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                    2008-10-14 
_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 InChI            InChI                1.02b InChI=1/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/f/h17,19-20H 
PY5 InChIKey         InChI                1.02b YYAMSLLSQINIQO-SDSCXEPSDK                                                                                                                                       
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                                                                                                                         
# 
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" 
# 
