data_YKD # _chem_comp.id YKD _chem_comp.name "(1S,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 YKD _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 YKD C14 C1 C 0 1 N N N N N N -10.957 -1.992 38.818 -4.704 -1.266 -0.251 C14 YKD 1 YKD C15 C2 C 0 1 N N R N N N -11.246 -0.474 38.919 -4.163 -2.473 0.517 C15 YKD 2 YKD C16 C3 C 0 1 N N N N N N -10.249 0.426 38.198 -5.229 -3.056 1.422 C16 YKD 3 YKD C18 C4 C 0 1 N N N N N N -12.322 0.985 37.162 -4.781 -4.737 0.031 C18 YKD 4 YKD C19 C5 C 0 1 N N N N N N -12.566 -0.094 38.258 -3.853 -3.640 -0.445 C19 YKD 5 YKD C25 C6 C 0 1 N N N N N N -16.112 3.726 41.376 4.504 1.635 1.757 C25 YKD 6 YKD C26 C7 C 0 1 N N N N N N -13.870 4.101 42.486 5.789 0.451 -0.029 C26 YKD 7 YKD C28 C8 C 0 1 N N N N N N -13.045 6.436 43.232 8.284 0.373 0.070 C28 YKD 8 YKD C01 C9 C 0 1 N N N N N N -14.087 3.026 40.162 4.432 -0.859 1.610 C01 YKD 9 YKD C02 C10 C 0 1 N N N N N N -14.673 3.159 41.560 4.505 0.439 0.802 C02 YKD 10 YKD C04 C11 C 0 1 N N N N N N -13.826 0.985 42.378 2.139 0.524 0.497 C04 YKD 11 YKD C06 C12 C 0 1 N N S N N N -13.263 -1.307 42.993 -0.287 0.715 0.365 C06 YKD 12 YKD C07 C13 C 0 1 N N N N N N -13.772 -2.444 43.906 -0.547 2.174 0.742 C07 YKD 13 YKD C08 C14 C 0 1 N N N N N N -14.025 -2.065 45.364 -1.824 2.265 1.579 C08 YKD 14 YKD C09 C15 C 0 1 N N N N N N -12.820 -1.366 45.990 -1.604 1.564 2.921 C09 YKD 15 YKD C10 C16 C 0 1 N N N N N N -14.467 -3.247 46.213 -2.172 3.735 1.823 C10 YKD 16 YKD C11 C17 C 0 1 N N N N N N -13.186 -1.817 41.568 -1.347 0.247 -0.598 C11 YKD 17 YKD C13 C18 C 0 1 N N S N N N -11.939 -2.882 39.651 -3.574 -0.628 -1.061 C13 YKD 18 YKD C21 C19 C 0 1 N N S N N N -11.485 -4.392 39.689 -4.144 0.482 -1.947 C21 YKD 19 YKD C27 C20 C 0 1 N N N N N N -13.986 5.640 42.354 7.000 0.361 0.902 C27 YKD 20 YKD C29 C21 C 0 1 N N N N N N -13.222 6.062 44.728 8.285 -0.822 -0.884 C29 YKD 21 YKD C32 C22 C 0 1 N N N N N N -13.184 4.524 44.905 7.074 -0.733 -1.815 C32 YKD 22 YKD C33 C23 C 0 1 N N N N N N -14.143 3.832 43.964 5.790 -0.745 -0.983 C33 YKD 23 YKD F30 F1 F 0 1 N N N N N N -12.275 6.674 45.474 9.459 -0.812 -1.645 F30 YKD 24 YKD F31 F2 F 0 1 N N N N N N -14.384 6.541 45.222 8.219 -2.009 -0.145 F31 YKD 25 YKD N05 N1 N 0 1 N N N N N N -14.171 -0.193 43.029 1.031 0.601 -0.266 N05 YKD 26 YKD N12 N2 N 0 1 N N N N N N -12.053 -2.399 41.042 -2.579 -0.060 -0.147 N12 YKD 27 YKD N17 N3 N 0 1 N N N N N N -10.885 1.224 37.247 -5.475 -4.317 1.039 N17 YKD 28 YKD O03 O1 O 0 1 N N N N N N -14.840 1.879 42.157 3.355 0.523 -0.081 O03 YKD 29 YKD O20 O2 O 0 1 N N N N N N -9.048 0.489 38.424 -5.770 -2.478 2.341 O20 YKD 30 YKD O22 O3 O 0 1 N N N N N N -11.344 -4.803 38.362 -5.195 -0.049 -2.756 O22 YKD 31 YKD O23 O4 O 0 1 N N N N N N -14.178 -1.686 40.864 -1.092 0.148 -1.780 O23 YKD 32 YKD O24 O5 O 0 1 N N N N N N -12.646 1.218 42.051 2.041 0.456 1.706 O24 YKD 33 YKD H1 H1 H 0 1 N N N N N N -11.032 -2.289 37.762 -5.496 -1.590 -0.926 H1 