data_PY4
# 
_chem_comp.id                                    PY4 
_chem_comp.name                                  "2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H19 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "VITAMIN B6 COMPLEXED WITH 2-AMINO-BUTYRIC ACID" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-08-18 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        334.262 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     PY4 
_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        1CQ6 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
PY4 N1   N1   N 0 1 Y N N N N N 26.666 4.870  -14.793 -3.607 0.472  0.356  N1   PY4 1  
PY4 C2   C2   C 0 1 Y N N N N N 26.345 6.074  -15.381 -3.544 0.240  -0.939 C2   PY4 2  
PY4 C2A  C2A  C 0 1 N N N N N N 27.100 6.197  -16.695 -4.775 0.417  -1.790 C2A  PY4 3  
PY4 C3   C3   C 0 1 Y N N N N N 25.405 6.953  -14.694 -2.355 -0.164 -1.528 C3   PY4 4  
PY4 O3   O3   O 0 1 N N N N N N 25.183 8.093  -15.396 -2.295 -0.403 -2.865 O3   PY4 5  
PY4 C4   C4   C 0 1 Y N N N N N 24.817 6.633  -13.473 -1.226 -0.323 -0.731 C4   PY4 6  
PY4 C4A  C4A  C 0 1 N N N N N N 23.828 7.560  -12.750 0.085  -0.762 -1.330 C4A  PY4 7  
PY4 C5   C5   C 0 1 Y N N N N N 25.259 5.353  -12.998 -1.338 -0.074 0.626  C5   PY4 8  
PY4 C6   C6   C 0 1 Y N N N N N 26.147 4.498  -13.611 -2.556 0.331  1.139  C6   PY4 9  
PY4 C5A  C5A  C 0 1 N N N N N N 24.780 4.772  -11.693 -0.144 -0.232 1.531  C5A  PY4 10 
PY4 O4P  O4P  O 0 1 N N N N N N 23.856 5.491  -10.988 -0.516 0.093  2.872  O4P  PY4 11 
PY4 P    P    P 0 1 N N N N N N 22.842 4.778  -10.038 0.799  -0.095 3.780  P    PY4 12 
PY4 O1P  O1P  O 0 1 N N N N N N 22.345 3.581  -10.642 1.866  0.808  3.296  O1P  PY4 13 
PY4 O2P  O2P  O 0 1 N N N N N N 21.946 5.861  -9.499  0.450  0.256  5.311  O2P  PY4 14 
PY4 O3P  O3P  O 0 1 N N N N N N 23.712 4.265  -8.943  1.304  -1.621 3.682  O3P  PY4 15 
PY4 N    N    N 0 1 N N N N N N 23.774 8.846  -13.578 0.853  0.418  -1.744 N    PY4 16 
PY4 CA   CA   C 0 1 N N R N N N 24.036 10.050 -12.707 2.113  -0.076 -2.316 CA   PY4 17 
PY4 C    C    C 0 1 N N N N N N 23.982 11.339 -13.527 1.938  -0.303 -3.795 C    PY4 18 
PY4 O    O    O 0 1 N N N N N N 24.182 11.085 -14.837 2.579  -1.162 -4.354 O    PY4 19 
PY4 CB   CB   C 0 1 N N N N N N 23.102 10.104 -11.505 3.218  0.956  -2.085 CB   PY4 20 
PY4 CG   CG   C 0 1 N N N N N N 23.687 9.453  -10.254 3.395  1.186  -0.583 CG   PY4 21 
PY4 OXT  OXT  O 0 1 N N N N N N 23.781 12.528 -13.032 1.072  0.448  -4.492 OXT  PY4 22 
PY4 H2A1 1H2A H 0 0 N N N N N N 26.840 7.171  -17.170 -5.326 -0.522 -1.831 H2A1 PY4 23 
PY4 H2A2 2H2A H 0 0 N N N N N N 28.199 6.065  -16.567 -5.409 1.191  -1.356 H2A2 PY4 24 
PY4 H2A3 3H2A H 0 0 N N N N N N 26.917 5.330  -17.372 -4.482 0.711  -2.798 H2A3 PY4 25 
PY4 HO3  HO3  H 0 1 N N N N N N 24.570 8.665  -14.948 -2.511 -1.337 -2.992 HO3  PY4 26 
PY4 H4A1 1H4A H 0 0 N N N N N N 22.827 7.097  -12.580 -0.104 -1.395 -2.196 H4A1 PY4 27 
PY4 H4A2 2H4A H 0 0 N N N N N N 24.081 7.731  -11.677 0.653  -1.323 -0.588 H4A2 PY4 28 
PY4 H6   H6   H 0 1 N N N N N N 26.437 3.532  -13.163 -2.649 0.531  2.197  H6   PY4 29 
PY4 H5A1 1H5A H 0 0 N N N N N N 24.392 3.741  -11.867 0.207  -1.263 1.493  H5A1 PY4 30 
PY4 H5A2 2H5A H 0 0 N N N N N N 25.657 4.556  -11.039 0.651  0.435  1.203  H5A2 PY4 31 
PY4 HOP2 2HOP H 0 0 N N N N N N 21.329 5.427  -8.921  1.263  0.130  5.819  HOP2 PY4 32 
PY4 HOP3 3HOP H 0 0 N N N N N N 23.095 3.831  -8.365  0.581  -2.176 4.005  HOP3 PY4 33 
PY4 HN2  HN2  H 0 1 N N N N N N 22.894 8.931  -14.087 1.094  0.918  -0.902 HN2  PY4 34 
PY4 HA   HA   H 0 1 N N N N N N 25.068 9.948  -12.299 2.386  -1.015 -1.834 HA   PY4 35 
PY4 HB1  1HB  H 0 1 N N N N N N 22.787 11.153 -11.295 2.945  1.894  -2.567 HB1  PY4 36 
