data_Y4P
# 
_chem_comp.id                                    Y4P 
_chem_comp.name                                  "(1R,2S)-2-((S)-2-(((((1R,2S,4S)-bicyclo[2.2.1]heptan-2-yl)methoxy)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 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                     2021-02-03 
_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                        503.609 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y4P 
_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        7LKS 
_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 
Y4P C11 C1  C 0 1 N N S N N N 8.986  19.765 27.710 3.110  0.296  -1.067 C11 Y4P 1  
Y4P C12 C2  C 0 1 N N N N N N 7.984  19.671 26.475 4.167  1.049  -0.257 C12 Y4P 2  
Y4P C13 C3  C 0 1 N N S N N N 7.596  21.032 25.901 3.598  2.396  0.196  C13 Y4P 3  
Y4P C14 C4  C 0 1 N N N N N N 6.615  20.973 24.729 4.622  3.157  1.009  C14 Y4P 4  
Y4P C16 C5  C 0 1 N N N N N N 5.750  22.651 26.161 3.706  4.698  -0.468 C16 Y4P 5  
Y4P C17 C6  C 0 1 N N N N N N 6.869  21.945 26.900 3.329  3.307  -1.025 C17 Y4P 6  
Y4P C19 C7  C 0 1 N N R N N N 9.208  18.357 28.309 3.721  -0.988 -1.633 C19 Y4P 7  
Y4P C23 C8  C 0 1 N N N N N N 9.764  25.809 25.213 -5.101 0.804  0.115  C23 Y4P 8  
Y4P C02 C9  C 0 1 N N N N N N 10.987 24.021 25.981 -2.784 0.233  0.048  C02 Y4P 9  
Y4P C04 C10 C 0 1 N N S N N N 12.073 22.193 27.169 -0.438 -0.412 0.177  C04 Y4P 10 
Y4P C05 C11 C 0 1 N N N N N N 13.182 21.971 28.198 -0.414 -1.840 0.724  C05 Y4P 11 
Y4P C06 C12 C 0 1 N N N N N N 14.560 22.436 27.746 0.727  -1.981 1.734  C06 Y4P 12 
Y4P C07 C13 C 0 1 N N N N N N 15.026 21.666 26.527 0.428  -1.120 2.963  C07 Y4P 13 
Y4P C08 C14 C 0 1 N N N N N N 15.592 22.325 28.902 0.856  -3.445 2.157  C08 Y4P 14 
Y4P C09 C15 C 0 1 N N N N N N 10.718 21.635 27.621 0.748  -0.200 -0.728 C09 Y4P 15 
Y4P C24 C16 C 0 1 N N S N N N 10.022 27.345 25.423 -6.318 0.849  -0.811 C24 Y4P 16 
Y4P C25 C17 C 0 1 N N R N N N 8.805  28.246 25.350 -7.530 1.505  -0.083 C25 Y4P 17 
Y4P C26 C18 C 0 1 N N N N N N 7.983  27.880 24.110 -7.586 0.794  1.303  C26 Y4P 18 
Y4P C27 C19 C 0 1 N N N N N N 8.910  28.122 22.993 -8.053 -0.645 0.986  C27 Y4P 19 
Y4P C28 C20 C 0 1 N N S N N N 10.089 28.867 23.614 -8.236 -0.668 -0.562 C28 Y4P 20 
Y4P C29 C21 C 0 1 N N N N N N 9.483  29.543 24.856 -8.726 0.817  -0.833 C29 Y4P 21 
Y4P C30 C22 C 0 1 N N N N N N 10.961 27.826 24.318 -6.790 -0.584 -1.149 C30 Y4P 22 
Y4P N03 N1  N 0 1 N N N N N N 11.930 23.610 26.860 -1.674 -0.200 -0.581 N03 Y4P 23 
Y4P N10 N2  N 0 1 N N N N N N 10.292 20.344 27.303 1.979  -0.042 -0.200 N10 Y4P 24 
Y4P N15 N3  N 0 1 N N N N N N 5.597  21.892 24.913 4.665  4.440  0.613  N15 Y4P 25 
