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                    2024-05-07 
_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 
# 
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 
# 
_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         ? 
# 
