data_S7N
# 
_chem_comp.id                                    S7N 
_chem_comp.name                                  "(phenylmethyl) ~{N}-[(2~{R})-3-methyl-1-[[(2~{S})-1-[[(3~{S})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H33 N3 O5 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         Z-VAM-FMK;zVAM.fmk 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-11-10 
_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                        451.580 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     S7N 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        7ARA 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
S7N C10 C1  C 0 1 N N N N N N -31.323 43.826 5.012  2.317   -1.589 2.009  C10 S7N 1  
S7N C20 C2  C 0 1 Y N N N N N -25.139 39.271 0.390  -7.195  1.003  -0.538 C20 S7N 2  
S7N C21 C3  C 0 1 Y N N N N N -25.371 38.279 -0.591 -8.150  0.442  0.289  C21 S7N 3  
S7N C22 C4  C 0 1 Y N N N N N -24.984 36.960 -0.353 -9.170  1.224  0.798  C22 S7N 4  
S7N C24 C5  C 0 1 Y N N N N N -24.148 37.611 1.817  -8.279  3.129  -0.346 C24 S7N 5  
S7N C26 C6  C 0 1 N N N N N N -28.278 44.724 0.764  -1.792  -2.806 0.316  C26 S7N 6  
S7N C28 C7  C 0 1 N N N N N N -27.782 45.602 1.914  -2.971  -3.430 -0.433 C28 S7N 7  
S7N C01 C8  C 0 1 N N N N N N -36.732 48.010 2.592  6.383   4.926  0.131  C01 S7N 8  
S7N C03 C9  C 0 1 N N N N N N -36.129 45.178 2.894  6.021   2.133  -0.228 C03 S7N 9  
S7N C04 C10 C 0 1 N N N N N N -35.789 43.870 2.131  6.609   0.724  -0.119 C04 S7N 10 
S7N C05 C11 C 0 1 N N S N N N -35.302 42.826 3.147  5.573   -0.298 -0.591 C05 S7N 11 
S7N C07 C12 C 0 1 N N N N N N -32.747 43.568 2.883  3.214   -0.686 -0.119 C07 S7N 12 
S7N C09 C13 C 0 1 N N S N N N -31.373 43.279 3.585  2.033   -0.673 0.817  C09 S7N 13 
S7N C12 C14 C 0 1 N N N N N N -29.560 42.842 1.987  -0.384  -0.775 0.522  C12 S7N 14 
S7N C14 C15 C 0 1 N N R N N N -28.327 43.262 1.145  -1.610  -1.356 -0.134 C14 S7N 15 
S7N C16 C16 C 0 1 N N N N N N -25.792 42.819 1.314  -3.873  -0.550 -0.545 C16 S7N 16 
S7N C19 C17 C 0 1 N N N N N N -25.564 40.722 0.136  -6.087  0.148  -1.098 C19 S7N 17 
S7N C23 C18 C 0 1 Y N N N N N -24.375 36.619 0.839  -9.234  2.568  0.480  C23 S7N 18 
S7N C25 C19 C 0 1 Y N N N N N -24.531 38.932 1.583  -7.260  2.346  -0.856 C25 S7N 19 
S7N C27 C20 C 0 1 N N N N N N -29.576 45.243 0.107  -2.068  -2.843 1.821  C27 S7N 20 
S7N C29 C21 C 0 1 N N N N N N -35.446 41.371 2.730  6.191   -1.672 -0.601 C29 S7N 21 
S7N C30 C22 C 0 1 N N N N N N -34.661 40.411 3.639  7.163   -2.054 -1.688 C30 S7N 22 
S7N N06 N1  N 0 1 N N N N N N -33.897 42.865 3.499  4.424   -0.285 0.318  N06 S7N 23 
S7N N11 N2  N 0 1 N N N N N N -30.245 43.766 2.820  0.843   -1.150 0.108  N11 S7N 24 
S7N N15 N3  N 0 1 N N N N N N -27.138 42.936 1.943  -2.787  -0.573 0.253  N15 S7N 25 
S7N O08 O1  O 0 1 N N N N N N -32.829 44.331 1.920  3.076   -1.057 -1.265 O08 S7N 26 
S7N O13 O2  O 0 1 N N N N N N -29.940 41.695 1.949  -0.501  0.028  1.423  O13 S7N 27 
S7N O17 O3  O 0 1 N N N N N N -25.235 43.816 0.845  -3.876  -1.177 -1.586 O17 S7N 28 
S7N O18 O4  O 0 1 N N N N N N -25.146 41.531 1.260  -4.954  0.169  -0.190 O18 S7N 29 
S7N O31 O5  O 0 1 N N N N N N -36.088 41.002 1.774  5.908   -2.467 0.263  O31 S7N 30 
S7N S02 S1  S 0 1 N N N N N N -36.691 46.417 1.761  7.249   3.345  0.331  S02 S7N 31 