Y4P O01 O1  O 0 1 N N N N N N 10.288 23.326 25.247 -2.738 0.535  1.224  O01 Y4P 26 
Y4P O18 O2  O 0 1 N N N N N N 6.755  20.212 23.787 5.304  2.678  1.890  O18 Y4P 27 
Y4P O20 O3  O 0 1 N N N N N N 10.067 18.538 29.449 2.771  -1.632 -2.484 O20 Y4P 28 
Y4P O21 O4  O 0 1 N N N N N N 9.978  22.362 28.274 0.597  -0.172 -1.931 O21 Y4P 29 
Y4P O22 O5  O 0 1 N N N N N N 10.798 25.362 25.912 -3.945 0.331  -0.626 O22 Y4P 30 
Y4P H1  H1  H 0 1 N N N N N N 8.524  20.405 28.476 2.764  0.925  -1.887 H1  Y4P 31 
Y4P H2  H2  H 0 1 N N N N N N 7.069  19.159 26.807 4.443  0.459  0.617  H2  Y4P 32 
Y4P H3  H3  H 0 1 N N N N N N 8.465  19.082 25.680 5.048  1.216  -0.876 H3  Y4P 33 
Y4P H4  H4  H 0 1 N N N N N N 8.510  21.543 25.565 2.684  2.249  0.771  H4  Y4P 34 
Y4P H5  H5  H 0 1 N N N N N N 6.022  23.696 25.950 4.169  5.303  -1.247 H5  Y4P 35 
Y4P H6  H6  H 0 1 N N N N N N 4.820  22.626 26.748 2.821  5.200  -0.076 H6  Y4P 36 
Y4P H7  H7  H 0 1 N N N N N N 6.452  21.343 27.721 3.971  3.036  -1.863 H7  Y4P 37 
Y4P H8  H8  H 0 1 N N N N N N 7.572  22.686 27.309 2.279  3.274  -1.312 H8  Y4P 38 
Y4P S1  S1  S 0 1 N Y N N N N 9.660  17.705 27.591 4.162  -2.100 -0.269 S1  Y4P 39 
Y4P H10 H10 H 0 1 N N N N N N 8.229  18.015 28.677 4.615  -0.743 -2.206 H10 Y4P 40 
Y4P H11 H11 H 0 1 N N N N N N 8.802  25.485 25.635 -4.900 1.804  0.501  H11 Y4P 41 
Y4P H12 H12 H 0 1 N N N N N N 9.817  25.517 24.154 -5.301 0.128  0.946  H12 Y4P 42 
Y4P H13 H13 H 0 1 N N N N N N 12.361 21.662 26.250 -0.394 0.295  1.005  H13 Y4P 43 
Y4P H14 H14 H 0 1 N N N N N N 12.917 22.520 29.114 -1.363 -2.057 1.215  H14 Y4P 44 
Y4P H15 H15 H 0 1 N N N N N N 13.237 20.895 28.418 -0.261 -2.541 -0.097 H15 Y4P 45 
Y4P H16 H16 H 0 1 N N N N N N 14.485 23.498 27.469 1.659  -1.651 1.276  H16 Y4P 46 
Y4P H17 H17 H 0 1 N N N N N N 16.022 22.024 26.225 -0.467 -1.493 3.460  H17 Y4P 47 
Y4P H18 H18 H 0 1 N N N N N N 15.079 20.594 26.769 1.272  -1.165 3.651  H18 Y4P 48 
Y4P H19 H19 H 0 1 N N N N N N 14.315 21.821 25.702 0.268  -0.087 2.653  H19 Y4P 49 
Y4P H20 H20 H 0 1 N N N N N N 15.230 22.891 29.773 1.069  -4.059 1.281  H20 Y4P 50 
Y4P H21 H21 H 0 1 N N N N N N 15.719 21.268 29.179 1.669  -3.545 2.876  H21 Y4P 51 
Y4P H22 H22 H 0 1 N N N N N N 16.557 22.736 28.572 -0.077 -3.775 2.614  H22 Y4P 52 
Y4P H23 H23 H 0 1 N N N N N N 10.515 27.484 26.396 -6.080 1.396  -1.723 H23 Y4P 53 
Y4P H24 H24 H 0 1 N N N N N N 8.231  28.346 26.283 -7.540 2.595  -0.061 H24 Y4P 54 
Y4P H25 H25 H 0 1 N N N N N N 7.093  28.520 24.027 -6.597 0.780  1.763  H25 Y4P 55 
Y4P H26 H26 H 0 1 N N N N N N 7.674  26.825 24.142 -8.301 1.292  1.957  H26 Y4P 56 
