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      ? 
# 
