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 ? ? #