PY4 HB2  2HB  H 0 1 N N N N N N 22.109 9.660  -11.754 4.153  0.588  -2.509 HB2  PY4 37 
PY4 HG1  HG1  H 0 1 N N N N N N 23.003 9.492  -9.374  4.183  1.921  -0.418 HG1  PY4 38 
PY4 HG2  HG2  H 0 1 N N N N N N 24.001 8.404  -10.464 2.461  1.553  -0.159 HG2  PY4 39 
PY4 HG3  HG3  H 0 1 N N N N N N 24.679 9.896  -10.004 3.668  0.247  -0.101 HG3  PY4 40 
PY4 HXT  HXT  H 0 1 N N N N N N 23.747 13.329 -13.541 0.960  0.303  -5.441 HXT  PY4 41 
# 
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 
PY4 N1  C2   DOUB Y N 1  
PY4 N1  C6   SING Y N 2  
PY4 C2  C2A  SING N N 3  
PY4 C2  C3   SING Y N 4  
PY4 C2A H2A1 SING N N 5  
PY4 C2A H2A2 SING N N 6  
PY4 C2A H2A3 SING N N 7  
PY4 C3  O3   SING N N 8  
PY4 C3  C4   DOUB Y N 9  
PY4 O3  HO3  SING N N 10 
PY4 C4  C4A  SING N N 11 
PY4 C4  C5   SING Y N 12 
PY4 C4A N    SING N N 13 
PY4 C4A H4A1 SING N N 14 
PY4 C4A H4A2 SING N N 15 
PY4 C5  C6   DOUB Y N 16 
PY4 C5  C5A  SING N N 17 
PY4 C6  H6   SING N N 18 
PY4 C5A O4P  SING N N 19 
PY4 C5A H5A1 SING N N 20 
PY4 C5A H5A2 SING N N 21 
PY4 O4P P    SING N N 22 
PY4 P   O1P  DOUB N N 23 
PY4 P   O2P  SING N N 24 
PY4 P   O3P  SING N N 25 
PY4 O2P HOP2 SING N N 26 
PY4 O3P HOP3 SING N N 27 
PY4 N   CA   SING N N 28 
PY4 N   HN2  SING N N 29 
PY4 CA  C    SING N N 30 
PY4 CA  CB   SING N N 31 
PY4 CA  HA   SING N N 32 
PY4 C   O    DOUB N N 33 
PY4 C   OXT  SING N N 34 
PY4 CB  CG   SING N N 35 
PY4 CB  HB1  SING N N 36 
PY4 CB  HB2  SING N N 37 
PY4 CG  HG1  SING N N 38 
PY4 CG  HG2  SING N N 39 
PY4 CG  HG3  SING N N 40 
PY4 OXT HXT  SING N N 41 
# 
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 
PY4 SMILES           ACDLabs              10.04 "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CC"                                                                                                        
PY4 SMILES_CANONICAL CACTVS               3.341 "CC[C@@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"                                                                                                 
PY4 SMILES           CACTVS               3.341 "CC[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"                                                                                                   
PY4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC[C@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O"                                                                                                    
PY4 SMILES           "OpenEye OEToolkits" 1.5.0 "CCC(C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O"                                                                                                        
PY4 InChI            InChI                1.03  "InChI=1S/C12H19N2O7P/c1-3-10(12(16)17)14-5-9-8(6-21-22(18,19)20)4-13-7(2)11(9)15/h4,10,14-15H,3,5-6H2,1-2H3,(H,16,17)(H2,18,19,20)/t10-/m1/s1" 
PY4 InChIKey         InChI                1.03  VRMPGTOTVVJQMU-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 
PY4 "SYSTEMATIC NAME" ACDLabs              10.04 "(2R)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]butanoic acid" 
PY4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]butanoic 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 
PY4 "Create component"  1999-08-18 RCSB 
PY4 "Modify descriptor" 2011-06-04 RCSB 
PY4 "Modify synonyms"   2021-03-01 PDBE 
PY4 "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      PY4 
_pdbx_chem_comp_synonyms.name         "VITAMIN B6 COMPLEXED WITH 2-AMINO-BUTYRIC ACID" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            PY4 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               CG 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
#