data_PY5
#

_chem_comp.id                                   PY5
_chem_comp.name                                 "2-[O-PHOSPHONOPYRIDOXYL]-AMINO-PENTANOIC ACID"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C13 H21 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "VITAMIN B6 COMPLEXED WITH 2-AMINO-PENTANOIC ACID"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-08-18
_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                       348.289
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    PY5
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1CQ7
_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
PY5  N1    N1    N  0  1  Y  N  N  26.691   3.739  -15.103   3.767   0.432  -0.541  N1    PY5   1  
PY5  C2    C2    C  0  1  Y  N  N  26.404   4.867  -15.834   3.777   0.071   0.726  C2    PY5   2  
PY5  C2A   C2A   C  0  1  N  N  N  27.113   4.794  -17.170   5.056   0.167   1.518  C2A   PY5   3  
PY5  C3    C3    C  0  1  Y  N  N  25.541   5.872  -15.247   2.624  -0.396   1.338  C3    PY5   4  
PY5  O3    O3    O  0  1  N  N  N  25.357   6.912  -16.096   2.640  -0.769   2.645  O3    PY5   5  
PY5  C4    C4    C  0  1  Y  N  N  24.965   5.755  -13.974   1.451  -0.480   0.594  C4    PY5   6  
PY5  C4A   C4A   C  0  1  N  N  N  24.054   6.846  -13.383   0.175  -0.983   1.219  C4A   PY5   7  
PY5  C5    C5    C  0  1  Y  N  N  25.356   4.524  -13.325   1.486  -0.095  -0.735  C5    PY5   8  
PY5  C6    C6    C  0  1  Y  N  N  26.176   3.538  -13.861   2.673   0.366  -1.273  C6    PY5   9  
PY5  C5A   C5A   C  0  1  N  N  N  24.867   4.126  -11.927   0.241  -0.166  -1.582  C5A   PY5  10  
PY5  O4P   O4P   O  0  1  N  N  N  23.666   4.635  -11.506   0.537   0.294  -2.902  O4P   PY5  11  
PY5  P     P     P  0  1  N  N  N  22.770   3.977  -10.396  -0.829   0.190  -3.748  P     PY5  12  
PY5  O1P   O1P   O  0  1  N  N  N  22.283   2.704  -10.802  -1.865   1.037  -3.116  O1P   PY5  13  
PY5  O2P   O2P   O  0  1  N  N  N  21.850   5.084   -9.948  -0.568   0.697  -5.254  O2P   PY5  14  
PY5  O3P   O3P   O  0  1  N  N  N  23.728   3.656   -9.286  -1.329  -1.339  -3.775  O3P   PY5  15  
PY5  N     N     N  0  1  N  N  N  24.522   8.151  -14.048  -0.566   0.146   1.794  N     PY5  16  
PY5  CA    CA    C  0  1  N  N  S  23.447   9.221  -13.968  -1.792  -0.409   2.384  CA    PY5  17  
PY5  C     C     C  0  1  N  N  N  23.937  10.505  -14.638  -2.888  -0.415   1.350  C     PY5  18  
PY5  O     O     O  0  1  N  N  N  24.577  10.243  -15.795  -3.751  -1.260   1.390  O     PY5  19  
PY5  CB    CB    C  0  1  N  N  N  23.061   9.487  -12.518  -2.219   0.449   3.575  CB    PY5  20  
PY5  CG    CG    C  0  1  N  N  N  24.200   9.965  -11.631  -1.106   0.456   4.625  CG    PY5  21  
PY5  CD    CD    C  0  1  N  N  N  23.875   9.871  -10.152  -1.534   1.315   5.817  CD    PY5  22  
PY5  OXT   OXT   O  0  1  N  N  N  23.760  11.699  -14.155  -2.906   0.516   0.384  OXT   PY5  23  
PY5  H2A1  1H2A  H  0  0  N  N  N  26.880   5.709  -17.763   5.607  -0.769   1.433  H2A1  PY5  24  
PY5  H2A2  2H2A  H  0  0  N  N  N  28.210   4.632  -17.057   5.664   0.983   1.129  H2A2  PY5  25  
PY5  H2A3  3H2A  H  0  0  N  N  N  26.870   3.858  -17.725   4.820   0.357   2.566  H2A3  PY5  26  
PY5  HO3   HO3   H  0  1  N  N  N  24.791   7.570  -15.711   2.862  -1.709   2.665  HO3   PY5  27  
PY5  H4A1  1H4A  H  0  0  N  N  N  22.964   6.641  -13.504   0.413  -1.699   2.006  H4A1  PY5  28  
PY5  H4A2  2H4A  H  0  0  N  N  N  24.052   6.880  -12.268  -0.435  -1.469   0.458  H4A2  PY5  29  
PY5  H6    H6    H  0  1  N  N  N  26.413   2.612  -13.310   2.705   0.671  -2.309  H6    PY5  30  
PY5  H5A1  1H5A  H  0  0  N  N  N  24.843   3.014  -11.847  -0.108  -1.198  -1.627  H5A1  PY5  31  
PY5  H5A2  2H5A  H  0  0  N  N  N  25.654   4.372  -11.177  -0.533   0.461  -1.143  H5A2  PY5  32  
PY5  HOP2  2HOP  H  0  0  N  N  N  21.308   4.686   -9.276  -1.409   0.619  -5.724  HOP2  PY5  33  
PY5  HOP3  3HOP  H  0  0  N  N  N  23.186   3.258   -8.614  -0.626  -1.855  -4.194  HOP3  PY5  34  
