data_VPP
#

_chem_comp.id                                   VPP
_chem_comp.name                                 "(2S,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C23 H29 N5 O8 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(5S)-Penicilloic Acid"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2013-07-18
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       535.570
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VPP
_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       4KQQ
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
VPP  S    S    S  0  1  N  N  N   -7.297   5.636  24.052   5.074  -1.254  -1.498  S    VPP   1  
VPP  O01  O01  O  0  1  N  N  N   -4.489   3.620  23.416   3.610  -3.061  -0.054  O01  VPP   2  
VPP  O02  O02  O  0  1  N  N  N   -7.923   4.789  19.678   5.859  -0.292   2.462  O02  VPP   3  
VPP  O03  O03  O  0  1  N  N  N   -9.791   5.857  19.940   7.563   0.984   1.866  O03  VPP   4  
VPP  O06  O06  O  0  1  N  N  N   -2.419   6.896  24.607  -0.227  -1.382  -0.930  O06  VPP   5  
VPP  O04  O04  O  0  1  N  N  N    0.406   9.686  21.863  -3.199   0.867   1.774  O04  VPP   6  
VPP  O05  O05  O  0  1  N  N  N    1.159   7.674  25.271  -5.538   1.016   2.012  O05  VPP   7  
VPP  O    O    O  0  1  N  N  N    3.523   7.861  26.511  -8.013   0.145   1.235  O    VPP   8  
VPP  N02  N02  N  0  1  N  N  N   -6.622   6.193  21.630   4.280   0.265   0.427  N02  VPP   9  
VPP  N03  N03  N  0  1  N  N  N   -3.836   6.931  22.727   1.395  -0.116  -0.100  N03  VPP  10  
VPP  N04  N04  N  0  1  N  N  N   -0.517   8.377  23.515  -2.294  -0.036  -0.042  N04  VPP  11  
VPP  N01  N01  N  0  1  N  N  N    1.883   9.026  23.533  -4.589  -0.147   0.371  N01  VPP  12  
VPP  N    N    N  0  1  N  N  N    4.534   8.640  24.581  -7.081  -1.376  -0.096  N    VPP  13  
VPP  C17  C17  C  0  1  N  N  S   -6.144   6.442  22.964   3.713  -0.181  -0.876  C17  VPP  14  
VPP  C19  C19  C  0  1  N  N  N   -8.641   5.531  22.910   6.420  -0.233  -0.776  C19  VPP  15  
VPP  C18  C18  C  0  1  N  N  S   -8.107   6.176  21.632   5.698   0.611   0.291  C18  VPP  16  
VPP  C20  C20  C  0  1  N  N  R   -4.737   5.959  23.240   2.427  -0.984  -0.673  C20  VPP  17  
VPP  C01  C01  C  0  1  N  N  N   -4.441   4.616  22.650   2.695  -2.132   0.266  C01  VPP  18  
VPP  C02  C02  C  0  1  N  N  N   -9.023   4.110  22.708   7.486  -1.123  -0.134  C02  VPP  19  
VPP  C03  C03  C  0  1  N  N  N   -9.833   6.352  23.454   7.045   0.668  -1.844  C03  VPP  20  
VPP  C04  C04  C  0  1  N  N  N   -8.627   5.578  20.351   6.379   0.401   1.619  C04  VPP  21  
VPP  C21  C21  C  0  1  N  N  N   -2.688   7.344  23.502   0.092  -0.404  -0.288  C21  VPP  22  
