data_XD2
# 
_chem_comp.id                                    XD2 
_chem_comp.name                                  "(2R)-2-[(1R)-1-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-2-oxoethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H20 N6 O5 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Cefamandole, bound form" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2010-06-09 
_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                        464.519 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XD2 
_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        3N8S 
_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 
XD2 CAA CAA C 0 1 N N N N N N -5.499  -4.252  0.908  -6.383 3.190  0.844  CAA XD2 1  
XD2 OAB OAB O 0 1 N N N N N N -11.209 -7.040  5.265  -2.998 -3.195 1.012  OAB XD2 2  
XD2 OAC OAC O 0 1 N N N N N N -9.009  -13.684 3.664  4.886  -1.725 1.011  OAC XD2 3  
XD2 OAD OAD O 0 1 N N N N N N -12.521 -10.681 4.442  2.976  -3.142 -1.310 OAD XD2 4  
XD2 OAE OAE O 0 1 N N N N N N -10.433 -6.282  3.617  -2.804 -1.449 2.370  OAE XD2 5  
XD2 OAF OAF O 0 1 N N N N N N -9.916  -14.644 1.239  6.988  -0.504 0.066  OAF XD2 6  
XD2 CAG CAG C 0 1 Y N N N N N -7.456  -11.105 -1.215 5.086  4.029  0.513  CAG XD2 7  
XD2 CAH CAH C 0 1 Y N N N N N -8.798  -10.939 -1.196 4.631  3.524  -0.690 CAH XD2 8  
XD2 CAI CAI C 0 1 Y N N N N N -6.926  -12.002 -0.330 5.751  3.205  1.402  CAI XD2 9  
XD2 CAJ CAJ C 0 1 Y N N N N N -9.635  -11.620 -0.306 4.838  2.194  -1.004 CAJ XD2 10 
XD2 CAK CAK C 0 1 Y N N N N N -7.758  -12.702 0.539  5.958  1.875  1.087  CAK XD2 11 
XD2 CAL CAL C 0 1 N N N N N N -11.704 -11.101 5.470  2.214  -2.901 -0.405 CAL XD2 12 
XD2 CAM CAM C 0 1 N N N N N N -8.714  -7.292  2.273  -3.422 -0.489 -0.614 CAM XD2 13 
XD2 CAN CAN C 0 1 N N N N N N -8.066  -9.731  2.907  -1.095 0.136  -1.500 CAN XD2 14 
XD2 NAO NAO N 0 1 Y N N N N N -5.885  -4.466  4.347  -7.592 0.216  -0.758 NAO XD2 15 
XD2 NAP NAP N 0 1 Y N N N N N -6.403  -5.555  4.130  -6.331 -0.021 -0.727 NAP XD2 16 
XD2 NAQ NAQ N 0 1 Y N N N N N -5.521  -3.882  3.346  -7.846 1.362  -0.225 NAQ XD2 17 
XD2 NAR NAR N 0 1 N N N N N N -10.483 -11.977 3.501  3.357  -0.764 -0.277 NAR XD2 18 
XD2 NAS NAS N 0 1 N N N N N N -10.004 -9.325  5.060  -0.128 -1.650 0.750  NAS XD2 19 
XD2 SAT SAT S 0 1 N N N N N N -6.985  -7.024  1.771  -3.949 1.089  0.099  SAT XD2 20 
XD2 SAU SAU S 0 1 N N N N N N -7.754  -10.698 4.407  0.558  -0.616 -1.601 SAU XD2 21 
XD2 CAV CAV C 0 1 N N N N N N -10.497 -7.115  4.387  -2.461 -2.004 1.345  CAV XD2 22 
XD2 CAW CAW C 0 1 N N N N N N -9.733  -12.959 2.999  4.627  -0.916 0.146  CAW XD2 23 
XD2 CAX CAX C 0 1 N N N N N N -8.878  -8.459  3.194  -1.925 -0.616 -0.500 CAX XD2 24 
XD2 CAY CAY C 0 1 N N N N N N -9.796  -8.380  4.209  -1.459 -1.375 0.465  CAY XD2 25 
XD2 CAZ CAZ C 0 1 Y N N N N N -9.112  -12.512 0.569  5.502  1.369  -0.116 CAZ XD2 26 
XD2 CBA CBA C 0 1 Y N N N N N -6.364  -5.664  2.817  -5.688 0.977  -0.161 CBA XD2 27 
XD2 CBB CBB C 0 1 N N R N N N -9.992  -13.280 1.512  5.727  -0.081 -0.458 CBB XD2 28 