YKD 34 YKD H2 H2 H 0 1 N N N N N N -9.934 -2.174 39.179 -5.104 -0.536 0.453 H2 YKD 35 YKD H3 H3 H 0 1 N N N N N N -11.282 -0.191 39.981 -3.277 -2.199 1.090 H3 YKD 36 YKD H4 H4 H 0 1 N N N N N N -13.041 1.445 36.500 -4.854 -5.722 -0.405 H4 YKD 37 YKD H5 H5 H 0 1 N N N N N N -13.252 0.308 39.018 -4.083 -3.361 -1.474 H5 YKD 38 YKD H6 H6 H 0 1 N N N N N N -13.013 -0.987 37.797 -2.812 -3.951 -0.353 H6 YKD 39 YKD H7 H7 H 0 1 N N N N N N -16.589 3.844 42.360 5.366 1.571 2.420 H7 YKD 40 YKD H8 H8 H 0 1 N N N N N N -16.059 4.704 40.874 4.555 2.559 1.181 H8 YKD 41 YKD H9 H9 H 0 1 N N N N N N -16.704 3.031 40.763 3.589 1.626 2.349 H9 YKD 42 YKD H10 H10 H 0 1 N N N N N N -12.810 3.861 42.319 5.840 1.375 -0.605 H10 YKD 43 YKD H11 H11 H 0 1 N N N N N N -12.008 6.226 42.930 8.336 1.298 -0.506 H11 YKD 44 YKD H12 H12 H 0 1 N N N N N N -13.254 7.508 43.103 9.147 0.310 0.733 H12 YKD 45 YKD H13 H13 H 0 1 N N N N N N -13.064 2.627 40.229 3.517 -0.867 2.203 H13 YKD 46 YKD H14 H14 H 0 1 N N N N N N -14.709 2.341 39.567 4.433 -1.711 0.931 H14 YKD 47 YKD H15 H15 H 0 1 N N N N N N -14.064 4.014 39.679 5.295 -0.922 2.273 H15 YKD 48 YKD H16 H16 H 0 1 N N N N N N -12.261 -0.999 43.327 -0.314 0.097 1.263 H16 YKD 49 YKD H17 H17 H 0 1 N N N N N N -14.718 -2.816 43.485 0.294 2.556 1.319 H17 YKD 50 YKD H18 H18 H 0 1 N N N N N N -13.022 -3.249 43.892 -0.665 2.768 -0.165 H18 YKD 51 YKD H19 H19 H 0 1 N N N N N N -14.852 -1.340 45.367 -2.643 1.781 1.047 H19 YKD 52 YKD H20 H20 H 0 1 N N N N N N -13.045 -1.112 47.036 -2.533 1.571 3.492 H20 YKD 53 YKD H21 H21 H 0 1 N N N N N N -11.949 -2.036 45.955 -1.293 0.534 2.747 H21 YKD 54 YKD H22 H22 H 0 1 N N N N N N -12.598 -0.446 45.429 -0.830 2.087 3.482 H22 YKD 55 YKD H23 H23 H 0 1 N N N N N N -14.633 -2.914 47.248 -2.328 4.234 0.866 H23 YKD 56 YKD H24 H24 H 0 1 N N N N N N -15.402 -3.661 45.807 -3.081 3.799 2.420 H24 YKD 57 YKD H25 H25 H 0 1 N N N N N N -13.686 -4.021 46.198 -1.353 4.218 2.355 H25 YKD 58 YKD H26 H26 H 0 1 N N N N N N -12.928 -2.838 39.172 -3.102 -1.385 -1.686 H26 YKD 59 YKD S1 S1 S 0 1 N Y N N N N -10.561 -4.497 40.219 -4.798 1.813 -0.902 S1 YKD 60 YKD H28 H28 H 0 1 N N N N N N -12.322 -4.950 40.134 -3.356 0.876 -2.588 H28 YKD 61 YKD H29 H29 H 0 1 N N N N N N -13.782 5.908 41.307 6.999 1.214 1.581 H29 YKD 62 YKD H30 H30 H 0 1 N N N N N N -15.016 5.927 42.612 6.948 -0.563 1.477 H30 YKD 63 YKD H31 H31 H 0 1 N N N N N N -13.460 4.277 45.941 7.126 0.191 -2.391 H31 YKD 64 YKD H32 H32 H 0 1 N N N N N N -12.164 4.166 44.702 7.075 -1.585 -2.495 H32 YKD 65 YKD H33 H33 H 0 1 N N N N N N -15.162 4.176 44.195 5.738 -1.669 -0.408 H33 YKD 66 YKD H34 H34 H 0 1 N N N N N N -14.074 2.748 44.136 4.927 -0.682 -1.646 H34 YKD 67 YKD H35 H35 H 0 1 N N N N N N -15.041 -0.265 43.517 1.105 0.581 -1.233 H35 YKD 68 YKD H36 H36 H 0 1 N N N N N N -11.258 -2.501 41.640 -2.808 0.095 0.783 H36 YKD 69 YKD H37 H37 H 0 1 N N N N N N -11.070 -5.712 38.339 -5.933 -0.418 -2.251 