data_PDD
# 
_chem_comp.id                                    PDD 
_chem_comp.name                                  "N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE" 
_chem_comp.type                                  "D-PEPTIDE LINKING" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C11 H17 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2002-03-18 
_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                        320.236 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     PDD 
_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        1L6G 
_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 
PDD N    N    N 0 1 N N N N N N 24.688 15.923 69.190 0.731  -0.122 1.963  N    PDD 1  
PDD N1   N1   N 0 1 Y N N N N N 23.966 10.714 69.264 -3.550 -0.520 -0.450 N1   PDD 2  
PDD C2   C2   C 0 1 Y N N N N N 25.093 11.460 69.401 -3.594 -0.174 0.821  C2   PDD 3  
PDD C2A  C2A  C 0 1 N N N N N N 26.340 10.727 69.790 -4.882 -0.321 1.590  C2A  PDD 4  
PDD C3   C3   C 0 1 Y N N N N N 25.100 12.856 69.192 -2.467 0.323  1.458  C3   PDD 5  
PDD O3A  O3A  O 0 1 N N N N N N 26.268 13.564 69.388 -2.517 0.679  2.769  O3A  PDD 6  
PDD C4   C4   C 0 1 Y N N N N N 23.898 13.510 68.743 -1.285 0.453  0.736  C4   PDD 7  
PDD C4A  C4A  C 0 1 N N N N N N 24.040 14.974 68.287 -0.037 0.989  1.388  C4A  PDD 8  
PDD C5   C5   C 0 1 Y N N N N N 22.676 12.725 68.644 -1.284 0.082  -0.598 C5   PDD 9  
PDD C5A  C5A  C 0 1 N N N N N N 21.334 13.298 68.246 -0.029 0.204  -1.423 C5A  PDD 10 
PDD OP4  OP4  O 0 1 N N N N N N 21.454 13.928 66.978 -0.287 -0.250 -2.753 OP4  PDD 11 
PDD P    P    P 0 1 N N N N N N 20.296 14.769 66.406 1.089  -0.092 -3.573 P    PDD 12 
PDD OP1  OP1  O 0 1 N N N N N N 19.098 13.895 66.278 2.141  -0.912 -2.933 OP1  PDD 13 
PDD OP2  OP2  O 0 1 N N N N N N 20.723 15.304 65.068 0.870  -0.589 -5.089 OP2  PDD 14 
PDD OP3  OP3  O 0 1 N N N N N N 19.988 15.915 67.296 1.539  1.452  -3.575 OP3  PDD 15 
PDD C6   C6   C 0 1 Y N N N N N 22.784 11.338 68.905 -2.446 -0.410 -1.162 C6   PDD 16 
PDD CA   CA   C 0 1 N N R N N N 24.892 17.350 68.809 1.927  0.465  2.580  CA   PDD 17 
PDD CB   CB   C 0 1 N N N N N N 23.766 17.929 67.928 3.058  0.520  1.550  CB   PDD 18 
PDD C    C    C 0 1 N N N N N N 26.258 17.582 68.097 2.356  -0.379 3.752  C    PDD 19 
PDD O    O    O 0 1 N N N N N N 26.422 18.844 67.664 1.729  -1.370 4.043  O    PDD 20 
PDD OXT  OXT  O 0 1 N Y N N N N 27.097 16.766 67.948 3.434  -0.032 4.471  OXT  PDD 21 
PDD H    HN   H 0 1 N N N N N N 25.595 15.536 69.453 1.051  -0.685 1.189  H    PDD 22 
PDD H2A1 1H2A H 0 0 N N N N N N 26.526 9.896  69.070 -5.462 0.597  1.506  H2A1 PDD 23 
PDD H2A2 2H2A H 0 0 N N N N N N 27.265 11.339 69.903 -5.457 -1.152 1.181  H2A2 PDD 24 
PDD H2A3 3H2A H 0 0 N N N N N N 26.158 10.149 70.726 -4.658 -0.515 2.639  H2A3 PDD 25 
PDD HO3  HO3  H 0 1 N N N N N N 26.273 14.504 69.247 -2.770 1.612  2.795  HO3  PDD 26 
PDD H4A1 1H4A H 0 0 N N N N N N 24.560 14.998 67.301 -0.311 1.688  2.179  H4A1 PDD 27 
PDD H4A2 2H4A H 0 0 N N N N N N 23.034 15.367 68.009 0.569  1.504  0.644  H4A2 PDD 28 
PDD H5A1 1H5A H 0 0 N N N N N N 20.919 13.983 69.022 0.287  1.246  -1.450 H5A1 PDD 29 
PDD H5A2 2H5A H 0 0 N N N N N N 20.524 12.532 68.263 0.758  -0.403 -0.977 H5A2 PDD 30 
PDD HOP2 2HOP H 0 0 N N N N N N 20.009 15.822 64.715 1.716  -0.479 -5.544 HOP2 PDD 31 
PDD HOP3 3HOP H 0 0 N N N N N N 19.274 16.433 66.943 0.827  1.950  -4.000 HOP3 PDD 32 
