data_X56
# 
_chem_comp.id                                    X56 
_chem_comp.name                                  Cefazolin 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C14 H14 N8 O4 S3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-10-30 
_chem_comp.pdbx_modified_date                    2024-11-13 
_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                        454.507 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     X56 
_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        8YXA 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_chem_comp.pdbx_pcm                              ? 
# 
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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
X56 S1  S1  S 0 1 N N N N N N -0.774 -13.899 -12.302 -0.969 1.933  -0.484 S1  X56 1  
X56 C1  C1  C 0 1 N N R N N N 0.874  -14.501 -11.940 -1.324 0.467  -1.508 C1  X56 2  
X56 C2  C2  C 0 1 N N R N N N 1.129  -16.067 -12.037 -2.645 -0.225 -1.225 C2  X56 3  
X56 C3  C3  C 0 1 N N N N N N 1.417  -16.007 -10.522 -1.737 -1.374 -0.853 C3  X56 4  
X56 C4  C4  C 0 1 N N N N N N 0.613  -13.850 -9.494  0.702  -0.682 -0.375 C4  X56 5  
X56 C5  C5  C 0 1 N N N N N N -0.014 -12.709 -9.863  1.336  0.461  -0.149 C5  X56 6  
X56 O1  O1  O 0 1 N N N N N N 1.816  -16.757 -9.668  -1.960 -2.543 -0.623 O1  X56 7  
X56 O2  O2  O 0 1 N N N N N N -0.078 -14.280 -7.303  1.333  -2.515 1.114  O2  X56 8  
X56 N1  N1  N 0 1 N N N N N N 0.967  -14.728 -10.498 -0.612 -0.668 -0.862 N1  X56 9  
X56 C6  C6  C 0 1 N N N N N N -0.575 -12.443 -11.244 0.845  1.850  -0.392 C6  X56 10 
X56 C7  C7  C 0 1 N N N N N N -0.213 -11.566 -8.911  2.724  0.342  0.427  C7  X56 11 
X56 C8  C8  C 0 1 N N N N N N 0.886  -14.212 -8.041  1.380  -1.965 -0.116 C8  X56 12 
X56 O3  O3  O 0 1 N N N N N N 2.040  -14.463 -7.744  1.980  -2.527 -1.010 O3  X56 13 
X56 N2  N2  N 0 1 N N N N N N 0.043  -16.920 -12.424 -3.395 0.342  -0.101 N2  X56 14 
X56 C9  C9  C 0 1 N N N N N N 0.002  -17.515 -13.619 -4.734 0.197  -0.043 C9  X56 15 
X56 O4  O4  O 0 1 N N N N N N -0.936 -18.227 -13.973 -5.318 -0.402 -0.922 O4  X56 16 
X56 C10 C10 C 0 1 N N N N N N 1.195  -17.255 -14.530 -5.505 0.780  1.113  C10 X56 17 
X56 N3  N3  N 0 1 Y N N N N N 1.214  -18.178 -15.651 -6.931 0.490  0.944  N3  X56 18 
X56 C11 C11 C 0 1 Y N N N N N -2.077 -9.736  -8.105  5.432  0.416  0.042  C11 X56 19 
X56 C12 C12 C 0 1 Y N N N N N 1.690  -19.416 -15.732 -7.732 -0.128 1.832  C12 X56 20 
X56 C13 C13 C 0 1 Y N N N N N -2.717 -7.463  -8.049  7.687  0.205  1.031  C13 X56 21 
X56 S2  S2  S 0 1 N N N N N N -1.964 -11.443 -8.444  3.944  0.605  -0.883 S2  X56 22 
X56 C14 C14 C 0 1 N N N N N N -3.373 -6.129  -8.197  9.137  0.119  1.431  C14 X56 23 
X56 N4  N4  N 0 1 Y N N N N N 0.707  -17.844 -16.849 -7.657 0.784  -0.082 N4  X56 24 
X56 N5  N5  N 0 1 Y N N N N N -1.065 -8.953  -7.898  5.517  0.153  1.315  N5  X56 25 
X56 N6  N6  N 0 1 Y N N N N N 1.494  -19.875 -16.944 -8.924 -0.185 1.289  N6  X56 26 
X56 N7  N7  N 0 1 Y N N N N N 0.877  -18.868 -17.622 -8.859 0.373  0.129  N7  X56 27 
X56 N8  N8  N 0 1 Y N N N N N -1.446 -7.618  -7.911  6.670  0.047  1.814  N8  X56 28 
X56 S3  S3  S 0 1 Y N N N N N -3.604 -8.945  -8.034  7.075  0.541  -0.590 S3  X56 29 
X56 H1  H1  H 0 1 N N N N N N 1.651  -13.875 -12.403 -1.095 0.606  -2.565 H1  X56 30 
X56 H2  H2  H 0 1 N N N N N N 2.049  -16.270 -12.605 -3.258 -0.404 -2.108 H2  X56 31 
X56 H3  H3  H 0 1 N N N N N N 0.202  -14.563 -6.441  1.792  -3.358 1.235  H3  X56 32 
X56 H4  H4  H 0 1 N N N N N N 0.102  -11.743 -11.755 1.264  2.214  -1.331 H4  X56 33 
X56 H5  H5  H 0 1 N N N N N N -1.563 -11.975 -11.123 1.189  2.493  0.418  H5  X56 34 
X56 H6  H6  H 0 1 N N N N N N 0.394  -11.734 -8.009  2.859  1.093  1.205  H6  X56 35 
X56 H7  H7  H 0 1 N N N N N N 0.101  -10.630 -9.395  2.856  -0.652 0.853  H7  X56 36 
