data_X5L
# 
_chem_comp.id                                    X5L 
_chem_comp.name                                  "(2~{S})-2-azanyl-6-[[(2~{R})-1-[[(1~{S})-2-methyl-1-sulfo-propyl]amino]-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-6-oxidanylidene-hexanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H25 N3 O7 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-31 
_chem_comp.pdbx_modified_date                    2024-06-07 
_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                        399.484 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     X5L 
_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        8P7O 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
X5L N   N1  N 0 1 N N N N N N 12.948 -2.950 -7.774  0.545  -0.275 0.526  N   X5L 1  
X5L C   C1  C 0 1 N N N N N N 13.393 -2.177 -8.767  1.747  -0.270 -0.084 C   X5L 2  
X5L O   O1  O 0 1 N N N N N N 13.229 -2.458 -9.952  1.848  -0.664 -1.227 O   X5L 3  
X5L C1  C2  C 0 1 N N R N N N 11.951 -3.987 -7.979  -0.637 -0.761 -0.189 C1  X5L 4  
X5L C10 C3  C 0 1 N N N N N N 14.212 1.607  -8.405  5.425  0.627  0.490  C10 X5L 5  
X5L C11 C4  C 0 1 N N S N N N 13.646 2.883  -9.030  6.649  0.527  -0.423 C11 X5L 6  
X5L C12 C5  C 0 1 N N N N N N 14.427 4.097  -8.550  7.842  1.134  0.269  C12 X5L 7  
X5L C2  C6  C 0 1 N N N N N N 11.995 -5.003 -6.844  -0.722 -2.283 -0.058 C2  X5L 8  
X5L C3  C7  C 0 1 N N N N N N 10.559 -3.364 -8.081  -1.875 -0.137 0.403  C3  X5L 9  
X5L C4  C8  C 0 1 N N S N N N 9.726  -5.345 -9.374  -4.291 0.168  0.478  C4  X5L 10 
X5L C5  C9  C 0 1 N N N N N N 9.585  -5.009 -10.898 -5.365 -0.906 0.665  C5  X5L 11 
X5L C6  C10 C 0 1 N N N N N N 10.330 -6.007 -11.770 -4.789 -2.065 1.482  C6  X5L 12 
X5L C7  C11 C 0 1 N N N N N N 8.128  -4.917 -11.323 -6.562 -0.306 1.405  C7  X5L 13 
X5L C8  C12 C 0 1 N N N N N N 14.125 -0.927 -8.343  2.964  0.224  0.653  C8  X5L 14 
X5L C9  C13 C 0 1 N N N N N N 13.477 0.350  -8.861  4.189  0.124  -0.259 C9  X5L 15 
X5L N1  N2  N 0 1 N N N N N N 9.573  -4.147 -8.539  -3.088 -0.440 -0.098 N1  X5L 16 
X5L N2  N3  N 0 1 N N N N N N 13.691 2.788  -10.502 6.923  -0.885 -0.722 N2  X5L 17 
X5L O1  O2  O 0 1 N N N N N N 9.278  -6.918 -7.453  -6.072 2.087  0.118  O1  X5L 18 
X5L O2  O3  O 0 1 N N N N N N 8.547  -7.688 -9.584  -3.963 2.505  -0.766 O2  X5L 19 
X5L O3  O4  O 0 1 N N N N N N 7.359  -5.916 -8.386  -5.517 0.872  -1.785 O3  X5L 20 
X5L O4  O5  O 0 1 N N N N N N 10.381 -2.197 -7.741  -1.778 0.638  1.331  O4  X5L 21 
X5L O5  O6  O 0 1 N N N N N N 14.242 4.357  -7.281  8.003  2.466  0.284  O5  X5L 22 
X5L O6  O7  O 0 1 N N N N N N 15.146 4.745  -9.281  8.654  0.421  0.811  O6  X5L 23 