PDD H6   H6   H 0 1 N N N N N N 21.887 10.701 68.823 -2.451 -0.704 -2.201 H6   PDD 33 
PDD HA   HA   H 0 1 N N N N N N 24.879 17.895 69.782 1.700  1.474  2.924  HA   PDD 34 
PDD HB1  1HB  H 0 1 N N N N N N 22.774 17.792 68.419 3.285  -0.488 1.206  HB1  PDD 35 
PDD HB2  2HB  H 0 1 N N N N N N 23.919 18.996 67.643 2.747  1.132  0.703  HB2  PDD 36 
PDD HB3  3HB  H 0 1 N N N N N N 23.615 17.299 67.021 3.945  0.957  2.008  HB3  PDD 37 
PDD HXT  HXT  H 0 1 N Y N N N N 27.930 16.908 67.514 3.709  -0.574 5.223  HXT  PDD 38 
# 
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 
PDD N   C4A  SING N N 1  
PDD N   CA   SING N N 2  
PDD N   H    SING N N 3  
PDD N1  C2   DOUB Y N 4  
PDD N1  C6   SING Y N 5  
PDD C2  C2A  SING N N 6  
PDD C2  C3   SING Y N 7  
PDD C2A H2A1 SING N N 8  
PDD C2A H2A2 SING N N 9  
PDD C2A H2A3 SING N N 10 
PDD C3  O3A  SING N N 11 
PDD C3  C4   DOUB Y N 12 
PDD O3A HO3  SING N N 13 
PDD C4  C4A  SING N N 14 
PDD C4  C5   SING Y N 15 
PDD C4A H4A1 SING N N 16 
PDD C4A H4A2 SING N N 17 
PDD C5  C5A  SING N N 18 
PDD C5  C6   DOUB Y N 19 
PDD C5A OP4  SING N N 20 
PDD C5A H5A1 SING N N 21 
PDD C5A H5A2 SING N N 22 
PDD OP4 P    SING N N 23 
PDD P   OP1  DOUB N N 24 
PDD P   OP2  SING N N 25 
PDD P   OP3  SING N N 26 
PDD OP2 HOP2 SING N N 27 
PDD OP3 HOP3 SING N N 28 
PDD C6  H6   SING N N 29 
PDD CA  CB   SING N N 30 
PDD CA  C    SING N N 31 
PDD CA  HA   SING N N 32 
PDD CB  HB1  SING N N 33 
PDD CB  HB2  SING N N 34 
PDD CB  HB3  SING N N 35 
PDD C   O    DOUB N N 36 
PDD C   OXT  SING N N 37 
PDD OXT HXT  SING N N 38 
# 
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 
PDD SMILES           ACDLabs              10.04 "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)C"                                                                                                  
PDD SMILES_CANONICAL CACTVS               3.341 "C[C@@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"                                                                                           
PDD SMILES           CACTVS               3.341 "C[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"                                                                                             
PDD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](C)C(=O)O)O"                                                                                            
PDD SMILES           "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)C(=O)O)O"                                                                                                
PDD InChI            InChI                1.03  "InChI=1S/C11H17N2O7P/c1-6-10(14)9(4-13-7(2)11(15)16)8(3-12-6)5-20-21(17,18)19/h3,7,13-14H,4-5H2,1-2H3,(H,15,16)(H2,17,18,19)/t7-/m1/s1" 
PDD InChIKey         InChI                1.03  WACJCHFWJNNBPR-SSDOTTSWSA-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 
PDD "SYSTEMATIC NAME" ACDLabs              10.04 "N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-alanine"             
PDD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]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 
PDD "Create component"  2002-03-18 RCSB 
PDD "Modify descriptor" 2011-06-04 RCSB 
PDD "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            PDD 
_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               CB 
_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      ? 
# 