XD2 CBC CBC C 0 1 N N R N N N -10.428 -11.619 4.914  2.288  -1.576 0.309  CBC XD2 29 
XD2 CBD CBD C 0 1 N N R N N N -9.374  -10.597 5.142  0.952  -0.843 0.164  CBD XD2 30 
XD2 NBE NBE N 0 1 Y N N N N N -5.762  -4.571  2.379  -6.615 1.902  0.185  NBE XD2 31 
XD2 H1  H1  H 0 1 N N N N N N -5.035  -3.258  0.825  -6.219 3.959  0.090  H1  XD2 32 
XD2 H2  H2  H 0 1 N N N N N N -4.823  -5.009  0.484  -7.253 3.451  1.446  H2  XD2 33 
XD2 H3  H3  H 0 1 N N N N N N -6.450  -4.259  0.356  -5.505 3.116  1.486  H3  XD2 34 
XD2 H4  H4  H 0 1 N N N N N N -11.685 -6.219  5.218  -3.651 -3.568 1.620  H4  XD2 35 
XD2 H6  H6  H 0 1 N N N N N N -9.532  -15.095 1.982  7.062  -0.422 1.026  H6  XD2 36 
XD2 H7  H7  H 0 1 N N N N N N -6.830  -10.553 -1.900 4.928  5.069  0.757  H7  XD2 37 
XD2 H8  H8  H 0 1 N N N N N N -9.243  -10.250 -1.899 4.111  4.168  -1.384 H8  XD2 38 
XD2 H9  H9  H 0 1 N N N N N N -5.859  -12.168 -0.305 6.108  3.599  2.342  H9  XD2 39 
XD2 H10 H10 H 0 1 N N N N N N -10.699 -11.435 -0.316 4.482  1.799  -1.944 H10 XD2 40 
XD2 H11 H11 H 0 1 N N N N N N -7.318  -13.421 1.214  6.477  1.230  1.782  H11 XD2 41 
XD2 H12 H12 H 0 1 N N N N N N -11.954 -11.060 6.520  1.480  -3.635 -0.107 H12 XD2 42 
XD2 H14 H14 H 0 1 N N N N N N -9.075  -6.388  2.784  -3.898 -1.308 -0.075 H14 XD2 43 
XD2 H15 H15 H 0 1 N N N N N N -9.318  -7.469  1.371  -3.711 -0.528 -1.664 H15 XD2 44 
XD2 H16 H16 H 0 1 N N N N N N -8.625  -10.354 2.194  -1.003 1.176  -1.188 H16 XD2 45 
XD2 H17 H17 H 0 1 N N N N N N -7.101  -9.443  2.464  -1.575 0.091  -2.478 H17 XD2 46 
XD2 H18 H18 H 0 1 N N N N N N -11.098 -11.474 2.894  3.150  -0.117 -0.970 H18 XD2 47 
XD2 H20 H20 H 0 1 N N N N N N -11.023 -12.955 1.308  5.724  -0.204 -1.541 H20 XD2 48 
XD2 H21 H21 H 0 1 N N N N N N -10.153 -12.518 5.485  2.497  -1.744 1.366  H21 XD2 49 
XD2 H22 H22 H 0 1 N N N N N N -9.133  -10.709 6.209  1.003  0.125  0.661  H22 XD2 50 
XD2 H5  H5  H 0 1 N N N N N N -9.833  -8.903  5.950  0.092  -2.385 1.344  H5  XD2 51 
# 
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 
XD2 CAG CAH DOUB Y N 1  
XD2 CAG CAI SING Y N 2  
XD2 CAH CAJ SING Y N 3  
XD2 CAI CAK DOUB Y N 4  
XD2 CAJ CAZ DOUB Y N 5  
XD2 CAK CAZ SING Y N 6  
XD2 CAZ CBB SING N N 7  
XD2 CAA NBE SING N N 8  
XD2 OAF CBB SING N N 9  
XD2 CBB CAW SING N N 10 
XD2 SAT CAM SING N N 11 
XD2 SAT CBA SING N N 12 
XD2 CAM CAX SING N N 13 
XD2 NBE CBA SING Y N 14 
XD2 NBE NAQ SING Y N 15 
XD2 CBA NAP DOUB Y N 16 
XD2 CAN CAX SING N N 17 
XD2 CAN SAU SING N N 18 
XD2 CAW NAR SING N N 19 
XD2 CAW OAC DOUB N N 20 
XD2 CAX CAY DOUB N N 21 
XD2 NAQ NAO DOUB Y N 22 
XD2 NAR CBC SING N N 23 
XD2 OAE CAV DOUB N N 24 
XD2 NAP NAO SING Y N 25 
XD2 CAY CAV SING N N 26 
XD2 CAY NAS SING N N 27 
XD2 CAV OAB SING N N 28 
XD2 SAU CBD SING N N 29 
XD2 OAD CAL DOUB N N 30 
XD2 CBC CBD SING N N 31 
XD2 CBC CAL SING N N 32 
XD2 NAS CBD SING N N 33 
XD2 CAA H1  SING N N 34 
XD2 CAA H2  SING N N 35 
XD2 CAA H3  SING N N 36 
XD2 OAB H4  SING N N 37 
XD2 OAF H6  SING N N 38 
XD2 CAG H7  SING N N 39 
XD2 CAH H8  SING N N 40 
XD2 CAI H9  SING N N 41 
XD2 CAJ H10 SING N N 42 
XD2 CAK H11 SING N N 43 
XD2 CAL H12 SING N N 44 
