data_VBP
#

_chem_comp.id                                   VBP
_chem_comp.name                                 "4-({3-[(2R)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H15 N3 O6"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(S)-1-(2-amino-2-carboxyethyl)-3-(4-carboxybenzyl)pyrimidine-2,4-dione"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2009-04-09
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       333.296
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VBP
_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       3H06
_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
VBP  C10   C10   C  0  1  N  N  N  4.362  16.551  12.352  -0.848   1.151  -1.642  C1   VBP   1  
VBP  C11   C11   C  0  1  Y  N  N  4.223  15.144  11.802  -2.075   0.516  -1.041  C2   VBP   2  
VBP  C12   C12   C  0  1  Y  N  N  5.294  14.097  12.151  -3.058   1.311  -0.480  C3   VBP   3  
VBP  C13   C13   C  0  1  Y  N  N  5.189  12.667  11.600  -4.184   0.736   0.071  C4   VBP   4  
VBP  C14   C14   C  0  1  Y  N  N  4.006  12.282  10.690  -4.331  -0.652   0.062  C5   VBP   5  
VBP  C15   C15   C  0  1  Y  N  N  2.922  13.339  10.333  -3.335  -1.449  -0.506  C6   VBP   6  
VBP  C16   C16   C  0  1  Y  N  N  3.024  14.783  10.890  -2.216  -0.861  -1.059  C7   VBP   7  
VBP  C17   C17   C  0  1  N  N  N  3.913  10.857  10.153  -5.534  -1.275   0.651  C8   VBP   8  
VBP  C20   C20   C  0  1  N  N  N  5.323  17.669  10.163   1.071   0.285  -0.421  C9   VBP   9  
VBP  C22   C22   C  0  1  N  N  N  7.290  18.798   5.752   5.224  -1.567   0.079  C10  VBP  10  
VBP  N01   N01   N  0  1  N  N  N  7.814  16.969   7.291   4.774   0.821   0.067  N1   VBP  11  
VBP  C02   C02   C  0  1  N  N  R  7.596  18.410   7.207   4.195  -0.502  -0.200  C11  VBP  12  
VBP  C03   C03   C  0  1  N  N  N  6.404  18.792   8.104   2.979  -0.719   0.703  C12  VBP  13  
VBP  N04   N04   N  0  1  N  N  N  6.446  18.443   9.504   2.031   0.383   0.517  N2   VBP  14  
VBP  C05   C05   C  0  1  N  N  N  7.626  18.862  10.306   2.129   1.501   1.300  C13  VBP  15  
VBP  C06   C06   C  0  1  N  N  N  7.704  18.510  11.767   1.255   2.516   1.128  C14  VBP  16  
VBP  C07   C07   C  0  1  N  N  N  6.574  17.719  12.432   0.250   2.400   0.138  C15  VBP  17  
VBP  O08   O08   O  0  1  N  N  N  6.636  17.374  13.789  -0.549   3.303  -0.036  O1   VBP  18  
VBP  N09   N09   N  0  1  N  N  N  5.398  17.305  11.640   0.187   1.282  -0.613  N3   VBP  19  
VBP  O18   O18   O  0  1  N  N  N  4.281  10.748   9.026  -5.672  -2.615   0.640  O2   VBP  20  
VBP  O19   O19   O  0  1  N  N  N  2.740  10.039  10.153  -6.398  -0.579   1.144  O3   VBP  21  
VBP  O21   O21   O  0  1  N  N  N  4.209  17.276   9.423   1.006  -0.715  -1.109  O4   VBP  22  
VBP  O23   O23   O  0  1  N  N  N  6.392  18.255   5.216   5.086  -2.790  -0.456  O5   VBP  23  
VBP  O24   O24   O  0  1  N  N  N  7.545  20.205   5.752   6.173  -1.320   0.785  O6   VBP  24  
VBP  H10   H10   H  0  1  N  N  N  3.401  17.073  12.237  -0.476   0.527  -2.454  H1   VBP  25  
VBP  H10A  H10A  H  0  0  N  N  N  4.650  16.482  13.411  -1.102   2.138  -2.029  H2   VBP  26  
VBP  H12   H12   H  0  1  N  N  N  6.124  14.368  12.787  -2.943   2.385  -0.474  H3   VBP  27  
VBP  H13   H13   H  0  1  N  N  N  5.942  11.934  11.849  -4.951   1.359   0.509  H4   VBP  28  
VBP  H15   H15   H  0  1  N  N  N  2.095  13.066   9.695  -3.442  -2.524  -0.516  H5   VBP  29  
VBP  H16   H16   H  0  1  N  N  N  2.274  15.522  10.647  -1.445  -1.476  -1.498  H6   VBP  30  
VBP  HN01  HN01  H  0  0  N  N  N  7.864  16.585   6.369   5.068   0.899   1.030  H7   VBP  31  
VBP  HN0A  HN0A  H  0  0  N  N  N  8.671  16.789   7.774   5.540   1.014  -0.561  H8   VBP  32  
