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      ? 
# 
