data_PDG
#

_chem_comp.id                                   PDG
_chem_comp.name                                 "N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C13 H19 N2 O9 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2005-04-25
_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                       378.272
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    PDG
_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       1X2A
_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
PDG  N1    N1    N  0  1  Y  N  N  40.416  103.523  -11.097   1.683   3.695   0.490  N1    PDG   1  
PDG  C2    C2    C  0  1  Y  N  N  40.019  104.639  -11.827   0.471   3.933   0.029  C2    PDG   2  
PDG  C2A   C2A   C  0  1  N  N  N  41.074  105.728  -11.680  -0.094   5.328   0.103  C2A   PDG   3  
PDG  C3    C3    C  0  1  Y  N  N  38.744  104.567  -12.556  -0.292   2.912  -0.520  C3    PDG   4  
PDG  O3    O3    O  0  1  N  N  N  38.501  105.724  -13.213  -1.540   3.163  -0.994  O3    PDG   5  
PDG  C4    C4    C  0  1  Y  N  N  37.898  103.406  -12.548   0.245   1.630  -0.587  C4    PDG   6  
PDG  C4A   C4A   C  0  1  N  N  N  36.555  103.313  -13.317  -0.547   0.493  -1.180  C4A   PDG   7  
PDG  C5    C5    C  0  1  Y  N  N  38.461  102.338  -11.739   1.521   1.423  -0.090  C5    PDG   8  
PDG  C6    C6    C  0  1  Y  N  N  39.668  102.378  -11.036   2.218   2.490   0.447  C6    PDG   9  
PDG  C5A   C5A   C  0  1  N  N  N  37.771  100.990  -11.557   2.144   0.052  -0.135  C5A   PDG  10  
PDG  OP4   OP4   O  0  1  N  N  N  37.280  100.364  -12.678   3.453   0.104   0.435  OP4   PDG  11  
PDG  P     P     P  0  1  N  N  N  36.683   98.874  -12.691   4.055  -1.387   0.355  P     PDG  12  
PDG  OP1   OP1   O  0  1  N  N  N  37.450   97.992  -13.527   4.003  -1.866  -1.044  OP1   PDG  13  
PDG  OP2   OP2   O  0  1  N  N  N  35.213   99.104  -12.989   5.584  -1.376   0.861  OP2   PDG  14  
PDG  OP3   OP3   O  0  1  N  N  N  36.879   98.350  -11.278   3.187  -2.367   1.291  OP3   PDG  15  
PDG  NA    NA    N  0  1  N  N  N  36.052  104.742  -13.471  -1.334  -0.158  -0.125  NA    PDG  16  
PDG  CAA   CAA   C  0  1  N  N  R  34.774  104.984  -12.697  -2.077  -1.251  -0.766  CAA   PDG  17  
PDG  CBA   CBA   C  0  1  N  N  N  33.631  104.021  -13.087  -3.332  -1.563   0.051  CBA   PDG  18  
PDG  CGA   CGA   C  0  1  N  N  N  32.447  103.935  -12.100  -4.275  -0.359   0.018  CGA   PDG  19  
PDG  CDA   CDA   C  0  1  N  N  N  32.901  103.755  -10.641  -5.511  -0.667   0.824  CDA   PDG  20  
PDG  OE1   OE1   O  0  1  N  N  N  32.918  104.757   -9.967  -6.485   0.251   0.936  OE1   PDG  21  
PDG  OE2   OE2   O  0  1  N  N  N  33.193  102.587  -10.337  -5.626  -1.739   1.368  OE2   PDG  22  
PDG  CA    CA    C  0  1  N  N  N  34.373  106.454  -12.898  -1.205  -2.478  -0.837  CA    PDG  23  
PDG  OA    OA    O  0  1  N  N  N  35.366  107.256  -12.436  -0.080  -2.446  -0.397  OA    PDG  24  
PDG  OXT   OXT   O  0  1  N  N  N  33.249  106.881  -13.436  -1.678  -3.607  -1.387  OXT   PDG  25  
PDG  H2A1  1H2A  H  0  0  N  N  N  40.755  106.622  -12.265   0.164   5.874  -0.805  H2A1  PDG  26  
PDG  H2A2  2H2A  H  0  0  N  N  N  41.286  105.972  -10.613  -1.179   5.276   0.200  H2A2  PDG  27  
PDG  H2A3  3H2A  H  0  0  N  N  N  42.092  105.374  -11.965   0.324   5.844   0.968  H2A3  PDG  28  
PDG  HO3   HO3   H  0  1  N  N  N  37.677  105.677  -13.684  -2.152   3.023  -0.258  HO3   PDG  29  
PDG  H4A1  1H4A  H  0  0  N  N  N  36.635  102.765  -14.284  -1.217   0.878  -1.948  H4A1  PDG  30  
PDG  H4A2  2H4A  H  0  0  N  N  N  35.814  102.632  -12.835   0.136  -0.232  -1.624  H4A2  PDG  31  
PDG  H6    H6    H  0  1  N  N  N  40.024  101.519  -10.442   3.213   2.335   0.835  H6    PDG  32  
PDG  H5A1  1H5A  H  0  0  N  N  N  38.459  100.295  -11.021   1.528  -0.645   0.434  H5A1  PDG  33  
PDG  H5A2  2H5A  H  0  0  N  N  N  36.952  101.095  -10.807   2.211  -0.284  -1.170  H5A2  PDG  34  
