data_B3D # _chem_comp.id B3D _chem_comp.name "3-AMINOPENTANEDIOIC 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 ASP _chem_comp.pdbx_synonyms BETA-HOMOASPARTATE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-02-28 _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 147.129 _chem_comp.one_letter_code D _chem_comp.three_letter_code B3D _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 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 B3D OE1 OE1 O 0 1 N N N N N N -3.773 -8.508 -0.815 3.689 -0.647 0.077 OE1 B3D 1 B3D CD CD C 0 1 N N N N N N -2.684 -8.200 -1.360 2.471 -0.086 0.147 CD B3D 2 B3D OE2 OE2 O 0 1 N N N N N N -2.435 -8.502 -2.546 2.360 1.085 0.421 OE2 B3D 3 B3D CG CG C 0 1 N N N N N N -1.591 -7.486 -0.614 1.242 -0.918 -0.117 CG B3D 4 B3D CA CB C 0 1 N N N Y N N -1.931 -6.074 -0.121 -0.005 -0.045 0.025 CB B3D 5 B3D N N N 0 1 N N N Y Y N -2.878 -5.366 -0.972 -0.003 0.987 -1.020 N B3D 6 B3D CB CA C 0 1 N N N Y N N -0.617 -5.300 -0.074 -1.256 -0.914 -0.120 CA B3D 7 B3D C C C 0 1 N N N Y N Y -0.677 -4.342 1.091 -2.482 -0.078 0.142 C B3D 8 B3D O O O 0 1 N N N Y N Y -0.421 -4.723 2.241 -2.368 1.093 0.417 O B3D 9 B3D OXT OXT O 0 1 N Y N Y N Y -1.038 -3.093 0.784 -3.702 -0.634 0.071 OXT B3D 10 B3D HE1 HE1 H 0 1 N N N N N N -4.318 -8.976 -1.437 4.447 -0.073 0.255 HE1 B3D 11 B3D HG3 HG3 H 0 1 N N N N N N -1.327 -8.095 0.263 1.288 -1.324 -1.128 HG3 B3D 12 B3D HG2 HG2 H 0 1 N N N N N N -0.721 -7.410 -1.282 1.197 -1.737 0.601 HG2 B3D 13 B3D HA HB H 0 1 N N N Y N N -2.334 -6.146 0.900 -0.005 0.431 1.006 HB B3D 14 B3D H H H 0 1 N N N Y Y N -3.053 -4.457 -0.593 0.780 1.615 -0.907 H B3D 15 B3D H2 H2 H 0 1 N Y N Y Y N -2.496 -5.275 -1.892 -0.003 0.571 -1.939 H2 B3D 16 B3D HB1 HA1 H 0 1 N N N Y N N 0.222 -5.998 0.061 -1.302 -1.319 -1.130 HA1 B3D 17 B3D HB2 HA2 H 0 1 N N N Y N N -0.481 -4.740 -1.011 -1.214 -1.733 0.599 HA2 B3D 18 B3D HXT HXT H 0 1 N Y N Y N Y -1.063 -2.567 1.575 -4.458 -0.058 0.247 HXT B3D 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 B3D OE1 CD SING N N 1 B3D OE1 HE1 SING N N 2 B3D CD OE2 DOUB N N 3 B3D CD CG SING N N 4 B3D CG CA SING N N 5 B3D CG HG3 SING N N 6 B3D CG HG2 SING N N 7 B3D CA N SING N N 8 B3D CA CB SING N N 9 B3D CA HA SING N N 10 B3D N H SING N N 11 B3D N H2 SING N N 12 B3D CB C SING N N 13 B3D CB HB1 SING N N 14 B3D CB HB2 SING N N 15 B3D C OXT SING N N 16 B3D C O DOUB N N 17 B3D OXT HXT SING N N 18 # 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 B3D SMILES ACDLabs 12.01 "O=C(O)CC(N)CC(=O)O" B3D InChI InChI 1.03 "InChI=1S/C5H9NO4/c6-3(1-4(7)8)2-5(9)10/h3H,1-2,6H2,(H,7,8)(H,9,10)" B3D InChIKey InChI 1.03 BBJIPMIXTXKYLZ-UHFFFAOYSA-N B3D SMILES_CANONICAL CACTVS 3.370 "NC(CC(O)=O)CC(O)=O" B3D SMILES CACTVS 3.370 "NC(CC(O)=O)CC(O)=O" B3D SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C(C(CC(=O)O)N)C(=O)O" B3D SMILES "OpenEye OEToolkits" 1.7.6 "C(C(CC(=O)O)N)C(=O)O" # 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 B3D "SYSTEMATIC NAME" ACDLabs 12.01 "3-aminopentanedioic acid" B3D "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "3-azanylpentanedioic 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 B3D "Create component" 2007-02-28 RCSB B3D "Modify descriptor" 2011-06-04 RCSB B3D "Other modification" 2011-12-12 RCSB B3D "Modify synonyms" 2020-06-05 PDBE B3D "Modify backbone" 2023-11-03 PDBE B3D "Other modification" 2024-05-07 PDBE B3D "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id B3D _pdbx_chem_comp_synonyms.name BETA-HOMOASPARTATE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id B3D _pdbx_chem_comp_pcm.modified_residue_id ASP _pdbx_chem_comp_pcm.type "Beta-amino acid" _pdbx_chem_comp_pcm.category "Named protein modification" _pdbx_chem_comp_pcm.position "Amino-acid backbone" _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 ? #