VPP  CA   CA   C  0  1  N  N  R   -1.821   8.396  22.893  -0.970   0.489   0.301  CA   VPP  23  
VPP  C05  C05  C  0  1  Y  N  N   -2.536   9.714  23.002  -0.821   1.881  -0.256  C05  VPP  24  
VPP  C06  C06  C  0  1  N  N  N    0.582   9.070  22.901  -3.355   0.251   0.739  C06  VPP  25  
VPP  C07  C07  C  0  1  Y  N  N   -3.150  10.247  21.841  -1.321   2.181  -1.510  C07  VPP  26  
VPP  C08  C08  C  0  1  Y  N  N   -2.604  10.402  24.221  -0.190   2.860   0.488  C08  VPP  27  
VPP  C09  C09  C  0  1  N  N  N    3.006   9.764  22.902  -4.761  -0.994  -0.810  C09  VPP  28  
VPP  C10  C10  C  0  1  N  N  N    4.387   9.073  23.175  -5.860  -2.026  -0.573  C10  VPP  29  
VPP  C11  C11  C  0  1  N  N  N    2.085   8.288  24.746  -5.661   0.232   1.095  C11  VPP  30  
VPP  C12  C12  C  0  1  Y  N  N   -3.838  11.474  21.921  -1.184   3.458  -2.021  C12  VPP  31  
VPP  C13  C13  C  0  1  Y  N  N   -3.282  11.636  24.285  -0.054   4.137  -0.023  C13  VPP  32  
VPP  C14  C14  C  0  1  N  N  N    3.400   8.248  25.354  -7.006  -0.329   0.752  C14  VPP  33  
VPP  C15  C15  C  0  1  N  N  N    5.887   8.606  25.151  -8.388  -1.857  -0.549  C15  VPP  34  
VPP  C16  C16  C  0  1  Y  N  N   -3.903  12.172  23.135  -0.549   4.435  -1.278  C16  VPP  35  
VPP  C    C    C  0  1  N  N  N    6.560   7.327  24.709  -8.787  -1.120  -1.829  C    VPP  36  
VPP  O07  O07  O  0  1  N  N  N   -4.133   4.472  21.419   2.086  -2.217   1.306  O07  VPP  37  
VPP  H1   H1   H  0  1  N  N  N   -4.271   2.834  22.929   3.747  -3.779   0.579  H1   VPP  38  
VPP  H2   H2   H  0  1  N  N  N   -9.961   5.392  19.129   7.961   0.820   2.732  H2   VPP  39  
VPP  H3   H3   H  0  1  N  N  N   -6.279   5.309  21.312   4.146  -0.437   1.139  H3   VPP  40  
VPP  H5   H5   H  0  1  N  N  N   -3.997   7.331  21.825   1.649   0.666   0.414  H5   VPP  41  
VPP  H6   H6   H  0  1  N  N  N   -0.379   7.882  24.373  -2.408  -0.589  -0.830  H6   VPP  42  
VPP  H7   H7   H  0  1  N  N  N   -6.207   7.516  23.194   3.545   0.665  -1.542  H7   VPP  43  
VPP  H8   H8   H  0  1  N  N  N   -8.440   7.224  21.649   5.779   1.664   0.021  H8   VPP  44  
VPP  H9   H9   H  0  1  N  N  N   -4.610   5.890  24.330   2.085  -1.371  -1.632  H9   VPP  45  
VPP  H10  H10  H  0  1  N  N  N   -9.400   3.693  23.654   8.241  -0.499   0.343  H10  VPP  46  
VPP  H11  H11  H  0  1  N  N  N   -9.809   4.047  21.941   7.020  -1.766   0.614  H11  VPP  47  
VPP  H12  H12  H  0  1  N  N  N   -8.143   3.537  22.379   7.955  -1.740  -0.901  H12  VPP  48  
VPP  H13  H13  H  0  1  N  N  N  -10.213   5.883  24.374   6.276   1.311  -2.272  H13  VPP  49  
VPP  H14  H14  H  0  1  N  N  N   -9.501   7.377  23.676   7.822   1.282  -1.390  H14  VPP  50  
VPP  H15  H15  H  0  1  N  N  N  -10.633   6.380  22.700   7.481   0.051  -2.629  H15  VPP  51  