PDG  HP2   HP2   H  0  1  N  N  N  34.859   98.222  -12.996   5.906  -2.286   0.798  HP2   PDG  35  
PDG  HP3   HP3   H  0  1  N  N  N  36.525   97.468  -11.285   3.248  -2.020   2.192  HP3   PDG  36  
PDG  HNA   HNA   H  0  1  N  N  N  35.940  104.990  -14.454  -0.675  -0.588   0.506  HNA   PDG  37  
PDG  HAA   HAA   H  0  1  N  N  N  34.962  104.775  -11.618  -2.366  -0.952  -1.774  HAA   PDG  38  
PDG  HBA1  1HBA  H  0  0  N  N  N  33.255  104.274  -14.105  -3.836  -2.431  -0.374  HBA1  PDG  39  
PDG  HBA2  2HBA  H  0  0  N  N  N  34.043  103.001  -13.271  -3.051  -1.776   1.082  HBA2  PDG  40  
PDG  HGA1  1HGA  H  0  0  N  N  N  31.775  104.818  -12.203  -3.771   0.509   0.444  HGA1  PDG  41  
PDG  HGA2  2HGA  H  0  0  N  N  N  31.734  103.131  -12.399  -4.557  -0.146  -1.013  HGA2  PDG  42  
PDG  HE1   HE1   H  0  1  N  N  N  33.198  104.645   -9.066  -7.278   0.053   1.453  HE1   PDG  43  
PDG  HXT   HXT   H  0  1  N  N  N  33.001  107.789  -13.560  -1.119  -4.395  -1.432  HXT   PDG  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
PDG  N1   C2    DOUB  Y  N   1  
PDG  N1   C6    SING  Y  N   2  
PDG  C2   C2A   SING  N  N   3  
PDG  C2   C3    SING  Y  N   4  
PDG  C2A  H2A1  SING  N  N   5  
PDG  C2A  H2A2  SING  N  N   6  
PDG  C2A  H2A3  SING  N  N   7  
PDG  C3   O3    SING  N  N   8  
PDG  C3   C4    DOUB  Y  N   9  
PDG  O3   HO3   SING  N  N  10  
PDG  C4   C4A   SING  N  N  11  
PDG  C4   C5    SING  Y  N  12  
PDG  C4A  NA    SING  N  N  13  
PDG  C4A  H4A1  SING  N  N  14  
PDG  C4A  H4A2  SING  N  N  15  
PDG  C5   C6    DOUB  Y  N  16  
PDG  C5   C5A   SING  N  N  17  
PDG  C6   H6    SING  N  N  18  
PDG  C5A  OP4   SING  N  N  19  
PDG  C5A  H5A1  SING  N  N  20  
PDG  C5A  H5A2  SING  N  N  21  
PDG  OP4  P     SING  N  N  22  
PDG  P    OP1   DOUB  N  N  23  
PDG  P    OP2   SING  N  N  24  
PDG  P    OP3   SING  N  N  25  
PDG  OP2  HP2   SING  N  N  26  
PDG  OP3  HP3   SING  N  N  27  
PDG  NA   CAA   SING  N  N  28  
PDG  NA   HNA   SING  N  N  29  
PDG  CAA  CBA   SING  N  N  30  
PDG  CAA  CA    SING  N  N  31  
PDG  CAA  HAA   SING  N  N  32  
PDG  CBA  CGA   SING  N  N  33  
PDG  CBA  HBA1  SING  N  N  34  
PDG  CBA  HBA2  SING  N  N  35  
PDG  CGA  CDA   SING  N  N  36  
PDG  CGA  HGA1  SING  N  N  37  
PDG  CGA  HGA2  SING  N  N  38  
PDG  CDA  OE1   SING  N  N  39  
PDG  CDA  OE2   DOUB  N  N  40  
PDG  OE1  HE1   SING  N  N  41  
PDG  CA   OA    DOUB  N  N  42  
PDG  CA   OXT   SING  N  N  43  
PDG  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
PDG  SMILES            ACDLabs               10.04  "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCC(=O)O"  
PDG  SMILES_CANONICAL  CACTVS                3.341  "Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CCC(O)=O)C(O)=O)c1O"  
PDG  SMILES            CACTVS                3.341  "Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CCC(O)=O)C(O)=O)c1O"  
PDG  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CCC(=O)O)C(=O)O)O"  
PDG  SMILES            "OpenEye OEToolkits"  1.5.0  "Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CCC(=O)O)C(=O)O)O"  
PDG  InChI             InChI                 1.03   "InChI=1S/C13H19N2O9P/c1-7-12(18)9(8(4-14-7)6-24-25(21,22)23)5-15-10(13(19)20)2-3-11(16)17/h4,10,15,18H,2-3,5-6H2,1H3,(H,16,17)(H,19,20)(H2,21,22,23)/t10-/m1/s1"  
PDG  InChIKey          InChI                 1.03   JMRKOGDJNHPMHS-SNVBAGLBSA-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
PDG  "SYSTEMATIC NAME"  ACDLabs               10.04  "N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-glutamic acid"  
PDG  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2R)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanedioic 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
PDG  "Create component"   2005-04-25  RCSB  
PDG  "Modify descriptor"  2011-06-04  RCSB  
PDG  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     PDG
_pdbx_chem_comp_synonyms.name        "N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