X5L S   S1  S 0 1 N N N N N N 11.809 -4.267 -5.202  0.767  -3.035 -0.771 S   X5L 24 
X5L S1  S2  S 0 1 N N N N N N 8.577  -6.563 -8.721  -4.912 1.455  -0.639 S1  X5L 25 
X5L H1  H1  H 0 1 N N N N N N 13.315 -2.810 -6.854  0.464  0.040  1.440  H1  X5L 26 
X5L H2  H2  H 0 1 N N N N N N 12.163 -4.513 -8.922  -0.562 -0.491 -1.242 H2  X5L 27 
X5L H3  H3  H 0 1 N N N N N N 15.271 1.517  -8.688  5.584  0.016  1.379  H3  X5L 28 
X5L H4  H4  H 0 1 N N N N N N 14.130 1.685  -7.311  5.275  1.665  0.784  H4  X5L 29 
X5L H5  H5  H 0 1 N N N N N N 12.600 2.992  -8.709  6.455  1.064  -1.351 H5  X5L 30 
X5L H6  H6  H 0 1 N N N N N N 11.181 -5.727 -6.994  -0.797 -2.554 0.995  H6  X5L 31 
X5L H7  H7  H 0 1 N N N N N N 12.962 -5.526 -6.883  -1.602 -2.645 -0.590 H7  X5L 32 
X5L H8  H8  H 0 1 N N N N N N 10.728 -5.770 -9.214  -4.048 0.611  1.444  H8  X5L 33 
X5L H9  H9  H 0 1 N N N N N N 10.042 -4.021 -11.056 -5.686 -1.273 -0.310 H9  X5L 34 
X5L H10 H10 H 0 1 N N N N N N 11.381 -6.062 -11.450 -4.468 -1.699 2.457  H10 X5L 35 
X5L H11 H11 H 0 1 N N N N N N 9.865  -6.999 -11.671 -5.554 -2.830 1.615  H11 X5L 36 
X5L H12 H12 H 0 1 N N N N N N 10.283 -5.683 -12.820 -3.936 -2.493 0.955  H12 X5L 37 
X5L H13 H13 H 0 1 N N N N N N 7.604  -4.192 -10.683 -7.057 0.423  0.764  H13 X5L 38 
X5L H14 H14 H 0 1 N N N N N N 8.072  -4.588 -12.371 -7.265 -1.099 1.662  H14 X5L 39 
X5L H15 H15 H 0 1 N N N N N N 7.654  -5.904 -11.222 -6.218 0.184  2.316  H15 X5L 40 
X5L H16 H16 H 0 1 N N N N N N 15.155 -0.977 -8.726  2.814  1.263  0.947  H16 X5L 41 
X5L H17 H17 H 0 1 N N N N N N 14.144 -0.889 -7.244  3.123  -0.386 1.543  H17 X5L 42 
X5L H18 H18 H 0 1 N N N N N N 12.441 0.394  -8.493  4.030  0.734  -1.148 H18 X5L 43 
X5L H19 H19 H 0 1 N N N N N N 13.474 0.323  -9.961  4.339  -0.914 -0.553 H19 X5L 44 
X5L H20 H20 H 0 1 N N N N N N 8.640  -3.890 -8.287  -3.166 -1.059 -0.840 H20 X5L 45 
X5L H21 H21 H 0 1 N N N N N N 13.174 1.986  -10.801 7.106  -1.405 0.123  H21 X5L 46 
X5L H22 H22 H 0 1 N N N N N N 13.289 3.612  -10.902 6.164  -1.298 -1.243 H22 X5L 47 
X5L H24 H24 H 0 1 N N N N N N 14.753 5.119  -7.036  8.784  2.809  0.740  H24 X5L 48 
X5L H25 H25 H 0 1 N N N N N N 11.879 -5.310 -4.429  0.558  -4.351 -0.590 H25 X5L 49 
X5L H23 H23 H 0 1 N N N N N N 8.756  -6.634 -6.712  -6.511 2.803  -0.361 H23 X5L 50 
# 
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 
X5L C6  C5  SING N N 1  
X5L C7  C5  SING N N 2  
X5L C5  C4  SING N N 3  
X5L N2  C11 SING N N 4  
X5L O   C   DOUB N N 5  
X5L O2  S1  DOUB N N 6  
X5L C4  S1  SING N N 7  
X5L C4  N1  SING N N 8  
X5L O6  C12 DOUB N N 9  
X5L C11 C12 SING N N 10 
X5L C11 C10 SING N N 11 
X5L C9  C10 SING N N 12 
