data_PNK
#

_chem_comp.id                                   PNK
_chem_comp.name                                 "(2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAD
_chem_comp.formula                              "C16 H20 N2 O5 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "Penicillin, hydroxylated form"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2009-06-22
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       352.405
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    PNK
_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       3HUO
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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.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
PNK  C1    C1    C  0  1  N  N  R  52.098  15.372  -18.847   0.157  -0.920   0.028  C1    PNK   1  
PNK  C2    C2    C  0  1  N  N  N  51.806  13.869  -18.966   0.041  -2.322   0.570  C2    PNK   2  
PNK  C3    C3    C  0  1  Y  N  N  56.578  19.028  -18.280  -5.313  -0.113   0.750  C3    PNK   3  
PNK  C4    C4    C  0  1  N  N  R  51.530  16.217  -20.027   1.579  -0.403   0.253  C4    PNK   4  
PNK  C5    C5    C  0  1  N  N  S  49.422  16.490  -21.234   3.178   1.253  -0.542  C5    PNK   5  
PNK  C6    C6    C  0  1  N  N  N  50.194  15.632  -22.328   4.015  -0.000  -0.864  C6    PNK   6  
PNK  C7    C7    C  0  1  Y  N  N  57.070  20.063  -19.066  -6.548  -0.198   0.134  C7    PNK   7  
PNK  C8    C8    C  0  1  Y  N  N  56.980  19.980  -20.447  -6.866   0.663  -0.899  C8    PNK   8  
PNK  C9    C9    C  0  1  N  N  N  49.349  17.958  -21.549   3.723   1.893   0.709  C9    PNK   9  
PNK  C10   C10   C  0  1  Y  N  N  56.405  18.868  -21.046  -5.949   1.609  -1.317  C10   PNK  10  
PNK  C11   C11   C  0  1  Y  N  N  55.916  17.834  -20.254  -4.714   1.694  -0.702  C11   PNK  11  
PNK  C12   C12   C  0  1  N  N  N  49.578  14.242  -22.411   4.578   0.079  -2.284  C12   PNK  12  
PNK  N1    N1    N  0  1  N  N  N  50.045  16.230  -19.905   1.758   0.953  -0.339  N1    PNK  13  
PNK  O1    O1    O  0  1  N  N  N  48.389  18.328  -22.260   4.816   2.671   0.643  O1    PNK  14  
PNK  O2    O2    O  0  1  N  N  N  50.207  18.700  -21.051   3.177   1.707   1.770  O2    PNK  15  
PNK  O3    O3    O  0  1  N  N  N  52.764  13.079  -18.708   0.369  -3.369  -0.203  O3    PNK  16  
PNK  O4    O4    O  0  1  N  N  N  50.638  13.540  -19.249  -0.348  -2.502   1.699  O4    PNK  17  
PNK  O5    O5    O  0  1  N  N  N  53.244  17.624  -17.691  -2.430  -0.621  -0.667  O5    PNK  18  
PNK  C16   C16   C  0  1  Y  N  N  56.000  17.918  -18.875  -4.396   0.834   0.332  C16   PNK  19  
PNK  C15   C15   C  0  1  N  N  N  55.477  16.788  -18.006  -3.050   0.927   1.003  C15   PNK  20  
PNK  C14   C14   C  0  1  N  N  N  53.968  16.710  -18.113  -2.071   0.030   0.291  C14   PNK  21  
PNK  N2    N2    N  0  1  N  N  N  53.522  15.610  -18.683  -0.795  -0.048   0.720  N2    PNK  22  
PNK  S1    S1    S  0  1  N  N  N  51.895  15.532  -21.679   2.802  -1.373  -0.724  S1    PNK  23  
PNK  C13   C13   C  0  1  N  N  N  50.166  16.333  -23.693   5.144  -0.170   0.154  C13   PNK  24  
PNK  H1    H1    H  0  1  N  N  N  51.567  15.712  -17.946  -0.063  -0.924  -1.040  H1    PNK  25  
PNK  H3    H3    H  0  1  N  N  N  56.646  19.089  -17.204  -5.066  -0.782   1.561  H3    PNK  26  
PNK  H4    H4    H  0  1  N  N  N  52.001  17.208  -19.955   1.832  -0.405   1.313  H4    PNK  27  
PNK  H5    H5    H  0  1  N  N  N  48.371  16.167  -21.227   3.271   1.959  -1.367  H5    PNK  28  
PNK  H7    H7    H  0  1  N  N  N  57.521  20.928  -18.603  -7.264  -0.938   0.461  H7    PNK  29  
PNK  H8    H8    H  0  1  N  N  N  57.359  20.785  -21.060  -7.830   0.595  -1.381  H8    PNK  30  
PNK  H10   H10   H  0  1  N  N  N  56.337  18.806  -22.122  -6.198   2.282  -2.125  H10   PNK  31  
PNK  H11   H11   H  0  1  N  N  N  55.471  16.965  -20.716  -3.998   2.434  -1.029  H11   PNK  32  
PNK  H12   H12   H  0  1  N  N  N  49.429  13.969  -23.466   5.214   0.960  -2.374  H12   PNK  33  
PNK  H12A  H12A  H  0  0  N  N  N  50.251  13.514  -21.935   5.166  -0.816  -2.492  H12A  PNK  34  
