data_YKA # _chem_comp.id YKA _chem_comp.name "(1R,2S)-2-((S)-2-((((2-(4,4-difluorocyclohexyl)propan-2-yl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 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 553.617 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YKA _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 7M00 _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 YKA C01 C1 C 0 1 N N N N N N -14.088 3.022 40.163 -3.793 2.590 0.954 C01 YKA 1 YKA C02 C2 C 0 1 N N N N N N -14.672 3.149 41.563 -4.025 1.080 1.024 C02 YKA 2 YKA C04 C3 C 0 1 N N N N N N -13.823 0.965 42.360 -1.692 0.591 0.906 C04 YKA 3 YKA C06 C4 C 0 1 N N S N N N -13.246 -1.333 42.957 0.713 0.200 0.927 C06 YKA 4 YKA C07 C5 C 0 1 N N N N N N -13.754 -2.473 43.872 0.938 -0.765 2.093 C07 YKA 5 YKA C08 C6 C 0 1 N N N N N N -14.027 -2.086 45.328 -0.039 -0.436 3.223 C08 YKA 6 YKA C09 C7 C 0 1 N N N N N N -12.838 -1.369 45.964 0.101 -1.476 4.337 C09 YKA 7 YKA C10 C8 C 0 1 N N N N N N -14.466 -3.265 46.181 0.275 0.954 3.781 C10 YKA 8 YKA C11 C9 C 0 1 N N N N N N -13.157 -1.833 41.522 1.754 -0.043 -0.135 C11 YKA 9 YKA C13 C10 C 0 1 N N S N N N -11.896 -2.878 39.591 4.078 -0.230 -0.844 C13 YKA 10 YKA C14 C11 C 0 1 N N N N N N -10.931 -1.975 38.771 5.061 0.934 -0.978 C14 YKA 11 YKA C15 C12 C 0 1 N N R N N N -11.227 -0.467 38.908 4.345 2.138 -1.593 C15 YKA 12 YKA C16 C13 C 0 1 N N N N N N -10.242 0.447 38.197 3.461 2.819 -0.567 C16 YKA 13 YKA C18 C14 C 0 1 N N N N N N -12.321 0.984 37.160 4.921 4.412 -1.104 C18 YKA 14 YKA C19 C15 C 0 1 N N N N N N -12.557 -0.083 38.268 5.355 3.245 -1.965 C19 YKA 15 YKA C21 C16 C 0 1 N N R N N N -11.428 -4.376 39.603 4.833 -1.488 -0.408 C21 YKA 16 YKA C25 C17 C 0 1 N N N N N N -16.111 3.717 41.382 -4.122 0.646 2.489 C25 YKA 17 YKA C26 C18 C 0 1 N N N N N N -13.868 4.091 42.489 -5.328 0.730 0.302 C26 YKA 18 YKA C27 C19 C 0 1 N N N N N N -13.981 5.630 42.356 -5.231 1.163 -1.163 C27 YKA 19 YKA C28 C20 C 0 1 N N N N N N -13.040 6.425 43.237 -6.533 0.813 -1.885 C28 YKA 20 YKA C29 C21 C 0 1 N N N N N N -13.221 6.051 44.732 -6.766 -0.697 -1.814 C29 YKA 21 YKA C32 C22 C 0 1 N N N N N N -13.185 4.513 44.909 -6.863 -1.131 -0.350 C32 YKA 22 YKA C33 C23 C 0 1 N N N N N N -14.143 3.821 43.966 -5.560 -0.781 0.372 C33 YKA 23 YKA F30 F1 F 0 1 N N N N N N -12.274 6.663 45.479 -7.957 -1.017 -2.475 F30 YKA 24 YKA F31 F2 F 0 1 N N N N N N -14.383 6.532 45.226 -5.699 -1.363 -2.428 F31 YKA 25 YKA N05 N1 N 0 1 N N