data_PTD
# 
_chem_comp.id                                    PTD 
_chem_comp.name                                  PENTANEDIAL 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C5 H8 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2000-07-12 
_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                        100.116 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     PTD 
_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        1F8Q 
_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 
PTD C1   C1   C 0 1 N N N N N N 67.125 91.954 4.264 -0.266 -0.416 -2.444 C1   PTD 1  
PTD C2   C2   C 0 1 N N N N N N 66.219 92.062 5.506 0.604  -0.210 -1.231 C2   PTD 2  
PTD C3   C3   C 0 1 N N N N N N 65.703 93.503 5.761 -0.278 0.000  0.000  C3   PTD 3  
PTD C4   C4   C 0 1 N N N N N N 64.835 94.038 4.583 0.604  0.208  1.231  C4   PTD 4  
PTD C5   C5   C 0 1 N N N N N N 64.279 95.458 4.825 -0.265 0.416  2.444  C5   PTD 5  
PTD O1   O1   O 0 1 N N N N N N 66.687 91.548 3.170 -0.186 0.343  -3.380 O1   PTD 6  
PTD O5   O5   O 0 1 N N N N N N 63.946 96.208 3.879 -0.187 -0.342 3.380  O5   PTD 7  
PTD HC1  HC1  H 0 1 N N N N N N 68.195 92.191 4.146 -0.964 -1.239 -2.475 HC1  PTD 8  
PTD HC21 1HC2 H 0 0 N N N N N N 65.370 91.341 5.442 1.232  -1.089 -1.082 HC21 PTD 9  
PTD HC22 2HC2 H 0 0 N N N N N N 66.733 91.658 6.409 1.234  0.665  -1.380 HC22 PTD 10 
PTD HC31 1HC3 H 0 0 N N N N N N 65.152 93.568 6.728 -0.906 0.878  -0.149 HC31 PTD 11 
PTD HC32 2HC3 H 0 0 N N N N N N 66.545 94.197 5.988 -0.909 -0.876 0.149  HC32 PTD 12 
PTD HC41 1HC4 H 0 0 N N N N N N 65.400 93.993 3.623 1.232  -0.669 1.380  HC41 PTD 13 
PTD HC42 2HC4 H 0 0 N N N N N N 64.010 93.326 4.344 1.235  1.085  1.082  HC42 PTD 14 
PTD HC5  HC5  H 0 1 N N N N N N 64.101 95.992 5.773 -0.957 1.245  2.476  HC5  PTD 15 
# 
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 
PTD C1 C2   SING N N 1  
PTD C1 O1   DOUB N N 2  
PTD C1 HC1  SING N N 3  
PTD C2 C3   SING N N 4  
PTD C2 HC21 SING N N 5  
PTD C2 HC22 SING N N 6  
PTD C3 C4   SING N N 7  
PTD C3 HC31 SING N N 8  
PTD C3 HC32 SING N N 9  
PTD C4 C5   SING N N 10 
PTD C4 HC41 SING N N 11 
PTD C4 HC42 SING N N 12 
PTD C5 O5   DOUB N N 13 
PTD C5 HC5  SING N N 14 
# 
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 
PTD SMILES           ACDLabs              10.04 O=CCCCC=O                                  
PTD SMILES_CANONICAL CACTVS               3.341 O=CCCCC=O                                  
PTD SMILES           CACTVS               3.341 O=CCCCC=O                                  
PTD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(CC=O)CC=O"                              
PTD SMILES           "OpenEye OEToolkits" 1.5.0 "C(CC=O)CC=O"                              
PTD InChI            InChI                1.03  InChI=1S/C5H8O2/c6-4-2-1-3-5-7/h4-5H,1-3H2 
PTD InChIKey         InChI                1.03  SXRSQZLOMIGNAQ-UHFFFAOYSA-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 
PTD "SYSTEMATIC NAME" ACDLabs              10.04 pentanedial 
PTD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 pentanedial 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
PTD "Create component"  2000-07-12 RCSB 
PTD "Modify descriptor" 2011-06-04 RCSB 
PTD "Modify PCM"        2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_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 
1 PTD ARG None Crosslinker "Amino-acid backbone"   N-terminal     C1 N   ? ? 
2 PTD ARG None Crosslinker "Amino-acid backbone"   N-terminal     C5 N   ? ? 
3 PTD ARG None Crosslinker "Amino-acid side chain" "Any position" C2 CZ  ? ? 
4 PTD ARG None Crosslinker "Amino-acid side chain" "Any position" C5 NH1 ? ? 
5 PTD LYS None Crosslinker "Amino-acid side chain" "Any position" C1 NZ  ? ? 
6 PTD LYS None Crosslinker "Amino-acid side chain" "Any position" C5 NZ  ? ? 
# 
