data_VB4
#

_chem_comp.id                                   VB4
_chem_comp.name                                 "(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C19 H20 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-07-22
_chem_comp.pdbx_modified_date                   2021-01-29
_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                       433.352
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VB4
_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       6XOY
_chem_comp.pdbx_subcomponent_list               "PLP TRP"
_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
VB4  N03   N1   N  0  1  Y  N  N   -7.178  -12.990  11.798  -2.847   2.938   1.518  N1    PLP   1  
VB4  C02   C10  C  0  1  Y  N  N   -7.407  -12.287  10.708  -1.671   3.530   1.468  C2    PLP   2  
VB4  C01   C9   C  0  1  N  N  N   -6.364  -12.267   9.595  -1.481   4.863   2.145  C2A   PLP   3  
VB4  C29   C19  C  0  1  Y  N  N   -8.576  -11.565  10.527  -0.607   2.942   0.801  C3    PLP   4  
VB4  O30   O7   O  0  1  N  N  N   -8.791  -10.833   9.354   0.603   3.556   0.754  O3    PLP   5  
VB4  C12   C14  C  0  1  Y  N  N   -9.524  -11.583  11.542  -0.802   1.699   0.176  C4    PLP   6  
VB4  C13   C1   C  0  1  N  N  N  -10.847  -10.827  11.424   0.298   1.031  -0.545  C4A   PLP   7  
VB4  C05   C12  C  0  1  Y  N  N   -9.255  -12.337  12.674  -2.070   1.113   0.259  C5    PLP   8  
VB4  C04   C11  C  0  1  Y  N  N   -8.065  -13.035  12.782  -3.070   1.772   0.944  C6    PLP   9  
VB4  C06   C13  C  0  1  N  N  N  -10.277  -12.379  13.803  -2.340  -0.219  -0.393  C5A   PLP  10  
VB4  O07   O1   O  0  1  N  N  N  -11.466  -12.937  13.314  -3.700  -0.595  -0.164  O4P   PLP  11  
VB4  P08   P1   P  0  1  N  N  N  -12.070  -14.263  14.046  -4.337  -1.965  -0.719  P     PLP  12  
VB4  O11   O4   O  0  1  N  N  N  -13.441  -14.544  13.494  -3.520  -3.111  -0.258  O1P   PLP  13  
VB4  O09   O2   O  0  1  N  N  N  -12.178  -13.966  15.540  -5.840  -2.121  -0.166  O2P   PLP  14  
VB4  O10   O3   O  0  1  N  N  N  -11.176  -15.476  13.855  -4.357  -1.934  -2.329  O3P   PLP  15  
VB4  N14   N2   N  0  1  N  N  N  -11.156  -10.167  10.398   1.463   1.589  -0.609  N     TRP  16  
VB4  C15   C2   C  0  1  N  N  R  -12.454   -9.517  10.401   2.555   0.926  -1.326  CA    TRP  17  
VB4  C26   C8   C  0  1  N  N  N  -12.511   -8.510   9.272   3.030   1.812  -2.448  C     TRP  18  
VB4  O28   O6   O  0  1  N  N  N  -12.578   -8.919   8.087   2.510   2.887  -2.631  O     TRP  19  
VB4  C16   C15  C  0  1  N  N  N  -13.516  -10.606  10.185   3.711   0.661  -0.360  CB    TRP  20  
VB4  C17   C3   C  0  1  Y  N  N  -14.967  -10.208  10.492   3.271  -0.323   0.693  CG    TRP  21  
VB4  C18   C16  C  0  1  Y  N  N  -15.953   -9.930   9.556   2.786  -0.026   1.909  CD1   TRP  22  
VB4  C21   C5   C  0  1  Y  N  N  -15.550  -10.086  11.775   3.285  -1.783   0.583  CD2   TRP  23  