VPP  H16  H16  H  0  1  N  N  N   -1.704   8.163  21.824  -0.860   0.517   1.385  H16  VPP  52  
VPP  H17  H17  H  0  1  N  N  N   -3.091   9.717  20.902  -1.817   1.417  -2.090  H17  VPP  53  
VPP  H18  H18  H  0  1  N  N  N   -2.140   9.990  25.105   0.196   2.627   1.470  H18  VPP  54  
VPP  H19  H19  H  0  1  N  N  N    3.033  10.786  23.309  -5.031  -0.371  -1.663  H19  VPP  55  
VPP  H20  H20  H  0  1  N  N  N    2.838   9.806  21.816  -3.824  -1.508  -1.023  H20  VPP  56  
VPP  H21  H21  H  0  1  N  N  N    4.476   8.191  22.523  -5.522  -2.747   0.171  H21  VPP  57  
VPP  H22  H22  H  0  1  N  N  N    5.191   9.786  22.939  -6.071  -2.547  -1.507  H22  VPP  58  
VPP  H23  H23  H  0  1  N  N  N   -4.318  11.879  21.042  -1.574   3.692  -3.001  H23  VPP  59  
VPP  H24  H24  H  0  1  N  N  N   -3.327  12.175  25.220   0.439   4.902   0.559  H24  VPP  60  
VPP  H25  H25  H  0  1  N  N  N    6.463   9.472  24.792  -8.333  -2.927  -0.748  H25  VPP  61  
VPP  H26  H26  H  0  1  N  N  N    5.828   8.634  26.249  -9.133  -1.669   0.225  H26  VPP  62  
VPP  H27  H27  H  0  1  N  N  N   -4.426  13.115  23.191  -0.442   5.433  -1.678  H27  VPP  63  
VPP  H28  H28  H  0  1  N  N  N    7.577   7.284  25.127  -9.760  -1.477  -2.166  H28  VPP  64  
VPP  H29  H29  H  0  1  N  N  N    5.979   6.464  25.067  -8.842  -0.049  -1.630  H29  VPP  65  
VPP  H30  H30  H  0  1  N  N  N    6.614   7.302  23.611  -8.043  -1.307  -2.603  H30  VPP  66  
#   #
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
VPP  O02  C04  DOUB  N  N   1  
VPP  O03  C04  SING  N  N   2  
VPP  C04  C18  SING  N  N   3  
VPP  O07  C01  DOUB  N  N   4  
VPP  N02  C18  SING  N  N   5  
VPP  N02  C17  SING  N  N   6  
VPP  C18  C19  SING  N  N   7  
VPP  C07  C12  DOUB  Y  N   8  
VPP  C07  C05  SING  Y  N   9  
VPP  O04  C06  DOUB  N  N  10  
VPP  C12  C16  SING  Y  N  11  
VPP  C01  C20  SING  N  N  12  
VPP  C01  O01  SING  N  N  13  
VPP  C02  C19  SING  N  N  14  
VPP  N03  C20  SING  N  N  15  
VPP  N03  C21  SING  N  N  16  
VPP  CA   C05  SING  N  N  17  
VPP  CA   C21  SING  N  N  18  
VPP  CA   N04  SING  N  N  19  
VPP  C06  N04  SING  N  N  20  
VPP  C06  N01  SING  N  N  21  
VPP  C09  C10  SING  N  N  22  
VPP  C09  N01  SING  N  N  23  
VPP  C19  C03  SING  N  N  24  
VPP  C19  S    SING  N  N  25  
VPP  C17  C20  SING  N  N  26  
VPP  C17  S    SING  N  N  27  
VPP  C05  C08  DOUB  Y  N  28  
VPP  C16  C13  DOUB  Y  N  29  
VPP  C10  N    SING  N  N  30  
VPP  C21  O06  DOUB  N  N  31  
VPP  N01  C11  SING  N  N  32  
VPP  C08  C13  SING  Y  N  33  
VPP  N    C15  SING  N  N  34  
VPP  N    C14  SING  N  N  35  
VPP  C    C15  SING  N  N  36  
VPP  C11  O05  DOUB  N  N  37  