N N N N -14.165 -0.225 42.993 -0.621 -0.020 0.362 N05 YKA 26 YKA N12 N2 N 0 1 N N N N N N -12.017 -2.412 40.993 3.062 0.101 0.158 N12 YKA 27 YKA N17 N3 N 0 1 N N N N N N -10.887 1.241 37.248 3.895 4.075 -0.392 N17 YKA 28 YKA O03 O1 O 0 1 N N N N N N -14.837 1.866 42.158 -2.918 0.389 0.387 O03 YKA 29 YKA O20 O2 O 0 1 N N N N N N -9.043 0.522 38.426 2.517 2.311 0.002 O20 YKA 30 YKA O22 O3 O 0 1 N N N N N N -12.460 -5.063 40.240 5.886 -1.757 -1.336 O22 YKA 31 YKA O23 O4 O 0 1 N N N N N N -14.143 -1.688 40.810 1.415 -0.368 -1.253 O23 YKA 32 YKA O24 O5 O 0 1 N N N N N N -12.645 1.201 42.029 -1.552 1.324 1.865 O24 YKA 33 YKA H1 H1 H 0 1 N N N N N N -13.065 2.623 40.227 -3.724 2.899 -0.089 H1 YKA 34 YKA H2 H2 H 0 1 N N N N N N -14.711 2.340 39.566 -4.624 3.109 1.432 H2 YKA 35 YKA H3 H3 H 0 1 N N N N N N -14.066 4.012 39.684 -2.865 2.840 1.469 H3 YKA 36 YKA H4 H4 H 0 1 N N N N N N -12.248 -1.018 43.296 0.791 1.227 1.285 H4 YKA 37 YKA H5 H5 H 0 1 N N N N N N -14.691 -2.858 43.443 0.773 -1.788 1.755 H5 YKA 38 YKA H6 H6 H 0 1 N N N N N N -12.996 -3.270 43.871 1.961 -0.663 2.456 H6 YKA 39 YKA H7 H7 H 0 1 N N N N N N -14.862 -1.370 45.316 -1.058 -0.451 2.838 H7 YKA 40 YKA H8 H8 H 0 1 N N N N N N -13.079 -1.111 47.006 1.120 -1.461 4.722 H8 YKA 41 YKA H9 H9 H 0 1 N N N N N N -11.958 -2.029 45.944 -0.595 -1.242 5.142 H9 YKA 42 YKA H10 H10 H 0 1 N N N N N N -12.620 -0.450 45.400 -0.123 -2.466 3.939 H10 YKA 43 YKA H11 H11 H 0 1 N N N N N N -14.646 -2.926 47.212 0.176 1.695 2.988 H11 YKA 44 YKA H12 H12 H 0 1 N N N N N N -15.392 -3.691 45.768 -0.421 1.188 4.587 H12 YKA 45 YKA H13 H13 H 0 1 N N N N N N -13.677 -4.032 46.180 1.295 0.969 4.166 H13 YKA 46 YKA H14 H14 H 0 1 N N N N N N -12.887 -2.838 39.115 3.595 -0.411 -1.805 H14 YKA 47 YKA H15 H15 H 0 1 N N N N N N -11.015 -2.251 37.709 5.443 1.202 0.007 H15 YKA 48 YKA H16 H16 H 0 1 N N N N N N -9.904 -2.160 39.117 5.890 0.637 -1.621 H16 YKA 49 YKA H17 H17 H 0 1 N N N N N N -11.254 -0.206 39.976 3.763 1.837 -2.464 H17 YKA 50 YKA H18 H18 H 0 1 N N N N N N -13.043 1.427 36.489 5.397 5.381 -1.086 H18 YKA 51 YKA H19 H19 H 0 1 N N N N N N -13.226 0.331 39.037 6.370 2.938 -1.714 H19 YKA 52 YKA H20 H20 H 0 1 N N N N N N -13.019 -0.976 37.822 5.278 3.497 -3.022 H20 YKA 53 YKA S1 S1 S 0 1 N Y N N N N -10.505 -4.488 40.133 3.690 -2.896 -0.367 S1 YKA 54 YKA H22 H22 H 0 1 N N N N N N -11.391 -4.698 38.552 5.254 -1.333 0.585 H22 YKA 55 YKA H23 H23 H 0 1 N N N N N N -16.587 3.832 42.367 -4.953 1.165 2.967 H23 YKA 56 YKA H24 H24 H 0 1 N N N N N N -16.059 4.696 40.884 -4.288 -0.430 2.539 H24 YKA 57 YKA H25 H25 H 0 1 N N N N N N -16.704 3.024 40.767 -3.194 0.896 3.003 H25 YKA 58 YKA H26 H26 H 0 1 N N N N N N -12.808 3.849 42.323 -6.159 1.248 0.780 H26 YKA 59 YKA H27 H27 H 0 1 N N N N N N -13.774 5.897 41.309 -5.065 2.239 -1.213 H27 YKA 60 YKA H28 H28 H 0 1 N N N N N N -15.011 5.919 42.611 -4.400 0.645 -1.640 H28 YKA 61 YKA H29 H29 H 0 1 N N N N N N -12.003 6.213 42.937 -7.365 1.331 -1.407 H29 YKA 62 YKA H30 H30 H 0 1 N N N N N N -13.248 7.497 43.108 -6.464 1.122 -2.928 H30 YKA 63 YKA H31 H31 H 0 1 N N N N N N -13.463 4.266 45.944 -7.694 -0.613 0.128 H31 YKA 64 YKA H32 H32 H 0 1 N N N N N N -12.165 4.154 44.708 -7.028 -2.207 -0.300 H32 YKA 65 YKA H33 H33 H 0 1 N N N N N N -15.162 4.164 44.196 -4.729 -1.299 -0.106 H33 YKA 66 YKA H34 H34 H 0 1 N N N N N N -14.074 2.737 44.138 -5.629 -1.089 1.415 H34 YKA 67 YKA H35 H35 H 0 1 N N N N N N -15.041 -0.310 43.469 -0.733 -0.605 -0.403 H35 YKA 68 YKA H36 H36 H 0 1 N N N N N N -11.225 -2.523 41.594 3.330 0.424 1.032 H36 YKA 69 YKA H37 H37 H 0 1 N N N N N N -12.245 -5.987 40.285 6.536 -1.044 -1.410 H37 YKA 70 YKA O3 O6 O 0 1 N Y N N N N ? ? ? 2.621 -2.488 0.637 O3 YKA 71 YKA O1 O7 O 0 1 N Y N N N N ? ? ? 2.989 -3.006 -1.599 O1 YKA 72 YKA O2 O8 O 0 1 N Y N N N N ? ? ? 4.313 -4.027 0.224 O2 YKA 73 YKA H21 H21 H 0 1 N N N N N N ? ? ? 1.930 -3.152 0.767 H21 YKA 74 # 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 YKA C18 N17 DOUB N N 1 YKA C18 C19 SING N N 2 YKA N17 C16 SING N N 3 YKA C16 O20 DOUB N N 4 YKA C16 C15 SING N N 5 YKA C19 C15 SING N N 6 YKA C14 C15 SING N N 7 YKA C14 C13 SING N N 8 YKA C13 C21 SING N N 9 YKA C13 N12 SING N N 10 YKA C21 O22 SING N N 11 YKA C01 C02 SING N N 12 YKA O23 C11 DOUB N N 13 YKA N12 C11 SING N N 14 YKA C25 C02 SING N N 15 YKA C11 C06 SING N N 16 YKA C02 O03 SING N N 17 YKA C02 C26 SING N N 18 YKA O24 C04 DOUB N N 19 YKA O03 C04 SING N N 20 YKA C27 C26 SING N N 21 YKA C27 C28 SING N N 22 YKA C04 N05 SING N N 23 YKA C26 C33 SING N N 24 YKA C06 N05 SING N N 25 YKA C06 C07 SING N N 26 YKA C28 C29 SING N N 27 YKA C07 C08 SING N N 28 YKA C33 C32 SING N N 29 YKA C29 C32 SING N N 30 YKA C29 F31 SING N N 31 YKA C29 F30 SING N N 32 YKA C08 C09 SING N N 33 YKA C08 C10 SING N N 34 YKA C01 H1 SING N N 35 YKA C01 H2 SING N N 36 YKA C01 H3 SING N N 37 YKA C06 H4 SING N N 38 YKA C07 H5 SING N N 39 YKA C07 H6 SING N N 40 YKA