VB4  N19   N3   N  0  1  Y  N  N  -17.082   -9.643  10.211   2.493  -1.177   2.588  NE1   TRP  24  
VB4  C20   C4   C  0  1  Y  N  N  -16.855   -9.730  11.561   2.787  -2.270   1.805  CE2   TRP  25  
VB4  C22   C6   C  0  1  Y  N  N  -15.061  -10.246  13.096   3.667  -2.677  -0.420  CE3   TRP  26  
VB4  C25   C18  C  0  1  Y  N  N  -17.729   -9.518  12.663   2.683  -3.644   1.999  CZ2   TRP  27  
VB4  C23   C17  C  0  1  Y  N  N  -15.922  -10.034  14.175   3.554  -4.022  -0.209  CZ3   TRP  28  
VB4  C24   C7   C  0  1  Y  N  N  -17.247   -9.674  13.952   3.068  -4.508   0.998  CH2   TRP  29  
VB4  O27   O5   O  0  1  N  N  N  -12.498   -7.281   9.523   4.032   1.406  -3.245  OXT   TRP  30  
VB4  H011  H7   H  0  0  N  N  N   -6.027  -11.233   9.427  -2.423   5.411   2.141  H2A1  PLP  31  
VB4  H012  H5   H  0  0  N  N  N   -5.505  -12.890   9.885  -1.157   4.706   3.174  H2A2  PLP  32  
VB4  H013  H6   H  0  0  N  N  N   -6.808  -12.663   8.670  -0.724   5.437   1.610  H2A3  PLP  33  
VB4  H301  H20  H  0  0  N  N  N   -9.637  -10.403   9.399   1.192   3.322   1.484  HO3   PLP  34  
VB4  H131  H1   H  0  0  N  N  N  -11.541  -10.860  12.250   0.131   0.075  -1.020  H4A   PLP  35  
VB4  H041  H8   H  0  0  N  N  N   -7.859  -13.617  13.668  -4.051   1.325   1.012  H6    PLP  36  
VB4  H061  H9   H  0  0  N  N  N   -9.891  -12.995  14.628  -2.160  -0.143  -1.465  H5A1  PLP  37  
VB4  H062  H10  H  0  0  N  N  N  -10.469  -11.359  14.166  -1.679  -0.973   0.034  H5A2  PLP  38  
VB4  H1    H17  H  0  1  N  N  N  -13.087  -14.021  15.809  -6.287  -2.927  -0.461  HOP2  PLP  39  
VB4  H2    H18  H  0  1  N  N  N  -11.666  -16.167  13.425  -4.875  -1.208  -2.701  HOP3  PLP  40  
VB4  H151  H2   H  0  0  N  N  N  -12.635   -9.012  11.361   2.199  -0.020  -1.735  HA    TRP  41  
VB4  H161  H12  H  0  0  N  N  N  -13.258  -11.459  10.830   4.557   0.249  -0.911  HB2   TRP  42  
VB4  H162  H11  H  0  0  N  N  N  -13.469  -10.916   9.131   4.009   1.595   0.116  HB3   TRP  43  
VB4  H181  H13  H  0  0  N  N  N  -15.829   -9.943   8.483   2.648   0.974   2.295  HD1   TRP  44  
VB4  H191  H16  H  0  0  N  N  N  -17.954   -9.403   9.785   2.130  -1.217   3.487  HE1   TRP  45  
VB4  H221  H3   H  0  0  N  N  N  -14.033  -10.529  13.266   4.049  -2.306  -1.360  HE3   TRP  46  
VB4  H251  H15  H  0  0  N  N  N  -18.759   -9.238  12.496   2.302  -4.032   2.932  HZ2   TRP  47  
VB4  H231  H14  H  0  0  N  N  N  -15.558  -10.150  15.185   3.849  -4.713  -0.985  HZ3   TRP  48  
VB4  H241  H4   H  0  0  N  N  N  -17.906   -9.515  14.792   2.987  -5.574   1.151  HH2   TRP  49  
VB4  H3    H19  H  0  1  N  N  N  -12.545   -6.791   8.711   4.302   2.009  -3.951  HXT   TRP  50  
#   #
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
VB4  O28  C26   DOUB  N  N   1  
VB4  C26  O27   SING  N  N   2  
VB4  C26  C15   SING  N  N   3  
VB4  O30  C29   SING  N  N   4  
VB4  C18  N19   SING  Y  N   5  
VB4  C18  C17   DOUB  Y  N   6  
VB4  C01  C02   SING  N  N   7  
VB4  C16  C15   SING  N  N   8  
