data_YBR
# 
_chem_comp.id                                    YBR 
_chem_comp.name                                  "N-methyl-D-glutamic acid" 
_chem_comp.type                                  "D-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                     2023-01-23 
_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                     YBR 
_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        8FVQ 
_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 
YBR C7  C7  C 0 1 N N N N N N 108.614 26.593 106.398 -2.059 -2.385 -0.213 C7  YBR 1  
YBR N   N   N 0 1 N N N Y Y N 107.824 27.816 106.142 -1.183 -1.434 0.485  N2  YBR 2  
YBR CA  CA  C 0 1 N N R Y N N 108.246 28.516 104.893 -0.995 -0.213 -0.309 CA  YBR 3  
YBR C   C   C 0 1 N N N Y N Y 107.059 29.074 104.053 -2.115 0.753  -0.018 C   YBR 4  
YBR O   O   O 0 1 N N N Y N Y 106.923 30.293 103.929 -2.690 0.709  1.044  O   YBR 5  
YBR CB  CB  C 0 1 N N N N N N 109.439 29.492 105.029 0.343  0.433  0.059  CB  YBR 6  
YBR CG  CG  C 0 1 N N N N N N 109.765 29.773 106.502 1.487  -0.496 -0.352 CG  YBR 7  
YBR CD  CD  C 0 1 N N N N N N 110.574 31.042 106.675 2.805  0.139  0.010  CD  YBR 8  
YBR OE2 OE2 O 0 1 N N N N N N 111.221 31.550 105.771 2.827  1.224  0.541  OE2 YBR 9  
YBR O1  O1  O 0 1 N N N N N N 110.481 31.555 107.934 3.954  -0.500 -0.258 OE1 YBR 10 
YBR OXT OXT O 0 1 N Y N Y N Y 106.196 28.256 103.448 -2.474 1.661  -0.938 O1  YBR 11 
YBR H1  H1  H 0 1 N N N N N N 108.264 26.117 107.326 -2.115 -3.313 0.356  H1  YBR 12 
YBR H4  H2  H 0 1 N N N N N N 108.489 25.894 105.558 -3.057 -1.957 -0.308 H2  YBR 13 
YBR H3  H3  H 0 1 N N N N N N 109.677 26.858 106.500 -1.656 -2.591 -1.204 H3  YBR 14 
YBR H   H   H 0 1 N Y N Y Y N 107.940 28.440 106.915 -0.296 -1.859 0.711  H4  YBR 15 
YBR HA  HA  H 0 1 N N N Y N N 108.647 27.710 104.261 -0.998 -0.464 -1.369 H6  YBR 16 
YBR HB2 HB2 H 0 1 N N N N N N 110.322 29.048 104.545 0.443  1.385  -0.463 H7  YBR 17 
YBR HB3 HB3 H 0 1 N N N N N N 109.185 30.440 104.531 0.381  0.603  1.135  H8  YBR 18 
YBR HG2 HG2 H 0 1 N N N N N N 108.823 29.874 107.061 1.388  -1.448 0.170  H9  YBR 19 
YBR HG3 HG3 H 0 1 N N N N N N 110.341 28.927 106.905 1.449  -0.666 -1.428 H10 YBR 20 
YBR HE2 HE2 H 0 1 N N N N N N 110.991 32.354 107.989 4.774  -0.052 -0.008 H11 YBR 21 
YBR HXT HXT H 0 1 N Y N Y N Y 105.553 28.769 102.973 -3.197 2.259  -0.706 H12 YBR 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 
YBR O   C   DOUB N N 1  
YBR C   CA  SING N N 2  
YBR CA  CB  SING N N 3  
YBR CA  N   SING N N 4  
YBR CB  CG  SING N N 5  
YBR OE2 CD  DOUB N N 6  
YBR N   C7  SING N N 7  
YBR CG  CD  SING N N 8  
YBR CD  O1  SING N N 9  
YBR C   OXT SING N N 10 
YBR C7  H1  SING N N 11 
YBR C7  H4  SING N N 12 
YBR C7  H3  SING N N 13 
YBR N   H   SING N N 14 
YBR CA  HA  SING N N 15 
YBR CB  HB2 SING N N 16 
YBR CB  HB3 SING N N 17 
YBR CG  HG2 SING N N 18 
YBR CG  HG3 SING N N 19 
YBR O1  HE2 SING N N 20 
YBR OXT HXT 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 
YBR SMILES           ACDLabs              12.01 "CNC(CCC(=O)O)C(=O)O"                                                                   
YBR InChI            InChI                1.06  "InChI=1S/C6H11NO4/c1-7-4(6(10)11)2-3-5(8)9/h4,7H,2-3H2,1H3,(H,8,9)(H,10,11)/t4-/m1/s1" 
YBR InChIKey         InChI                1.06  XLBVNMSMFQMKEY-SCSAIBSYSA-N                                                             
YBR SMILES_CANONICAL CACTVS               3.385 "CN[C@H](CCC(O)=O)C(O)=O"                                                               
YBR SMILES           CACTVS               3.385 "CN[CH](CCC(O)=O)C(O)=O"                                                                
YBR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN[C@H](CCC(=O)O)C(=O)O"                                                               
YBR SMILES           "OpenEye OEToolkits" 2.0.7 "CNC(CCC(=O)O)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 
YBR "SYSTEMATIC NAME" ACDLabs              12.01 "N-methyl-D-glutamic acid"                 
YBR "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-2-(methylamino)pentanedioic 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 
YBR "Create component" 2023-01-23 RCSB 
YBR "Modify backbone"  2023-11-03 PDBE 
YBR "Modify PCM"       2024-09-27 PDBE 
YBR "Initial release"  2024-10-16 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YBR 
_pdbx_chem_comp_pcm.modified_residue_id                DGL 
_pdbx_chem_comp_pcm.type                               Methylation 
_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      ? 
# 