XD2 CAM H14 SING N N 45 
XD2 CAM H15 SING N N 46 
XD2 CAN H16 SING N N 47 
XD2 CAN H17 SING N N 48 
XD2 NAR H18 SING N N 49 
XD2 CBB H20 SING N N 50 
XD2 CBC H21 SING N N 51 
XD2 CBD H22 SING N N 52 
XD2 NAS H5  SING N N 53 
# 
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 
XD2 SMILES           ACDLabs              12.01 "O=CC(NC(=O)C(O)c1ccccc1)C2SCC(=C(N2)C(=O)O)CSc3nnnn3C"                                                                                                                                    
XD2 InChI            InChI                1.03  "InChI=1S/C18H20N6O5S2/c1-24-18(21-22-23-24)31-9-11-8-30-16(20-13(11)17(28)29)12(7-25)19-15(27)14(26)10-5-3-2-4-6-10/h2-7,12,14,16,20,26H,8-9H2,1H3,(H,19,27)(H,28,29)/t12-,14-,16-/m1/s1" 
XD2 InChIKey         InChI                1.03  CTWPBVTUYYLUGC-XNRPHZJLSA-N                                                                                                                                                                
XD2 SMILES_CANONICAL CACTVS               3.370 "Cn1nnnc1SCC2=C(N[C@H](SC2)[C@H](NC(=O)[C@H](O)c3ccccc3)C=O)C(O)=O"                                                                                                                        
XD2 SMILES           CACTVS               3.370 "Cn1nnnc1SCC2=C(N[CH](SC2)[CH](NC(=O)[CH](O)c3ccccc3)C=O)C(O)=O"                                                                                                                           
XD2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cn1c(nnn1)SCC2=C(N[C@H](SC2)[C@@H](C=O)NC(=O)[C@@H](c3ccccc3)O)C(=O)O"                                                                                                                    
XD2 SMILES           "OpenEye OEToolkits" 1.7.6 "Cn1c(nnn1)SCC2=C(NC(SC2)C(C=O)NC(=O)C(c3ccccc3)O)C(=O)O"                                                                                                                                  
# 
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 
XD2 "SYSTEMATIC NAME" ACDLabs              12.01 "(2R)-2-[(1R)-1-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-2-oxoethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid"                  
XD2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-5-[(1-methyl-1,2,3,4-tetrazol-5-yl)sulfanylmethyl]-2-[(1R)-2-oxidanylidene-1-[[(2R)-2-oxidanyl-2-phenyl-ethanoyl]amino]ethyl]-3,6-dihydro-2H-1,3-thiazine-4-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 
XD2 "Create component"     2010-06-09 RCSB 
XD2 "Modify aromatic_flag" 2011-06-04 RCSB 
XD2 "Modify descriptor"    2011-06-04 RCSB 
XD2 "Other modification"   2012-05-16 RCSB 
XD2 "Modify synonyms"      2021-03-13 RCSB 
XD2 "Modify PCM"           2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      XD2 
_pdbx_chem_comp_synonyms.name         "Cefamandole, bound form" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            XD2 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_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               CAL 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