C08 H7 SING N N 41 YKA C09 H8 SING N N 42 YKA C09 H9 SING N N 43 YKA C09 H10 SING N N 44 YKA C10 H11 SING N N 45 YKA C10 H12 SING N N 46 YKA C10 H13 SING N N 47 YKA C13 H14 SING N N 48 YKA C14 H15 SING N N 49 YKA C14 H16 SING N N 50 YKA C15 H17 SING N N 51 YKA C18 H18 SING N N 52 YKA C19 H19 SING N N 53 YKA C19 H20 SING N N 54 YKA C21 S1 SING N N 55 YKA C21 H22 SING N N 56 YKA C25 H23 SING N N 57 YKA C25 H24 SING N N 58 YKA C25 H25 SING N N 59 YKA C26 H26 SING N N 60 YKA C27 H27 SING N N 61 YKA C27 H28 SING N N 62 YKA C28 H29 SING N N 63 YKA C28 H30 SING N N 64 YKA C32 H31 SING N N 65 YKA C32 H32 SING N N 66 YKA C33 H33 SING N N 67 YKA C33 H34 SING N N 68 YKA N05 H35 SING N N 69 YKA N12 H36 SING N N 70 YKA O22 H37 SING N N 71 YKA S1 O3 SING N N 72 YKA S1 O1 DOUB N N 73 YKA S1 O2 DOUB N N 74 YKA O3 H21 SING N N 75 # 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 YKA SMILES ACDLabs 12.01 "O=C1N=CCC1CC(NC(=O)C(CC(C)C)NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(O)S(=O)(=O)O" YKA InChI InChI 1.03 "InChI=1S/C23H37F2N3O8S/c1-13(2)11-16(28-21(32)36-22(3,4)15-5-8-23(24,25)9-6-15)19(30)27-17(20(31)37(33,34)35)12-14-7-10-26-18(14)29/h10,13-17,20,31H,5-9,11-12H2,1-4H3,(H,27,30)(H,28,32)(H,33,34,35)/t14-,16-,17-,20+/m0/s1" YKA InChIKey InChI 1.03 AFVXFMYQWMALEA-JWWIWJDOSA-N YKA SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(=O)N[C@@H](C[C@@H]2CC=NC2=O)[C@H](O)[S](O)(=O)=O" YKA SMILES CACTVS 3.385 "CC(C)C[CH](NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(=O)N[CH](C[CH]2CC=NC2=O)[CH](O)[S](O)(=O)=O" YKA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CC=NC1=O)C(O)S(=O)(=O)O)NC(=O)OC(C)(C)C2CCC(CC2)(F)F" YKA SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CC=NC1=O)C(O)S(=O)(=O)O)NC(=O)OC(C)(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 YKA "SYSTEMATIC NAME" ACDLabs 12.01 "(1R,2S)-2-{[N-({[2-(4,4-difluorocyclohexyl)propan-2-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propane-1-sulfonic acid" YKA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(2~{S})-2-[2-[4,4-bis(fluoranyl)cyclohexyl]propan-2-yloxycarbonylamino]-4-methyl-pentanoyl]amino]-1-oxidanyl-3-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-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 YKA "Create component" 2021-03-11 RCSB YKA "Initial release" 2021-03-24 RCSB YKA "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id YKA _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 ? #