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 ? #