data_A1D9O
# 
_chem_comp.id                                    A1D9O 
_chem_comp.name                                  "(2~{S},3~{S},4~{S})-3,4-bis(oxidanyl)pyrrolidine-2-carboxylic acid" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C5 H9 N O4" 
_chem_comp.mon_nstd_parent_comp_id               PRO 
_chem_comp.pdbx_synonyms                         
;HEPTULOSE-2-PHOSPHATE; 1-deoxy-2-O-phosphono-alpha-D-gluco-hept-2-ulose; 1-deoxy-2-O-phosphono-D-gluco-hept-2-ulose;
1-deoxy-2-O-phosphono-gluco-hept-2-ulose
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-07-04 
_chem_comp.pdbx_modified_date                    2025-01-03 
_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                        147.129 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D9O 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        9IKM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1D9O N   N1  N 0 1 N N N Y Y N 177.557 176.018 252.809 -0.176 1.552  -0.148 N   A1D9O 1  
A1D9O CA  C1  C 0 1 N N S N Y N 176.829 176.478 251.597 0.378  0.379  0.576  CA  A1D9O 2  
A1D9O C   C2  C 0 1 N N N N Y Y 177.345 175.845 250.287 1.806  0.133  0.163  C   A1D9O 3  
A1D9O O   O1  O 0 1 N N N N Y Y 178.308 175.040 250.310 2.229  0.610  -0.863 O   A1D9O 4  
A1D9O CB  C3  C 0 1 N N S N N N 176.968 177.992 251.525 -0.520 -0.802 0.147  CB  A1D9O 5  
A1D9O CG  C4  C 0 1 N N S N N N 177.158 178.403 252.974 -1.852 -0.156 -0.285 CG  A1D9O 6  
A1D9O CD  C5  C 0 1 N N N N N N 177.723 177.195 253.686 -1.648 1.360  -0.082 CD  A1D9O 7  
A1D9O OD1 O2  O 0 1 N N N N N N 175.888 178.730 253.553 -2.922 -0.627 0.536  OD1 A1D9O 8  
A1D9O OD2 O3  O 0 1 N N N N N N 178.150 178.302 250.756 0.071  -1.502 -0.950 OD2 A1D9O 9  
A1D9O OXT O4  O 0 1 N Y N N Y Y 176.728 176.214 249.167 2.609  -0.616 0.936  OXT A1D9O 10 
A1D9O H   H1  H 0 1 N Y N Y Y N 177.029 175.311 253.279 0.097  2.414  0.299  H   A1D9O 11 
A1D9O HA  H3  H 0 1 N N N N Y N 175.763 176.229 251.704 0.315  0.532  1.653  HA  A1D9O 12 
A1D9O HB2 H4  H 0 1 N N N N N N 176.063 178.451 251.100 -0.682 -1.478 0.986  HB2 A1D9O 13 
A1D9O HG2 H5  H 0 1 N N N N N N 177.860 179.248 253.040 -2.056 -0.375 -1.334 HG2 A1D9O 14 
A1D9O HD2 H6  H 0 1 N N N N N N 177.183 177.034 254.631 -2.027 1.668  0.893  HD2 A1D9O 15 
A1D9O HD3 H7  H 0 1 N N N N N N 178.791 177.354 253.897 -2.140 1.921  -0.877 HD3 A1D9O 16 
A1D9O H8  H8  H 0 1 N N N N N N 176.009 178.987 254.460 -3.785 -0.255 0.310  H8  A1D9O 17 
A1D9O H9  H9  H 0 1 N N N N N N 178.254 179.245 250.700 -0.449 -2.255 -1.262 H9  A1D9O 18 
A1D9O HXT H10 H 0 1 N Y N N Y Y 177.130 175.778 248.425 3.517  -0.746 0.630  HXT A1D9O 19 
# 
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 
A1D9O C   O   DOUB N N 1  
A1D9O C   CA  SING N N 2  
A1D9O OD2 CB  SING N N 3  
A1D9O CB  CA  SING N N 4  
A1D9O CB  CG  SING N N 5  
A1D9O CA  N   SING N N 6  
A1D9O N   CD  SING N N 7  
A1D9O CG  OD1 SING N N 8  
A1D9O CG  CD  SING N N 9  
A1D9O C   OXT SING N N 10 
A1D9O N   H   SING N N 11 
A1D9O CA  HA  SING N N 12 
A1D9O CB  HB2 SING N N 13 
A1D9O CG  HG2 SING N N 14 
A1D9O CD  HD2 SING N N 15 
A1D9O CD  HD3 SING N N 16 
A1D9O OD1 H8  SING N N 17 
A1D9O OD2 H9  SING N N 18 
A1D9O OXT HXT SING N N 19 
# 
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 
A1D9O InChI            InChI                1.06  "InChI=1S/C5H9NO4/c7-2-1-6-3(4(2)8)5(9)10/h2-4,6-8H,1H2,(H,9,10)/t2-,3-,4+/m0/s1" 
A1D9O InChIKey         InChI                1.06  HWNGLKPRXKKTPK-YVZJFKFKSA-N                                                       
A1D9O SMILES_CANONICAL CACTVS               3.385 "O[C@H]1CN[C@@H]([C@@H]1O)C(O)=O"                                                 
A1D9O SMILES           CACTVS               3.385 "O[CH]1CN[CH]([CH]1O)C(O)=O"                                                      
A1D9O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H]([C@H](N1)C(=O)O)O)O"                                              
A1D9O SMILES           "OpenEye OEToolkits" 2.0.7 "C1C(C(C(N1)C(=O)O)O)O"                                                           
# 
_pdbx_chem_comp_identifier.comp_id           A1D9O 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{S},3~{S},4~{S})-3,4-bis(oxidanyl)pyrrolidine-2-carboxylic 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 
A1D9O "Create component" 2024-07-04 PDBC 
A1D9O "Modify PCM"       2024-09-27 PDBE 
A1D9O "Initial release"  2025-01-08 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1D9O 
_pdbx_chem_comp_pcm.modified_residue_id                PRO 
_pdbx_chem_comp_pcm.type                               Hydroxylation 
_pdbx_chem_comp_pcm.category                           "Named protein 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               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