PNK  H12B  H12B  H  0  0  N  N  N  48.608  14.239  -21.892   3.757   0.148  -2.997  H12B  PNK  35  
PNK  HN1   HN1   H  0  1  N  N  N  49.735  15.343  -19.564   1.242   1.041  -1.202  HN1   PNK  36  
PNK  HO1   HO1   H  0  1  N  N  N  48.416  19.272  -22.363   5.128   3.059   1.472  HO1   PNK  37  
PNK  HO3   HO3   H  0  1  N  N  N  52.458  12.181  -18.762   0.278  -4.249   0.189  HO3   PNK  38  
PNK  H15   H15   H  0  1  N  N  N  55.915  15.837  -18.343  -2.695   1.957   0.964  H15   PNK  39  
PNK  H15A  H15A  H  0  0  N  N  N  55.756  16.977  -16.959  -3.141   0.614   2.043  H15A  PNK  40  
PNK  HN2   HN2   H  0  1  N  N  N  54.175  14.926  -19.009  -0.508   0.472   1.486  HN2   PNK  41  
PNK  H13   H13   H  0  1  N  N  N  50.159  17.423  -23.546   4.721  -0.275   1.153  H13   PNK  42  
PNK  H13A  H13A  H  0  0  N  N  N  51.057  16.047  -24.270   5.723  -1.060  -0.091  H13A  PNK  43  
PNK  H13B  H13B  H  0  0  N  N  N  49.261  16.032  -24.241   5.794   0.705   0.125  H13B  PNK  44  
#   #
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
PNK  C1   C2    SING  N  N   1  
PNK  C1   C4    SING  N  N   2  
PNK  C1   N2    SING  N  N   3  
PNK  C2   O3    SING  N  N   4  
PNK  C2   O4    DOUB  N  N   5  
PNK  C3   C7    DOUB  Y  N   6  
PNK  C3   C16   SING  Y  N   7  
PNK  C4   N1    SING  N  N   8  
PNK  C4   S1    SING  N  N   9  
PNK  C5   C6    SING  N  N  10  
PNK  C5   C9    SING  N  N  11  
PNK  C5   N1    SING  N  N  12  
PNK  C6   C12   SING  N  N  13  
PNK  C6   S1    SING  N  N  14  
PNK  C6   C13   SING  N  N  15  
PNK  C7   C8    SING  Y  N  16  
PNK  C8   C10   DOUB  Y  N  17  
PNK  C9   O1    SING  N  N  18  
PNK  C9   O2    DOUB  N  N  19  
PNK  C10  C11   SING  Y  N  20  
PNK  C11  C16   DOUB  Y  N  21  
PNK  O5   C14   DOUB  N  N  22  
PNK  C16  C15   SING  N  N  23  
PNK  C15  C14   SING  N  N  24  
PNK  C14  N2    SING  N  N  25  
PNK  C1   H1    SING  N  N  26  
PNK  C3   H3    SING  N  N  27  
PNK  C4   H4    SING  N  N  28  
PNK  C5   H5    SING  N  N  29  
PNK  C7   H7    SING  N  N  30  
PNK  C8   H8    SING  N  N  31  
PNK  C10  H10   SING  N  N  32  
PNK  C11  H11   SING  N  N  33  
PNK  C12  H12   SING  N  N  34  
PNK  C12  H12A  SING  N  N  35  
PNK  C12  H12B  SING  N  N  36  
PNK  N1   HN1   SING  N  N  37  
PNK  O1   HO1   SING  N  N  38  
PNK  O3   HO3   SING  N  N  39  
PNK  C15  H15   SING  N  N  40  
PNK  C15  H15A  SING  N  N  41  
PNK  N2   HN2   SING  N  N  42  
PNK  C13  H13   SING  N  N  43  
PNK  C13  H13A  SING  N  N  44  
PNK  C13  H13B  SING  N  N  45  
#   #
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
PNK  SMILES            ACDLabs               10.04  "O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)Cc2ccccc2"  
PNK  SMILES_CANONICAL  CACTVS                3.341  "CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)Cc2ccccc2)C(O)=O"  
PNK  SMILES            CACTVS                3.341  "CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)Cc2ccccc2)C(O)=O"  
PNK  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)Cc2ccccc2)C(=O)O)C"  
PNK  SMILES            "OpenEye OEToolkits"  1.5.0  "CC1(C(NC(S1)C(C(=O)O)NC(=O)Cc2ccccc2)C(=O)O)C"  
PNK  InChI             InChI                 1.03   "InChI=1S/C16H20N2O5S/c1-16(2)12(15(22)23)18-13(24-16)11(14(20)21)17-10(19)8-9-6-4-3-5-7-9/h3-7,11-13,18H,8H2,1-2H3,(H,17,19)(H,20,21)(H,22,23)/t11-,12-,13+/m0/s1"  
PNK  InChIKey          InChI                 1.03   HCYWNSXLUZRKJX-RWMBFGLXSA-N  
#   #
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
PNK  "SYSTEMATIC NAME"  ACDLabs               10.04  "(2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid"  
PNK  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2R,4S)-2-[(1R)-2-hydroxy-2-oxo-1-(2-phenylethanoylamino)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
PNK  "Create component"      2009-06-22  PDBJ  
PNK  "Modify aromatic_flag"  2011-06-04  RCSB  
PNK  "Modify descriptor"     2011-06-04  RCSB  
PNK  "Modify synonyms"       2012-05-10  RCSB  
PNK  "Modify synonyms"       2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     PNK
_pdbx_chem_comp_synonyms.name        "Penicillin, hydroxylated form"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