PY5  HN2   HN2   H  0  1  N  N  N  24.826   7.994  -15.009  -0.854   0.728   1.021  HN2   PY5  35  
PY5  HA    HA    H  0  1  N  N  N  22.540   8.858  -14.506  -1.603  -1.428   2.720  HA    PY5  36  
PY5  HB1   1HB   H  0  1  N  N  N  22.208  10.203  -12.470  -3.129   0.037   4.013  HB1   PY5  37  
PY5  HB2   2HB   H  0  1  N  N  N  22.579   8.584  -12.074  -2.408   1.469   3.239  HB2   PY5  38  
PY5  HG1   HG1   H  0  1  N  N  N  25.144   9.421  -11.867  -0.197   0.869   4.187  HG1   PY5  39  
PY5  HG2   HG2   H  0  1  N  N  N  24.512  10.999  -11.905  -0.918  -0.563   4.961  HG2   PY5  40  
PY5  HD1   HD1   H  0  1  N  N  N  24.710  10.221   -9.501  -0.741   1.320   6.564  HD1   PY5  41  
PY5  HD2   HD2   H  0  1  N  N  N  22.930  10.414   -9.915  -1.723   2.335   5.480  HD2   PY5  42  
PY5  HD3   HD3   H  0  1  N  N  N  23.562   8.836   -9.877  -2.443   0.903   6.254  HD3   PY5  43  
PY5  HXT   HXT   H  0  1  N  N  N  24.064  12.496  -14.571  -3.609   0.512  -0.278  HXT   PY5  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
PY5  N1   C2    DOUB  Y  N   1  
PY5  N1   C6    SING  Y  N   2  
PY5  C2   C2A   SING  N  N   3  
PY5  C2   C3    SING  Y  N   4  
PY5  C2A  H2A1  SING  N  N   5  
PY5  C2A  H2A2  SING  N  N   6  
PY5  C2A  H2A3  SING  N  N   7  
PY5  C3   O3    SING  N  N   8  
PY5  C3   C4    DOUB  Y  N   9  
PY5  O3   HO3   SING  N  N  10  
PY5  C4   C4A   SING  N  N  11  
PY5  C4   C5    SING  Y  N  12  
PY5  C4A  N     SING  N  N  13  
PY5  C4A  H4A1  SING  N  N  14  
PY5  C4A  H4A2  SING  N  N  15  
PY5  C5   C6    DOUB  Y  N  16  
PY5  C5   C5A   SING  N  N  17  
PY5  C6   H6    SING  N  N  18  
PY5  C5A  O4P   SING  N  N  19  
PY5  C5A  H5A1  SING  N  N  20  
PY5  C5A  H5A2  SING  N  N  21  
PY5  O4P  P     SING  N  N  22  
PY5  P    O1P   DOUB  N  N  23  
PY5  P    O2P   SING  N  N  24  
PY5  P    O3P   SING  N  N  25  
PY5  O2P  HOP2  SING  N  N  26  
PY5  O3P  HOP3  SING  N  N  27  
PY5  N    CA    SING  N  N  28  
PY5  N    HN2   SING  N  N  29  
PY5  CA   C     SING  N  N  30  
PY5  CA   CB    SING  N  N  31  
PY5  CA   HA    SING  N  N  32  
PY5  C    O     DOUB  N  N  33  
PY5  C    OXT   SING  N  N  34  
PY5  CB   CG    SING  N  N  35  
PY5  CB   HB1   SING  N  N  36  
PY5  CB   HB2   SING  N  N  37  
PY5  CG   CD    SING  N  N  38  
PY5  CG   HG1   SING  N  N  39  
PY5  CG   HG2   SING  N  N  40  
PY5  CD   HD1   SING  N  N  41  
PY5  CD   HD2   SING  N  N  42  
PY5  CD   HD3   SING  N  N  43  
PY5  OXT  HXT   SING  N  N  44  
#   #
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
PY5  SMILES            ACDLabs               10.04  "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCC"  
PY5  SMILES_CANONICAL  CACTVS                3.341  "CCC[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"  
PY5  SMILES            CACTVS                3.341  "CCC[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"  
PY5  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CCC[C@@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O"  
PY5  SMILES            "OpenEye OEToolkits"  1.5.0  "CCCC(C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O"  
PY5  InChI             InChI                 1.03   "InChI=1S/C13H21N2O7P/c1-3-4-11(13(17)18)15-6-10-9(7-22-23(19,20)21)5-14-8(2)12(10)16/h5,11,15-16H,3-4,6-7H2,1-2H3,(H,17,18)(H2,19,20,21)/t11-/m0/s1"  
PY5  InChIKey          InChI                 1.03   YYAMSLLSQINIQO-NSHDSACASA-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
PY5  "SYSTEMATIC NAME"  ACDLabs               10.04  "N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-norvaline"  
PY5  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2S)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanoic 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
PY5  "Create component"   1999-08-18  RCSB  
PY5  "Modify descriptor"  2011-06-04  RCSB  
PY5  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     PY5
_pdbx_chem_comp_synonyms.name        "VITAMIN B6 COMPLEXED WITH 2-AMINO-PENTANOIC ACID"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##