VB4  C16  C17   SING  N  N   9  
VB4  N19  C20   SING  Y  N  10  
VB4  N14  C15   SING  N  N  11  
VB4  N14  C13   DOUB  N  N  12  
VB4  C17  C21   SING  Y  N  13  
VB4  C29  C02   DOUB  Y  N  14  
VB4  C29  C12   SING  Y  N  15  
VB4  C02  N03   SING  Y  N  16  
VB4  C13  C12   SING  N  N  17  
VB4  C12  C05   DOUB  Y  N  18  
VB4  C20  C21   DOUB  Y  N  19  
VB4  C20  C25   SING  Y  N  20  
VB4  C21  C22   SING  Y  N  21  
VB4  N03  C04   DOUB  Y  N  22  
VB4  C25  C24   DOUB  Y  N  23  
VB4  C05  C04   SING  Y  N  24  
VB4  C05  C06   SING  N  N  25  
VB4  C22  C23   DOUB  Y  N  26  
VB4  O07  C06   SING  N  N  27  
VB4  O07  P08   SING  N  N  28  
VB4  O11  P08   DOUB  N  N  29  
VB4  O10  P08   SING  N  N  30  
VB4  C24  C23   SING  Y  N  31  
VB4  P08  O09   SING  N  N  32  
VB4  C13  H131  SING  N  N  33  
VB4  C15  H151  SING  N  N  34  
VB4  C22  H221  SING  N  N  35  
VB4  C24  H241  SING  N  N  36  
VB4  C01  H012  SING  N  N  37  
VB4  C01  H013  SING  N  N  38  
VB4  C01  H011  SING  N  N  39  
VB4  C04  H041  SING  N  N  40  
VB4  C06  H061  SING  N  N  41  
VB4  C06  H062  SING  N  N  42  
VB4  C16  H162  SING  N  N  43  
VB4  C16  H161  SING  N  N  44  
VB4  C18  H181  SING  N  N  45  
VB4  C23  H231  SING  N  N  46  
VB4  C25  H251  SING  N  N  47  
VB4  N19  H191  SING  N  N  48  
VB4  O09  H1    SING  N  N  49  
VB4  O10  H2    SING  N  N  50  
VB4  O27  H3    SING  N  N  51  
VB4  O30  H301  SING  N  N  52  
#   #
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
VB4  SMILES            ACDLabs               12.01  "n1cc(c(c(c1C)O)[C@H]=NC(C(O)=O)Cc3c2ccccc2nc3)COP(O)(=O)O"  
VB4  InChI             InChI                 1.03   "InChI=1S/C19H20N3O7P/c1-11-18(23)15(13(8-20-11)10-29-30(26,27)28)9-22-17(19(24)25)6-12-7-21-16-5-3-2-4-14(12)16/h2-5,7-9,17,21,23H,6,10H2,1H3,(H,24,25)(H2,26,27,28)/b22-9+/t17-/m1/s1"  
VB4  InChIKey          InChI                 1.03   MFRRQHVPLFTBMS-KCBMDGGTSA-N  
VB4  SMILES_CANONICAL  CACTVS                3.385  "Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H](Cc2c[nH]c3ccccc23)C(O)=O)c1O"  
VB4  SMILES            CACTVS                3.385  "Cc1ncc(CO[P](O)(O)=O)c(C=N[CH](Cc2c[nH]c3ccccc23)C(O)=O)c1O"  
VB4  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H](Cc2c[nH]c3c2cccc3)C(=O)O)O"  
VB4  SMILES            "OpenEye OEToolkits"  2.0.7  "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(Cc2c[nH]c3c2cccc3)C(=O)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
VB4  "SYSTEMATIC NAME"  ACDLabs               12.01  "(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan"  
VB4  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{R})-3-(1~{H}-indol-3-yl)-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanoic 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
VB4  "Create component"          2020-07-22  RCSB  
VB4  "Modify subcomponent list"  2020-07-27  RCSB  
VB4  "Initial release"           2021-02-03  RCSB  
##