Y4P H27 H27 H 0 1 N N N N N N 8.429  28.736 22.218 -7.291 -1.363 1.289  H27 Y4P 57 
Y4P H28 H28 H 0 1 N N N N N N 9.242  27.170 22.553 -8.998 -0.860 1.484  H28 Y4P 58 
Y4P H29 H29 H 0 1 N N N N N N 10.627 29.543 22.933 -8.859 -1.470 -0.957 H29 Y4P 59 
Y4P H30 H30 H 0 1 N N N N N N 10.240 29.931 25.553 -9.681 1.027  -0.352 H30 Y4P 60 
Y4P H31 H31 H 0 1 N N N N N N 8.767  30.342 24.611 -8.749 1.053  -1.897 H31 Y4P 61 
Y4P H32 H32 H 0 1 N N N N N N 11.236 27.006 23.639 -6.807 -0.754 -2.226 H32 Y4P 62 
Y4P H33 H33 H 0 1 N N N N N N 11.873 28.280 24.734 -6.139 -1.307 -0.659 H33 Y4P 63 
Y4P H34 H34 H 0 1 N N N N N N 12.530 24.280 27.298 -1.693 -0.370 -1.536 H34 Y4P 64 
Y4P H35 H35 H 0 1 N N N N N N 10.908 19.770 26.764 2.115  -0.153 0.754  H35 Y4P 65 
Y4P H36 H36 H 0 1 N N N N N N 4.843  22.024 24.270 5.255  5.111  0.993  H36 Y4P 66 
Y4P H37 H37 H 0 1 N N N N N N 10.235 17.696 29.856 1.948  -1.879 -2.040 H37 Y4P 67 
Y4P O1  O6  O 0 1 N Y N N N N ?      ?      ?      5.243  -1.563 0.481  O1  Y4P 68 
Y4P O2  O7  O 0 1 N Y N N N N ?      ?      ?      2.993  -2.587 0.375  O2  Y4P 69 
Y4P O3  O8  O 0 1 N Y N N N N ?      ?      ?      4.751  -3.325 -0.953 O3  Y4P 70 
Y4P H9  H9  H 0 1 N Y N N N N ?      ?      ?      5.037  -4.017 -0.342 H9  Y4P 71 
# 
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 
Y4P C27 C28 SING N N 1  
Y4P C27 C26 SING N N 2  
Y4P C28 C30 SING N N 3  
Y4P C28 C29 SING N N 4  
Y4P O18 C14 DOUB N N 5  
Y4P C26 C25 SING N N 6  
Y4P C30 C24 SING N N 7  
Y4P C14 N15 SING N N 8  
Y4P C14 C13 SING N N 9  
Y4P C29 C25 SING N N 10 
Y4P N15 C16 SING N N 11 
Y4P C23 C24 SING N N 12 
Y4P C23 O22 SING N N 13 
Y4P O01 C02 DOUB N N 14 
Y4P C25 C24 SING N N 15 
Y4P C13 C12 SING N N 16 
Y4P C13 C17 SING N N 17 
Y4P O22 C02 SING N N 18 
Y4P C02 N03 SING N N 19 
Y4P C16 C17 SING N N 20 
Y4P C12 C11 SING N N 21 
Y4P C07 C06 SING N N 22 
Y4P N03 C04 SING N N 23 
Y4P C04 C09 SING N N 24 
Y4P C04 C05 SING N N 25 
Y4P N10 C09 SING N N 26 
Y4P N10 C11 SING N N 27 
Y4P C09 O21 DOUB N N 28 
Y4P C11 C19 SING N N 29 
Y4P C06 C05 SING N N 30 
Y4P C06 C08 SING N N 31 
Y4P C19 O20 SING N N 32 
Y4P C11 H1  SING N N 33 
Y4P C12 H2  SING N N 34 
Y4P C12 H3  SING N N 35 
Y4P C13 H4  SING N N 36 
Y4P C16 H5  SING N N 37 
Y4P C16 H6  SING N N 38 
Y4P C17 H7  SING N N 39 
Y4P C17 H8  SING N N 40 
Y4P C19 S1  SING N N 41 
Y4P C19 H10 SING N N 42 
Y4P C23 H11 SING N N 43 
Y4P C23 H12 SING N N 44 
Y4P C04 H13 SING N N 45 
Y4P C05 H14 SING N N 46 
Y4P C05 H15 SING N N 47 
Y4P C06 H16 SING N N 48 
Y4P C07 H17 SING N N 49 
Y4P C07 H18 SING N N 50 
Y4P C07 H19 SING N N 51 
Y4P C08 H20 SING N N 52 
Y4P C08 H21 SING N N 53 
Y4P C08 H22 SING N N 54 