VBP  H02   H02   H  0  1  N  N  N  8.498  18.943   7.543   3.887  -0.560  -1.244  H9   VBP  33  
VBP  H03   H03   H  0  1  N  N  N  6.318  19.888   8.058   2.496  -1.661   0.443  H10  VBP  34  
VBP  H03A  H03A  H  0  0  N  N  N  5.564  18.206   7.703   3.300  -0.750   1.744  H11  VBP  35  
VBP  H05   H05   H  0  1  N  N  N  8.426  19.418   9.840   2.902   1.571   2.051  H12  VBP  36  
VBP  H06   H06   H  0  1  N  N  N  8.561  18.817  12.349   1.321   3.404   1.740  H13  VBP  37  
VBP  HO18  HO18  H  0  0  N  N  N  3.686  10.179   8.552  -6.476  -2.977   1.037  H14  VBP  38  
VBP  HO23  HO23  H  0  0  N  N  N  5.850  18.899   4.775   5.772  -3.440  -0.248  H15  VBP  39  
#   #
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
VBP  C11  C10   SING  N  N   1  
VBP  C11  C12   SING  Y  N   2  
VBP  C13  C12   DOUB  Y  N   3  
VBP  C14  C13   SING  Y  N   4  
VBP  C15  C14   DOUB  Y  N   5  
VBP  C15  C16   SING  Y  N   6  
VBP  C16  C11   DOUB  Y  N   7  
VBP  C17  C14   SING  N  N   8  
VBP  C17  O19   DOUB  N  N   9  
VBP  C20  N09   SING  N  N  10  
VBP  C22  C02   SING  N  N  11  
VBP  C02  N01   SING  N  N  12  
VBP  C02  C03   SING  N  N  13  
VBP  C03  N04   SING  N  N  14  
VBP  N04  C20   SING  N  N  15  
VBP  N04  C05   SING  N  N  16  
VBP  C05  C06   DOUB  N  N  17  
VBP  C06  C07   SING  N  N  18  
VBP  C07  O08   DOUB  N  N  19  
VBP  N09  C10   SING  N  N  20  
VBP  N09  C07   SING  N  N  21  
VBP  O18  C17   SING  N  N  22  
VBP  O21  C20   DOUB  N  N  23  
VBP  O23  C22   SING  N  N  24  
VBP  O24  C22   DOUB  N  N  25  
VBP  C10  H10   SING  N  N  26  
VBP  C10  H10A  SING  N  N  27  
VBP  C12  H12   SING  N  N  28  
VBP  C13  H13   SING  N  N  29  
VBP  C15  H15   SING  N  N  30  
VBP  C16  H16   SING  N  N  31  
VBP  N01  HN01  SING  N  N  32  
VBP  N01  HN0A  SING  N  N  33  
VBP  C02  H02   SING  N  N  34  
VBP  C03  H03   SING  N  N  35  
VBP  C03  H03A  SING  N  N  36  
VBP  C05  H05   SING  N  N  37  
VBP  C06  H06   SING  N  N  38  
VBP  O18  HO18  SING  N  N  39  
VBP  O23  HO23  SING  N  N  40  
#   #
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
VBP  SMILES            ACDLabs               10.04  "O=C(O)c1ccc(cc1)CN2C(=O)C=CN(C2=O)CC(N)C(=O)O"  
VBP  SMILES_CANONICAL  CACTVS                3.341  "N[C@H](CN1C=CC(=O)N(Cc2ccc(cc2)C(O)=O)C1=O)C(O)=O"  
VBP  SMILES            CACTVS                3.341  "N[CH](CN1C=CC(=O)N(Cc2ccc(cc2)C(O)=O)C1=O)C(O)=O"  
VBP  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1cc(ccc1CN2C(=O)C=CN(C2=O)C[C@H](C(=O)O)N)C(=O)O"  
VBP  SMILES            "OpenEye OEToolkits"  1.5.0  "c1cc(ccc1CN2C(=O)C=CN(C2=O)CC(C(=O)O)N)C(=O)O"  
VBP  InChI             InChI                 1.03   "InChI=1S/C15H15N3O6/c16-11(14(22)23)8-17-6-5-12(19)18(15(17)24)7-9-1-3-10(4-2-9)13(20)21/h1-6,11H,7-8,16H2,(H,20,21)(H,22,23)/t11-/m1/s1"  
VBP  InChIKey          InChI                 1.03   XLRLZPOBHPIDFX-LLVKDONJSA-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
VBP  "SYSTEMATIC NAME"  ACDLabs               10.04  "4-({3-[(2R)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid"  
VBP  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "4-[[3-[(2R)-2-amino-3-hydroxy-3-oxo-propyl]-2,6-dioxo-pyrimidin-1-yl]methyl]benzoic 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
VBP  "Create component"      2009-04-09  RCSB  
VBP  "Modify aromatic_flag"  2011-06-04  RCSB  
VBP  "Modify descriptor"     2011-06-04  RCSB  
VBP  "Modify synonyms"       2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VBP
_pdbx_chem_comp_synonyms.name        "(S)-1-(2-amino-2-carboxyethyl)-3-(4-carboxybenzyl)pyrimidine-2,4-dione"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