X56 H8  H8  H 0 1 N N N N N N -0.706 -17.074 -11.780 -2.928 0.820  0.601  H8  X56 37 
X56 H9  H9  H 0 1 N N N N N N 2.122  -17.376 -13.950 -5.153 0.338  2.045  H9  X56 38 
X56 H10 H10 H 0 1 N N N N N N 1.135  -16.226 -14.914 -5.355 1.859  1.142  H10 X56 39 
X56 H12 H12 H 0 1 N N N N N N 2.163  -19.958 -14.927 -7.448 -0.505 2.803  H12 X56 40 
X56 H14 H14 H 0 1 N N N N N N -4.461 -6.263  -8.289  9.490  1.104  1.735  H14 X56 41 
X56 H15 H15 H 0 1 N N N N N N -3.153 -5.512  -7.313  9.244  -0.578 2.262  H15 X56 42 
X56 H16 H16 H 0 1 N N N N N N -2.988 -5.629  -9.098  9.728  -0.233 0.584  H16 X56 43 
# 
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 
X56 N7  N6  SING Y N 1  
X56 N7  N4  DOUB Y N 2  
X56 N6  C12 DOUB Y N 3  
X56 N4  N3  SING Y N 4  
X56 C12 N3  SING Y N 5  
X56 N3  C10 SING N N 6  
X56 C10 C9  SING N N 7  
X56 O4  C9  DOUB N N 8  
X56 C9  N2  SING N N 9  
X56 N2  C2  SING N N 10 
X56 S1  C1  SING N N 11 
X56 S1  C6  SING N N 12 
X56 C2  C1  SING N N 13 
X56 C2  C3  SING N N 14 
X56 C1  N1  SING N N 15 
X56 C6  C5  SING N N 16 
X56 C3  N1  SING N N 17 
X56 C3  O1  DOUB N N 18 
X56 N1  C4  SING N N 19 
X56 C5  C4  DOUB N N 20 
X56 C5  C7  SING N N 21 
X56 C4  C8  SING N N 22 
X56 C7  S2  SING N N 23 
X56 S2  C11 SING N N 24 
X56 C14 C13 SING N N 25 
X56 C11 S3  SING Y N 26 
X56 C11 N5  DOUB Y N 27 
X56 C13 S3  SING Y N 28 
X56 C13 N8  DOUB Y N 29 
X56 C8  O3  DOUB N N 30 
X56 C8  O2  SING N N 31 
X56 N8  N5  SING Y N 32 
X56 C1  H1  SING N N 33 
X56 C2  H2  SING N N 34 
X56 O2  H3  SING N N 35 
X56 C6  H4  SING N N 36 
X56 C6  H5  SING N N 37 
X56 C7  H6  SING N N 38 
X56 C7  H7  SING N N 39 
X56 N2  H8  SING N N 40 
X56 C10 H9  SING N N 41 
X56 C10 H10 SING N N 42 
X56 C12 H12 SING N N 43 
X56 C14 H14 SING N N 44 
X56 C14 H15 SING N N 45 
X56 C14 H16 SING N N 46 
# 
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 
X56 InChI            InChI                1.06  "InChI=1S/C14H14N8O4S3/c1-6-17-18-14(29-6)28-4-7-3-27-12-9(11(24)22(12)10(7)13(25)26)16-8(23)2-21-5-15-19-20-21/h5,9,12H,2-4H2,1H3,(H,16,23)(H,25,26)/t9-,12-/m1/s1" 
X56 InChIKey         InChI                1.06  MLYYVTUWGNIJIB-BXKDBHETSA-N                                                                                                                                          
X56 SMILES_CANONICAL CACTVS               3.385 "Cc1sc(SCC2=C(N3[C@H](SC2)[C@H](NC(=O)Cn4cnnn4)C3=O)C(O)=O)nn1"                                                                                                      
X56 SMILES           CACTVS               3.385 "Cc1sc(SCC2=C(N3[CH](SC2)[CH](NC(=O)Cn4cnnn4)C3=O)C(O)=O)nn1"                                                                                                        
X56 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1nnc(s1)SCC2=C(N3[C@@H]([C@@H](C3=O)NC(=O)Cn4cnnn4)SC2)C(=O)O"                                                                                                    
X56 SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1nnc(s1)SCC2=C(N3C(C(C3=O)NC(=O)Cn4cnnn4)SC2)C(=O)O"                                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           X56 
_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        "(6~{R},7~{R})-3-[(5-methyl-1,3,4-thiadiazol-2-yl)sulfanylmethyl]-8-oxidanylidene-7-[2-(1,2,3,4-tetrazol-1-yl)ethanoylamino]-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic 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 
X56 "Create component"              2023-10-30 PDBC 
X56 "Initial release"               2024-08-07 RCSB 
X56 "Modify coordinates"            2024-11-13 PDBJ 
X56 "Modify descriptor"             2024-11-13 PDBJ 
X56 "Modify processing site"        2024-11-13 PDBJ 
X56 "Modify model coordinates code" 2024-11-13 PDBJ 
# 