S7N H1  H1  H 0 1 N N N N N N -32.185 43.448 5.581  2.488   -2.605 1.655  H1  S7N 32 
S7N H2  H2  H 0 1 N N N N N N -30.392 43.499 5.498  3.202   -1.234 2.537  H2  S7N 33 
S7N H3  H3  H 0 1 N N N N N N -31.356 44.925 4.985  1.462   -1.579 2.686  H3  S7N 34 
S7N H4  H4  H 0 1 N N N N N N -25.847 38.542 -1.524 -8.100  -0.608 0.538  H4  S7N 35 
S7N H5  H5  H 0 1 N N N N N N -25.161 36.203 -1.103 -9.916  0.785  1.444  H5  S7N 36 
S7N H6  H6  H 0 1 N N N N N N -23.675 37.346 2.751  -8.329  4.179  -0.595 H6  S7N 37 
S7N H7  H7  H 0 1 N N N N N N -27.507 44.801 -0.017 -0.884  -3.370 0.100  H7  S7N 38 
S7N H8  H8  H 0 1 N N N N N N -26.859 45.173 2.331  -2.774  -3.404 -1.505 H8  S7N 39 
S7N H9  H9  H 0 1 N N N N N N -27.579 46.616 1.540  -3.100  -4.463 -0.113 H9  S7N 40 
S7N H10 H10 H 0 1 N N N N N N -28.552 45.648 2.698  -3.878  -2.866 -0.217 H10 S7N 41 
S7N H11 H11 H 0 1 N N N N N N -37.081 48.782 1.890  7.037   5.741  0.442  H11 S7N 42 
S7N H12 H12 H 0 1 N N N N N N -37.418 47.958 3.450  6.109   5.060  -0.916 H12 S7N 43 
S7N H13 H13 H 0 1 N N N N N N -35.722 48.265 2.945  5.483   4.927  0.745  H13 S7N 44 
S7N H14 H14 H 0 1 N N N N N N -35.229 45.541 3.412  5.756   2.337  -1.266 H14 S7N 45 
S7N H15 H15 H 0 1 N N N N N N -36.920 44.974 3.631  5.130   2.204  0.395  H15 S7N 46 
S7N H16 H16 H 0 1 N N N N N N -36.687 43.497 1.616  7.500   0.653  -0.743 H16 S7N 47 
S7N H17 H17 H 0 1 N N N N N N -34.998 44.066 1.392  6.873   0.521  0.918  H17 S7N 48 
S7N H18 H18 H 0 1 N N N N N N -35.892 42.965 4.065  5.242   -0.042 -1.598 H18 S7N 49 
S7N H19 H19 H 0 1 N N N N N N -31.285 42.185 3.658  1.861   0.343  1.171  H19 S7N 50 
S7N H20 H20 H 0 1 N N N N N N -28.320 42.659 0.225  -1.493  -1.323 -1.217 H20 S7N 51 
S7N H21 H21 H 0 1 N N N N N N -25.087 41.092 -0.784 -6.442  -0.876 -1.213 H21 S7N 52 
S7N H22 H22 H 0 1 N N N N N N -26.658 40.774 0.029  -5.782  0.539  -2.068 H22 S7N 53 
S7N H23 H23 H 0 1 N N N N N N -24.074 35.598 1.022  -10.031 3.179  0.877  H23 S7N 54 
S7N H24 H24 H 0 1 N N N N N N -24.352 39.688 2.333  -6.514  2.785  -1.502 H24 S7N 55 
S7N H25 H25 H 0 1 N N N N N N -29.462 46.309 -0.140 -2.119  -3.879 2.156  H25 S7N 56 
S7N H26 H26 H 0 1 N N N N N N -29.775 44.673 -0.813 -1.265  -2.329 2.350  H26 S7N 57 
S7N H27 H27 H 0 1 N N N N N N -30.416 45.116 0.805  -3.015  -2.346 2.029  H27 S7N 58 
S7N H28 H28 H 0 1 N N N N N N -34.785 39.379 3.278  7.293   -1.214 -2.370 H28 S7N 59 
S7N H29 H29 H 0 1 N N N N N N -33.594 40.680 3.622  8.124   -2.312 -1.242 H29 S7N 60 
S7N H30 H30 H 0 1 N N N N N N -35.042 40.487 4.668  6.775   -2.912 -2.237 H30 S7N 61 
S7N H31 H31 H 0 1 N N N N N N -33.661 42.319 4.303  4.535   0.011  1.235  H31 S7N 62 
S7N H32 H32 H 0 1 N N N N N N -29.957 44.722 2.876  0.938   -1.735 -0.660 H32 S7N 63 
S7N H33 H33 H 0 1 N N N N N N -27.233 42.790 2.928  -2.785  -0.073 1.084  H33 S7N 64 
# 
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 
S7N C21 C22 DOUB Y N 1  
S7N C21 C20 SING Y N 2  
S7N C22 C23 SING Y N 3  
S7N C27 C26 SING N N 4  
S7N C19 C20 SING N N 5  
S7N C19 O18 SING N N 6  
S7N C20 C25 DOUB Y N 7  
S7N C26 C14 SING N N 8  
S7N C26 C28 SING N N 9  
S7N C23 C24 DOUB Y N 10 
S7N O17 C16 DOUB N N 11 
S7N C14 N15 SING N N 12 
S7N C14 C12 SING N N 13 
S7N O18 C16 SING N N 14 
S7N C16 N15 SING N N 15 
