data_ZI0
# 
_chem_comp.id                                    ZI0 
_chem_comp.name                                  N-MALONYL-PROLINE 
_chem_comp.type                                  "L-PEPTIDE LINKING" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C8 H11 N O5" 
_chem_comp.mon_nstd_parent_comp_id               PRO 
_chem_comp.pdbx_synonyms                         "1-(3-oxidanyl-3-oxidanylidene-propanoyl)pyrrolidine-2-carboxylic acid" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-01-22 
_chem_comp.pdbx_modified_date                    2025-04-04 
_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                        201.177 
_chem_comp.one_letter_code                       P 
_chem_comp.three_letter_code                     ZI0 
_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        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
ZI0 O1  O1  O 0 1 N N N N N N 3.786  0.486  -1.489 4.367  -0.386 0.389  O1  ZI0 1  
ZI0 C1  C1  C 0 1 N N N N N N 3.099  -0.473 -0.921 3.152  0.055  0.026  C1  ZI0 2  
ZI0 O2  O2  O 0 1 N N N N N N 3.075  -1.608 -1.335 3.034  1.137  -0.498 O2  ZI0 3  
ZI0 C2  C2  C 0 1 N N N N N N 2.325  -0.066 0.307  1.936  -0.801 0.271  C2  ZI0 4  
ZI0 C3  C3  C 0 1 N N N N N N 1.080  0.739  0.004  0.708  -0.082 -0.225 C3  ZI0 5  
ZI0 O3  O3  O 0 1 N N N N N N 1.153  1.952  -0.127 0.811  1.017  -0.728 O3  ZI0 6  
ZI0 N   N   N 0 1 N N N Y Y N -0.089 0.085  -0.122 -0.504 -0.660 -0.110 N   ZI0 7  
ZI0 CD  CD  C 0 1 N N N N N N -0.249 -1.189 -0.840 -0.771 -1.985 0.478  CD  ZI0 8  
ZI0 CG  CG  C 0 1 N N N N N N -1.734 -1.205 -1.130 -2.107 -2.440 -0.160 CG  ZI0 9  
ZI0 CB  CB  C 0 1 N N N N N N -2.357 -0.515 0.065  -2.887 -1.101 -0.239 CB  ZI0 10 
ZI0 CA  CA  C 0 1 N N S N Y N -1.344 0.584  0.435  -1.779 -0.071 -0.545 CA  ZI0 11 
ZI0 C   C   C 0 1 N N N N Y Y -1.329 0.812  1.941  -2.039 1.205  0.213  C   ZI0 12 
ZI0 OXT OXT O 0 1 N Y N N Y Y -2.002 1.866  2.333  -3.154 1.913  -0.026 OXT ZI0 13 
ZI0 O   O   O 0 1 N N N N Y Y -0.742 0.066  2.690  -1.243 1.591  1.037  O   ZI0 14 
ZI0 H1  H1  H 0 1 N N N N N N 4.240  0.143  -2.250 5.117  0.198  0.212  H1  ZI0 15 
ZI0 H4  H4  H 0 1 N N N N N N 2.026  -0.977 0.847  2.044  -1.746 -0.262 H4  ZI0 16 
ZI0 H3  H3  H 0 1 N N N N N N 2.983  0.540  0.947  1.837  -0.994 1.339  H3  ZI0 17 
ZI0 HD2 HD2 H 0 1 N N N N N N 0.339  -1.200 -1.769 0.028  -2.681 0.224  HD2 ZI0 18 
ZI0 HD3 HD3 H 0 1 N N N N N N 0.044  -2.042 -0.210 -0.876 -1.906 1.560  HD3 ZI0 19 
ZI0 HG2 HG2 H 0 1 N N N N N N -1.956 -0.655 -2.057 -1.943 -2.856 -1.155 HG2 ZI0 20 
ZI0 HG3 HG3 H 0 1 N N N N N N -2.102 -2.238 -1.219 -2.623 -3.156 0.481  HG3 ZI0 21 
ZI0 HB2 HB2 H 0 1 N N N N N N -3.330 -0.076 -0.201 -3.622 -1.130 -1.043 HB2 ZI0 22 
ZI0 HB3 HB3 H 0 1 N N N N N N -2.489 -1.221 0.898  -3.365 -0.877 0.714  HB3 ZI0 23 