H37 YKD 70 YKD O1 O6 O 0 1 N Y N N N N ? ? ? -5.881 1.341 -0.112 O1 YKD 71 YKD O2 O7 O 0 1 N Y N N N N ? ? ? -3.737 2.558 -0.321 O2 YKD 72 YKD O3 O8 O 0 1 N Y N N N N ? ? ? -5.443 2.782 -1.883 O3 YKD 73 YKD H27 H27 H 0 1 N N N N N N ? ? ? -5.842 3.557 -1.464 H27 YKD 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 YKD C18 N17 DOUB N N 1 YKD C18 C19 SING N N 2 YKD N17 C16 SING N N 3 YKD C16 O20 DOUB N N 4 YKD C16 C15 SING N N 5 YKD C19 C15 SING N N 6 YKD O22 C21 SING N N 7 YKD C14 C15 SING N N 8 YKD C14 C13 SING N N 9 YKD C13 C21 SING N N 10 YKD C13 N12 SING N N 11 YKD C01 C02 SING N N 12 YKD O23 C11 DOUB N N 13 YKD N12 C11 SING N N 14 YKD C25 C02 SING N N 15 YKD C02 O03 SING N N 16 YKD C02 C26 SING N N 17 YKD C11 C06 SING N N 18 YKD O24 C04 DOUB N N 19 YKD O03 C04 SING N N 20 YKD C27 C26 SING N N 21 YKD C27 C28 SING N N 22 YKD C04 N05 SING N N 23 YKD C26 C33 SING N N 24 YKD C06 N05 SING N N 25 YKD C06 C07 SING N N 26 YKD C28 C29 SING N N 27 YKD C07 C08 SING N N 28 YKD C33 C32 SING N N 29 YKD C29 C32 SING N N 30 YKD C29 F31 SING N N 31 YKD C29 F30 SING N N 32 YKD C08 C09 SING N N 33 YKD C08 C10 SING N N 34 YKD C14 H1 SING N N 35 YKD C14 H2 SING N N 36 YKD C15 H3 SING N N 37 YKD C18 H4 SING N N 38 YKD C19 H5 SING N N 39 YKD C19 H6 SING N N 40 YKD C25 H7 SING N N 41 YKD C25 H8 SING N N 42 YKD C25 H9 SING N N 43 YKD C26 H10 SING N N 44 YKD C28 H11 SING N N 45 YKD C28 H12 SING N N 46 YKD C01 H13 SING N N 47 YKD C01 H14 SING N N 48 YKD C01 H15 SING N N 49 YKD C06 H16 SING N N 50 YKD C07 H17 SING N N 51 YKD C07 H18 SING N N 52 YKD C08 H19 SING N N 53 YKD C09 H20 SING N N 54 YKD C09 H21 SING N N 55 YKD C09 H22 SING N N 56 YKD C10 H23 SING N N 57 YKD C10 H24 SING N N 58 YKD C10 H25 SING N N 59 YKD C13 H26 SING N N 60 YKD C21 S1 SING N N 61 YKD C21 H28 SING N N 62 YKD C27 H29 SING N N 63 YKD C27 H30 SING N N 64 YKD C32 H31 SING N N 65 YKD C32 H32 SING N N 66 YKD C33 H33 SING N N 67 YKD C33 H34 SING N N 68 YKD N05 H35 SING N N 69 YKD N12 H36 SING N N 70 YKD O22 H37 SING N N 71 YKD S1 O1 DOUB N N 72 YKD S1 O2 DOUB N N 73 YKD S1 O3 SING N N 74 YKD O3 H27 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 YKD 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" YKD 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" YKD InChIKey InChI 1.03 AFVXFMYQWMALEA-VERUCKTNSA-N YKD 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" YKD 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" YKD 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" YKD 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 YKD "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,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" YKD "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 YKD "Create component" 2021-03-11 RCSB YKD "Initial release" 2021-03-24 RCSB YKD "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id YKD _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 ? #