S7N C25 C24 SING Y N 16 
S7N S02 C01 SING N N 17 
S7N S02 C03 SING N N 18 
S7N O31 C29 DOUB N N 19 
S7N O08 C07 DOUB N N 20 
S7N O13 C12 DOUB N N 21 
S7N C12 N11 SING N N 22 
S7N C04 C03 SING N N 23 
S7N C04 C05 SING N N 24 
S7N C29 C05 SING N N 25 
S7N C29 C30 SING N N 26 
S7N N11 C09 SING N N 27 
S7N C07 N06 SING N N 28 
S7N C07 C09 SING N N 29 
S7N C05 N06 SING N N 30 
S7N C09 C10 SING N N 31 
S7N C10 H1  SING N N 32 
S7N C10 H2  SING N N 33 
S7N C10 H3  SING N N 34 
S7N C21 H4  SING N N 35 
S7N C22 H5  SING N N 36 
S7N C24 H6  SING N N 37 
S7N C26 H7  SING N N 38 
S7N C28 H8  SING N N 39 
S7N C28 H9  SING N N 40 
S7N C28 H10 SING N N 41 
S7N C01 H11 SING N N 42 
S7N C01 H12 SING N N 43 
S7N C01 H13 SING N N 44 
S7N C03 H14 SING N N 45 
S7N C03 H15 SING N N 46 
S7N C04 H16 SING N N 47 
S7N C04 H17 SING N N 48 
S7N C05 H18 SING N N 49 
S7N C09 H19 SING N N 50 
S7N C14 H20 SING N N 51 
S7N C19 H21 SING N N 52 
S7N C19 H22 SING N N 53 
S7N C23 H23 SING N N 54 
S7N C25 H24 SING N N 55 
S7N C27 H25 SING N N 56 
S7N C27 H26 SING N N 57 
S7N C27 H27 SING N N 58 
S7N C30 H28 SING N N 59 
S7N C30 H29 SING N N 60 
S7N C30 H30 SING N N 61 
S7N N06 H31 SING N N 62 
S7N N11 H32 SING N N 63 
S7N N15 H33 SING N N 64 
# 
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 
S7N InChI            InChI                1.03  "InChI=1S/C22H33N3O5S/c1-14(2)19(25-22(29)30-13-17-9-7-6-8-10-17)21(28)23-15(3)20(27)24-18(16(4)26)11-12-31-5/h6-10,14-15,18-19H,11-13H2,1-5H3,(H,23,28)(H,24,27)(H,25,29)/t15-,18-,19+/m0/s1" 
S7N InChIKey         InChI                1.03  XQQSDBOJVLTWFC-ZYSHUDEJSA-N                                                                                                                                                                    
S7N SMILES_CANONICAL CACTVS               3.385 "CSCC[C@H](NC(=O)[C@H](C)NC(=O)[C@H](NC(=O)OCc1ccccc1)C(C)C)C(C)=O"                                                                                                                            
S7N SMILES           CACTVS               3.385 "CSCC[CH](NC(=O)[CH](C)NC(=O)[CH](NC(=O)OCc1ccccc1)C(C)C)C(C)=O"                                                                                                                               
S7N SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](C(=O)N[C@@H](CCSC)C(=O)C)NC(=O)[C@@H](C(C)C)NC(=O)OCc1ccccc1"                                                                                                                         
S7N SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)C(C(=O)NC(C)C(=O)NC(CCSC)C(=O)C)NC(=O)OCc1ccccc1"                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           S7N 
_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        "(phenylmethyl) ~{N}-[(2~{R})-3-methyl-1-[[(2~{S})-1-[[(3~{S})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate" 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 S7N Z-VAM-FMK ? ? 
2 S7N zVAM.fmk  ? ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
S7N "Create component" 2020-11-10 PDBE 
S7N "Initial release"  2021-07-28 RCSB 
S7N "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            S7N 
_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               C30 
_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      ? 
# 