X5L C9  C8  SING N N 13 
X5L C   C8  SING N N 14 
X5L C   N   SING N N 15 
X5L S1  O3  DOUB N N 16 
X5L S1  O1  SING N N 17 
X5L C12 O5  SING N N 18 
X5L N1  C3  SING N N 19 
X5L C3  C1  SING N N 20 
X5L C3  O4  DOUB N N 21 
X5L C1  N   SING N N 22 
X5L C1  C2  SING N N 23 
X5L C2  S   SING N N 24 
X5L N   H1  SING N N 25 
X5L C1  H2  SING N N 26 
X5L C10 H3  SING N N 27 
X5L C10 H4  SING N N 28 
X5L C11 H5  SING N N 29 
X5L C2  H6  SING N N 30 
X5L C2  H7  SING N N 31 
X5L C4  H8  SING N N 32 
X5L C5  H9  SING N N 33 
X5L C6  H10 SING N N 34 
X5L C6  H11 SING N N 35 
X5L C6  H12 SING N N 36 
X5L C7  H13 SING N N 37 
X5L C7  H14 SING N N 38 
X5L C7  H15 SING N N 39 
X5L C8  H16 SING N N 40 
X5L C8  H17 SING N N 41 
X5L C9  H18 SING N N 42 
X5L C9  H19 SING N N 43 
X5L N1  H20 SING N N 44 
X5L N2  H21 SING N N 45 
X5L N2  H22 SING N N 46 
X5L O5  H24 SING N N 47 
X5L S   H25 SING N N 48 
X5L O1  H23 SING N N 49 
# 
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 
X5L InChI            InChI                1.06  "InChI=1S/C13H25N3O7S2/c1-7(2)12(25(21,22)23)16-11(18)9(6-24)15-10(17)5-3-4-8(14)13(19)20/h7-9,12,24H,3-6,14H2,1-2H3,(H,15,17)(H,16,18)(H,19,20)(H,21,22,23)/t8-,9-,12-/m0/s1" 
X5L InChIKey         InChI                1.06  SLYPAEUXHCDCFQ-AUTRQRHGSA-N                                                                                                                                                    
X5L SMILES_CANONICAL CACTVS               3.385 "CC(C)[C@@H](NC(=O)[C@H](CS)NC(=O)CCC[C@H](N)C(O)=O)[S](O)(=O)=O"                                                                                                              
X5L SMILES           CACTVS               3.385 "CC(C)[CH](NC(=O)[CH](CS)NC(=O)CCC[CH](N)C(O)=O)[S](O)(=O)=O"                                                                                                                  
X5L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)[C@@H](NC(=O)[C@H](CS)NC(=O)CCC[C@@H](C(=O)O)N)S(=O)(=O)O"                                                                                                               
X5L SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)C(NC(=O)C(CS)NC(=O)CCCC(C(=O)O)N)S(=O)(=O)O"                                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           X5L 
_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-azanyl-6-[[(2~{R})-1-[[(1~{S})-2-methyl-1-sulfo-propyl]amino]-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-6-oxidanylidene-hexanoic 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 
X5L "Create component" 2023-05-31 PDBE 
X5L "Initial release"  2024-06-12 RCSB 
# 
