8  O 0 1 N Y N N N N ?      ?      ?      4.378  -3.977 -0.791 O3  YKM 72 
YKM H23 H23 H 0 1 N Y N N N N ?      ?      ?      4.596  -4.654 -0.137 H23 YKM 73 
# 
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 
YKM F29 C28 SING N N 1  
YKM O20 C16 DOUB N N 2  
YKM C28 F30 SING N N 3  
YKM C28 C27 SING N N 4  
YKM C28 C31 SING N N 5  
YKM C26 C27 SING N N 6  
YKM C26 C25 SING N N 7  
YKM C32 C31 SING N N 8  
YKM C32 C25 SING N N 9  
YKM C16 N17 SING N N 10 
YKM C16 C15 SING N N 11 
YKM N17 C18 SING N N 12 
YKM O24 C04 DOUB N N 13 
YKM C25 C02 SING N N 14 
YKM C02 C01 SING N N 15 
YKM C02 O03 SING N N 16 
YKM C15 C14 SING N N 17 
YKM C15 C19 SING N N 18 
YKM C04 O03 SING N N 19 
YKM C04 N05 SING N N 20 
YKM C18 C19 SING N N 21 
YKM C10 C08 SING N N 22 
YKM C14 C13 SING N N 23 
YKM N05 C06 SING N N 24 
YKM C06 C11 SING N N 25 
YKM C06 C07 SING N N 26 
YKM N12 C13 SING N N 27 
YKM N12 C11 SING N N 28 
YKM C13 C21 SING N N 29 
YKM C11 O23 DOUB N N 30 
YKM C08 C07 SING N N 31 
YKM C08 C09 SING N N 32 
YKM C21 O22 SING N N 33 
YKM C01 H1  SING N N 34 
YKM C01 H2  SING N N 35 
YKM C01 H3  SING N N 36 
YKM C02 H4  SING N N 37 
YKM C06 H5  SING N N 38 
YKM C07 H6  SING N N 39 
YKM C07 H7  SING N N 40 
YKM C08 H8  SING N N 41 
YKM C09 H9  SING N N 42 
YKM C09 H10 SING N N 43 
YKM C09 H11 SING N N 44 
YKM C10 H12 SING N N 45 
YKM C10 H13 SING N N 46 
YKM C10 H14 SING N N 47 
YKM C13 H15 SING N N 48 
YKM C14 H16 SING N N 49 
YKM C14 H17 SING N N 50 
YKM C15 H18 SING N N 51 
YKM C18 H19 SING N N 52 
YKM C18 H20 SING N N 53 
YKM C19 H21 SING N N 54 
YKM C19 H22 SING N N 55 
YKM C21 S1  SING N N 56 
YKM C21 H24 SING N N 57 
YKM C25 H25 SING N N 58 
YKM C26 H26 SING N N 59 
YKM C26 H27 SING N N 60 
YKM C27 H28 SING N N 61 
YKM C27 H29 SING N N 62 
YKM C31 H30 SING N N 63 
YKM C31 H31 SING N N 64 
YKM C32 H32 SING N N 65 
YKM C32 H33 SING N N 66 
YKM N05 H34 SING N N 67 
YKM N12 H35 SING N N 68 
YKM N17 H36 SING N N 69 
YKM O22 H37 SING N N 70 
YKM S1  O1  DOUB N N 71 
YKM S1  O2  DOUB N N 72 
YKM S1  O3  SING N N 73 
YKM O3  H23 SING N N 74 
# 
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 
YKM SMILES           ACDLabs              12.01 "CC(C)CC(NC(=O)OC(C)C1CCC(F)(F)CC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O"                                                                                                                                                            
YKM InChI            InChI                1.03  "InChI=1S/C22H37F2N3O8S/c1-12(2)10-16(27-21(31)35-13(3)14-4-7-22(23,24)8-5-14)19(29)26-17(20(30)36(32,33)34)11-15-6-9-25-18(15)28/h12-17,20,30H,4-11H2,1-3H3,(H,25,28)(H,26,29)(H,27,31)(H,32,33,34)/t13-,15-,16-,17-,20+/m0/s1" 
YKM InChIKey         InChI                1.03  YRNJEPAFOLVHMN-GINSCSNVSA-N                                                                                                                                                                                                      
YKM SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)O[C@@H](C)C1CCC(F)(F)CC1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O"                                                                                                                                   
YKM SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)O[CH](C)C1CCC(F)(F)CC1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O"                                                                                                                                           
YKM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](C1CCC(CC1)(F)F)OC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)C(O)S(=O)(=O)O"                                                                                                                                        
YKM SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC(C)C2CCC(CC2)(F)F"                                                                                                                                                            
# 
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 
YKM "SYSTEMATIC NAME" ACDLabs              12.01 "(1R,2S)-2-[(N-{[(1S)-1-(4,4-difluorocyclohexyl)ethoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid"                                               
YKM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(2~{S})-2-[[(1~{S})-1-[4,4-bis(fluoranyl)cyclohexyl]ethoxy]carbonylamino]-4-methyl-pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YKM "Create component" 2021-03-11 RCSB 
YKM "Initial release"  2021-03-24 RCSB 
YKM "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YKM 
_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               C21 
_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      ? 
# 
