data_XD1
# 
_chem_comp.id                                    XD1 
_chem_comp.name                                  "(2R,4S)-2-[(1R)-1-amino-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C8 H14 N2 O3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "6-aminopenicillian, bound form" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2010-06-08 
_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                        218.273 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XD1 
_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        3N6I 
_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 
XD1 C    C    C 0 1 N N N N N N -11.712 -11.275 5.361 2.816  0.167  1.037  C    XD1 1  
XD1 N    N    N 0 1 N N N N N N -10.421 -11.930 3.422 3.049  0.886  -1.272 N    XD1 2  
XD1 O    O    O 0 1 N N N N N N -12.531 -10.799 4.231 3.747  -0.564 0.798  O    XD1 3  
XD1 CA   CA   C 0 1 N N R N N N -10.464 -11.688 4.906 2.275  1.074  -0.038 CA   XD1 4  
XD1 CB   CB   C 0 1 N N R N N N -9.545  -10.474 5.312 0.806  0.734  -0.300 CB   XD1 5  
XD1 CAA  CAA  C 0 1 N N N N N N -7.817  -7.532  4.730 -2.121 -1.086 -1.242 CAA  XD1 6  
XD1 CAB  CAB  C 0 1 N N N N N N -8.064  -8.255  2.283 -1.325 -2.441 0.721  CAB  XD1 7  
XD1 OAE  OAE  O 0 1 N N N N N N -10.572 -6.845  5.276 -3.607 0.682  0.385  OAE  XD1 8  
XD1 OAF  OAF  O 0 1 N N N N N N -10.694 -6.303  3.283 -1.985 2.007  -0.320 OAF  XD1 9  
XD1 NAH  NAH  N 0 1 N N N N N N -10.307 -9.232  5.139 0.002  0.830  0.950  NAH  XD1 10 
XD1 SAI  SAI  S 0 1 N N N N N N -8.042  -10.247 4.324 0.601  -1.049 -0.711 SAI  XD1 11 
XD1 CAJ  CAJ  C 0 1 N N N N N N -10.457 -7.049  4.172 -2.308 0.995  0.255  CAJ  XD1 12 
XD1 CAM  CAM  C 0 1 N N S N N N -9.966  -8.474  3.927 -1.253 0.082  0.825  CAM  XD1 13 
XD1 CAN  CAN  C 0 1 N N N N N N -8.443  -8.527  3.754 -1.123 -1.156 -0.085 CAN  XD1 14 
XD1 HA   HA   H 0 1 N N N N N N -12.034 -11.299 6.392 2.369  0.168  2.020  HA   XD1 15 
XD1 HN   HN   H 0 1 N N N N N N -9.502  -12.223 3.158 2.990  -0.069 -1.594 HN   XD1 16 
XD1 HNA  HNA  H 0 1 N N N N N N -11.080 -12.643 3.181 2.747  1.528  -1.989 HNA  XD1 17 
XD1 HAA  HAA  H 0 1 N N N N N N -10.120 -12.587 5.439 2.355  2.111  0.287  HAA  XD1 18 
XD1 HB   HB   H 0 1 N N N N N N -9.223  -10.594 6.357 0.393  1.368  -1.084 HB   XD1 19 
XD1 HAAA HAAA H 0 0 N N N N N N -8.125  -7.781  5.756 -3.137 -1.086 -0.846 HAAA XD1 20 
XD1 HAAB HAAB H 0 0 N N N N N N -6.721  -7.584  4.654 -1.954 -0.171 -1.811 HAAB XD1 21 
XD1 HAAC HAAC H 0 0 N N N N N N -8.154  -6.514  4.482 -1.985 -1.949 -1.893 HAAC XD1 22 
XD1 HAB  HAB  H 0 1 N N N N N N -8.545  -9.003  1.636 -1.188 -3.304 0.069  HAB  XD1 23 
XD1 HABA HABA H 0 0 N N N N N N -8.405  -7.249  1.997 -0.598 -2.479 1.532  HABA XD1 24 
XD1 HABB HABB H 0 0 N N N N N N -6.972  -8.319  2.168 -2.333 -2.455 1.136  HABB XD1 25 
XD1 HOAE HOAE H 0 0 N N N N N N -10.897 -5.961  5.403 -4.247 1.298  0.003  HOAE XD1 26 
XD1 HNAH HNAH H 0 0 N N N N N N -11.279 -9.464  5.099 0.533  0.514  1.748  HNAH XD1 27 
XD1 HAM  HAM  H 0 1 N N N N N N -10.462 -8.900  3.042 -1.569 -0.244 1.816  HAM  XD1 28 
# 
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 
XD1 O   C    DOUB N N 1  
XD1 CA  C    SING N N 2  
XD1 C   HA   SING N N 3  
XD1 N   CA   SING N N 4  
XD1 N   HN   SING N N 5  
XD1 N   HNA  SING N N 6  
XD1 CA  CB   SING N N 7  
XD1 CA  HAA  SING N N 8  
XD1 SAI CB   SING N N 9  
XD1 NAH CB   SING N N 10 
XD1 CB  HB   SING N N 11 
XD1 CAN CAA  SING N N 12 
XD1 CAA HAAA SING N N 13 
XD1 CAA HAAB SING N N 14 
XD1 CAA HAAC SING N N 15 
XD1 CAB CAN  SING N N 16 
XD1 CAB HAB  SING N N 17 
XD1 CAB HABA SING N N 18 
XD1 CAB HABB SING N N 19 
XD1 CAJ OAE  SING N N 20 
XD1 OAE HOAE SING N N 21 
XD1 OAF CAJ  DOUB N N 22 
XD1 CAM NAH  SING N N 23 
XD1 NAH HNAH SING N N 24 
XD1 CAN SAI  SING N N 25 
XD1 CAM CAJ  SING N N 26 
XD1 CAN CAM  SING N N 27 
XD1 CAM HAM  SING N N 28 
# 
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 
XD1 SMILES           ACDLabs              12.01 "O=C(O)C1NC(SC1(C)C)C(N)C=O"                                                                           
XD1 InChI            InChI                1.03  "InChI=1S/C8H14N2O3S/c1-8(2)5(7(12)13)10-6(14-8)4(9)3-11/h3-6,10H,9H2,1-2H3,(H,12,13)/t4-,5+,6-/m1/s1" 
XD1 InChIKey         InChI                1.03  SVTWYXMNISTMAS-NGJCXOISSA-N                                                                            
XD1 SMILES_CANONICAL CACTVS               3.370 "CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](N)C=O"                                                              
XD1 SMILES           CACTVS               3.370 "CC1(C)S[CH](N[CH]1C(O)=O)[CH](N)C=O"                                                                  
XD1 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1([C@@H](N[C@H](S1)[C@@H](C=O)N)C(=O)O)C"                                                           
XD1 SMILES           "OpenEye OEToolkits" 1.7.6 "CC1(C(NC(S1)C(C=O)N)C(=O)O)C"                                                                         
# 
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 
XD1 "SYSTEMATIC NAME" ACDLabs              12.01 "(2R,4S)-2-[(1R)-1-amino-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid"             
XD1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R,4S)-2-[(1R)-1-azanyl-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidine-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 
XD1 "Create component"  2010-06-08 RCSB 
XD1 "Modify descriptor" 2011-06-04 RCSB 
XD1 "Modify synonyms"   2012-03-22 RCSB 
XD1 "Modify synonyms"   2021-03-13 RCSB 
XD1 "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      XD1 
_pdbx_chem_comp_synonyms.name         "6-aminopenicillian, 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                            XD1 
_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               C 
_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      ? 
# 