Y4P C24 H23 SING N N 55 
Y4P C25 H24 SING N N 56 
Y4P C26 H25 SING N N 57 
Y4P C26 H26 SING N N 58 
Y4P C27 H27 SING N N 59 
Y4P C27 H28 SING N N 60 
Y4P C28 H29 SING N N 61 
Y4P C29 H30 SING N N 62 
Y4P C29 H31 SING N N 63 
Y4P C30 H32 SING N N 64 
Y4P C30 H33 SING N N 65 
Y4P N03 H34 SING N N 66 
Y4P N10 H35 SING N N 67 
Y4P N15 H36 SING N N 68 
Y4P O20 H37 SING N N 69 
Y4P S1  O1  DOUB N N 70 
Y4P S1  O2  DOUB N N 71 
Y4P S1  O3  SING N N 72 
Y4P O3  H9  SING N N 73 
# 
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 
Y4P InChI            InChI                1.03  "InChI=1S/C22H37N3O8S/c1-12(2)7-17(25-22(29)33-11-16-9-13-3-4-14(16)8-13)20(27)24-18(21(28)34(30,31)32)10-15-5-6-23-19(15)26/h12-18,21,28H,3-11H2,1-2H3,(H,23,26)(H,24,27)(H,25,29)(H,30,31,32)/t13-,14+,15-,16+,17-,18-,21+/m0/s1" 
Y4P InChIKey         InChI                1.03  CDEICDIJDMTLMS-NFFJHMNLSA-N                                                                                                                                                                                                         
Y4P SMILES_CANONICAL CACTVS               3.385 "CC(C)C[C@H](NC(=O)OC[C@H]1C[C@H]2CC[C@@H]1C2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)[S](O)(=O)=O"                                                                                                                                    
Y4P SMILES           CACTVS               3.385 "CC(C)C[CH](NC(=O)OC[CH]1C[CH]2CC[CH]1C2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O"                                                                                                                                              
Y4P SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC[C@H]2C[C@H]3CC[C@@H]2C3"                                                                                                                                         
Y4P SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CC3CCC2C3"                                                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           Y4P 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{S})-2-[[(2~{S})-2-[[(1~{R},2~{S},4~{S})-2-bicyclo[2.2.1]heptanyl]methoxycarbonylamino]-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 
Y4P "Create component"   2021-02-03 RCSB 
Y4P "Other modification" 2021-02-09 RCSB 
Y4P "Modify name"        2021-02-09 RCSB 
Y4P "Initial release"    2021-02-17 RCSB 
Y4P "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y4P 
_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               C19 
_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      ? 
# 