VPP  C11  C14  SING  N  N  38  
VPP  C14  O    DOUB  N  N  39  
VPP  O01  H1   SING  N  N  40  
VPP  O03  H2   SING  N  N  41  
VPP  N02  H3   SING  N  N  42  
VPP  N03  H5   SING  N  N  43  
VPP  N04  H6   SING  N  N  44  
VPP  C17  H7   SING  N  N  45  
VPP  C18  H8   SING  N  N  46  
VPP  C20  H9   SING  N  N  47  
VPP  C02  H10  SING  N  N  48  
VPP  C02  H11  SING  N  N  49  
VPP  C02  H12  SING  N  N  50  
VPP  C03  H13  SING  N  N  51  
VPP  C03  H14  SING  N  N  52  
VPP  C03  H15  SING  N  N  53  
VPP  CA   H16  SING  N  N  54  
VPP  C07  H17  SING  N  N  55  
VPP  C08  H18  SING  N  N  56  
VPP  C09  H19  SING  N  N  57  
VPP  C09  H20  SING  N  N  58  
VPP  C10  H21  SING  N  N  59  
VPP  C10  H22  SING  N  N  60  
VPP  C12  H23  SING  N  N  61  
VPP  C13  H24  SING  N  N  62  
VPP  C15  H25  SING  N  N  63  
VPP  C15  H26  SING  N  N  64  
VPP  C16  H27  SING  N  N  65  
VPP  C    H28  SING  N  N  66  
VPP  C    H29  SING  N  N  67  
VPP  C    H30  SING  N  N  68  
#   #
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
VPP  SMILES            ACDLabs               12.01  "O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)NC(=O)N3C(=O)C(=O)N(CC)CC3"  
VPP  InChI             InChI                 1.03   "InChI=1S/C23H29N5O8S/c1-4-27-10-11-28(19(31)18(27)30)22(36)25-13(12-8-6-5-7-9-12)16(29)24-14(20(32)33)17-26-15(21(34)35)23(2,3)37-17/h5-9,13-15,17,26H,4,10-11H2,1-3H3,(H,24,29)(H,25,36)(H,32,33)(H,34,35)/t13-,14+,15+,17+/m1/s1"  
VPP  InChIKey          InChI                 1.03   OKSUEATVFIVTFV-AESZEHBQSA-N  
VPP  SMILES_CANONICAL  CACTVS                3.385  "CCN1CCN(C(=O)N[C@@H](C(=O)N[C@@H]([C@H]2N[C@@H](C(O)=O)C(C)(C)S2)C(O)=O)c3ccccc3)C(=O)C1=O"  
VPP  SMILES            CACTVS                3.385  "CCN1CCN(C(=O)N[CH](C(=O)N[CH]([CH]2N[CH](C(O)=O)C(C)(C)S2)C(O)=O)c3ccccc3)C(=O)C1=O"  
VPP  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C@@H]([C@H]3N[C@H](C(S3)(C)C)C(=O)O)C(=O)O"  
VPP  SMILES            "OpenEye OEToolkits"  1.7.6  "CCN1CCN(C(=O)C1=O)C(=O)NC(c2ccccc2)C(=O)NC(C3NC(C(S3)(C)C)C(=O)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
VPP  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2S,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid"  
VPP  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "(2S,4S)-2-[(1R)-1-[[(2R)-2-[[4-ethyl-2,3-bis(oxidanylidene)piperazin-1-yl]carbonylamino]-2-phenyl-ethanoyl]amino]-2-oxidanyl-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
VPP  "Create component"  2013-07-18  RCSB  
VPP  "Initial release"   2013-11-06  RCSB  
VPP  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VPP
_pdbx_chem_comp_synonyms.name        "(5S)-Penicilloic Acid"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