ZI0 HA  HA  H 0 1 N N N N Y N -1.633 1.519  -0.068 -1.748 0.131  -1.615 HA  ZI0 24 
ZI0 HXT HXT H 0 1 N Y N N Y Y -1.951 1.941  3.279  -3.277 2.724  0.485  HXT ZI0 25 
# 
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 
ZI0 O1  C1  SING N N 1  
ZI0 C1  O2  DOUB N N 2  
ZI0 C1  C2  SING N N 3  
ZI0 C2  C3  SING N N 4  
ZI0 C3  O3  DOUB N N 5  
ZI0 C3  N   SING N N 6  
ZI0 N   CD  SING N N 7  
ZI0 CD  CG  SING N N 8  
ZI0 CG  CB  SING N N 9  
ZI0 CB  CA  SING N N 10 
ZI0 CA  C   SING N N 11 
ZI0 C   OXT SING N N 12 
ZI0 C   O   DOUB N N 13 
ZI0 N   CA  SING N N 14 
ZI0 O1  H1  SING N N 15 
ZI0 C2  H4  SING N N 16 
ZI0 C2  H3  SING N N 17 
ZI0 CD  HD2 SING N N 18 
ZI0 CD  HD3 SING N N 19 
ZI0 CG  HG2 SING N N 20 
ZI0 CG  HG3 SING N N 21 
ZI0 CB  HB2 SING N N 22 
ZI0 CB  HB3 SING N N 23 
ZI0 CA  HA  SING N N 24 
ZI0 OXT HXT SING N N 25 
# 
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 
ZI0 InChI            InChI                1.06  "InChI=1S/C8H11NO5/c10-6(4-7(11)12)9-3-1-2-5(9)8(13)14/h5H,1-4H2,(H,11,12)(H,13,14)/t5-/m0/s1" 
ZI0 InChIKey         InChI                1.06  OFSJFCHZCUQYDU-YFKPBYRVSA-N                                                                    
ZI0 SMILES_CANONICAL CACTVS               3.385 "OC(=O)CC(=O)N1CCC[C@H]1C(O)=O"                                                                
ZI0 SMILES           CACTVS               3.385 "OC(=O)CC(=O)N1CCC[CH]1C(O)=O"                                                                 
ZI0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1CC(N(C1)C(=O)CC(=O)O)C(=O)O"                                                                
ZI0 SMILES           "OpenEye OEToolkits" 2.0.7 "C1CC(N(C1)C(=O)CC(=O)O)C(=O)O"                                                                
# 
_pdbx_chem_comp_identifier.comp_id           ZI0 
_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        "1-(3-oxidanyl-3-oxidanylidene-propanoyl)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 
ZI0 "Create component"   2024-02-14 PDBE 
ZI0 "Modify descriptor"  2024-02-14 PDBE 
ZI0 "Other modification" 2024-02-14 PDBE 
ZI0 "Modify PCM"         2024-09-27 PDBE 
ZI0 "Initial release"    2025-04-09 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      ZI0 
_pdbx_chem_comp_synonyms.name         "1-(3-oxidanyl-3-oxidanylidene-propanoyl)pyrrolidine-2-carboxylic acid" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            ZI0 
_pdbx_chem_comp_pcm.modified_residue_id                PRO 
_pdbx_chem_comp_pcm.type                               Malonylation 
_pdbx_chem_comp_pcm.category                           "Named protein modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid backbone" 
_pdbx_chem_comp_pcm.polypeptide_position               N-terminal 
_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      ? 
# 
