data_YD5
# 
_chem_comp.id                                    YD5 
_chem_comp.name                                  "N-(2-carboxyethyl)-L-alanine" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C6 H11 N O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-25 
_chem_comp.pdbx_modified_date                    2024-10-11 
_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                        161.156 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YD5 
_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        8FVP 
_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 
YD5 C4  C4  C 0 1 N N N N N N 17.232 36.475 -29.786 3.246  0.049  -0.100 C4  YD5 1  
YD5 O   O   O 0 1 N N N Y N Y 14.578 31.888 -28.230 -2.809 1.528  0.059  O2  YD5 2  
YD5 O5  O5  O 0 1 N N N N N N 16.838 37.474 -29.191 3.257  -0.980 -0.733 O5  YD5 3  
YD5 CA  CA  C 0 1 N N S Y N N 14.833 34.111 -29.108 -1.624 -0.502 -0.107 C21 YD5 4  
YD5 C   C   C 0 1 N N N Y N Y 15.214 32.636 -28.967 -2.863 0.350  -0.205 C31 YD5 5  
YD5 C41 C41 C 0 1 N N N N N N 13.858 34.642 -28.033 -1.854 -1.621 0.910  C41 YD5 6  
YD5 N   N   N 0 1 N N N Y Y N 14.554 34.535 -30.504 -0.492 0.329  0.326  N1  YD5 7  
YD5 C32 C32 C 0 1 N N N N N N 16.532 36.030 -31.068 1.937  0.642  0.353  C32 YD5 8  
YD5 C33 C33 C 0 1 N N N N N N 15.002 35.903 -30.864 0.784  -0.249 -0.115 C33 YD5 9  
YD5 HA  HA2 H 0 1 N N N Y N N 15.771 34.633 -28.866 -1.403 -0.936 -1.082 H2  YD5 10 
YD5 H4  H4  H 0 1 N N N N N N 14.161 34.266 -27.045 -2.693 -2.237 0.589  H4  YD5 11 
YD5 H5  H5  H 0 1 N N N N N N 13.880 35.742 -28.029 -0.957 -2.237 0.982  H5  YD5 12 
YD5 H6  H6  H 0 1 N N N N N N 12.839 34.297 -28.260 -2.074 -1.187 1.885  H6  YD5 13 
YD5 H   H   H 0 1 N Y N Y Y N 13.565 34.488 -30.647 -0.502 0.461  1.327  H7  YD5 14 
YD5 H9  H9  H 0 1 N N N N N N 16.934 35.053 -31.374 1.925  0.708  1.441  H9  YD5 15 
YD5 H10 H10 H 0 1 N N N N N N 16.727 36.771 -31.857 1.822  1.638  -0.073 H10 YD5 16 
YD5 H11 H11 H 0 1 N N N N N N 14.702 36.589 -30.058 0.899  -1.246 0.311  H11 YD5 17 
YD5 H12 H12 H 0 1 N N N N N N 14.503 36.196 -31.799 0.796  -0.315 -1.203 H12 YD5 18 
YD5 OXT OXT O 0 1 N Y N Y N Y 16.265 32.233 -29.687 -4.027 -0.200 -0.586 O1  YD5 19 
YD5 O3  O3  O 0 1 N Y N N N N 18.265 35.745 -29.357 4.401  0.661  0.204  O3  YD5 20 
YD5 HXT HXT H 0 1 N Y N Y N Y 16.421 31.309 -29.531 -4.794 0.386  -0.634 H1  YD5 21 
YD5 H3  H3  H 0 1 N Y N N N N 18.611 36.124 -28.557 5.215  0.241  -0.105 H3  YD5 22 
# 
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 
YD5 C32 C33 SING N N 1  
YD5 C32 C4  SING N N 2  
YD5 C33 N   SING N N 3  
YD5 N   CA  SING N N 4  
YD5 C4  O5  DOUB N N 5  
YD5 CA  C   SING N N 6  
YD5 CA  C41 SING N N 7  
YD5 C   O   DOUB N N 8  
YD5 CA  HA  SING N N 9  
YD5 C41 H4  SING N N 10 
YD5 C41 H5  SING N N 11 
YD5 C41 H6  SING N N 12 
YD5 N   H   SING N N 13 
YD5 C32 H9  SING N N 14 
YD5 C32 H10 SING N N 15 
YD5 C33 H11 SING N N 16 
YD5 C33 H12 SING N N 17 
YD5 C   OXT SING N N 18 
YD5 C4  O3  SING N N 19 
YD5 OXT HXT SING N N 20 
YD5 O3  H3  SING N N 21 
# 
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 
YD5 SMILES           ACDLabs              12.01 "OC(=O)CCNC(C)C(=O)O"                                                                   
YD5 InChI            InChI                1.06  "InChI=1S/C6H11NO4/c1-4(6(10)11)7-3-2-5(8)9/h4,7H,2-3H2,1H3,(H,8,9)(H,10,11)/t4-/m0/s1" 
YD5 InChIKey         InChI                1.06  OAWHMSFCLIYBHE-BYPYZUCNSA-N                                                             
YD5 SMILES_CANONICAL CACTVS               3.385 "C[C@H](NCCC(O)=O)C(O)=O"                                                               
YD5 SMILES           CACTVS               3.385 "C[CH](NCCC(O)=O)C(O)=O"                                                                
YD5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](C(=O)O)NCCC(=O)O"                                                              
YD5 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C(=O)O)NCCC(=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 
YD5 "SYSTEMATIC NAME" ACDLabs              12.01 "N-(2-carboxyethyl)-L-alanine"                         
YD5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-(3-hydroxy-3-oxopropylamino)propanoic 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 
YD5 "Create component" 2023-01-25 RCSB 
YD5 "Modify backbone"  2023-11-03 PDBE 
YD5 "Modify PCM"       2024-09-27 PDBE 
YD5 "Initial release"  2024-10-16 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YD5 
_pdbx_chem_comp_pcm.modified_residue_id                ALA 
_pdbx_chem_comp_pcm.type                               Carboxyethylation 
_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      ? 
# 
