data_A1D5B
# 
_chem_comp.id                                    A1D5B 
_chem_comp.name                                  "methyl (2~{S})-2,6-bis(azanyl)hexanoate" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C7 H16 N2 O2" 
_chem_comp.mon_nstd_parent_comp_id               LYS 
_chem_comp.pdbx_synonyms                         "Methyl lysinate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-01-02 
_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                        160.214 
_chem_comp.one_letter_code                       K 
_chem_comp.three_letter_code                     A1D5B 
_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        8XIQ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1D5B N   N1  N 0 1 N N N Y Y N 147.732 124.567 102.821 0.816  2.066  0.165  N   A1D5B 1  
A1D5B CA  C1  C 0 1 N N S N Y N 148.177 123.737 103.934 0.921  0.636  0.483  CA  A1D5B 2  
A1D5B CB  C2  C 0 1 N N N N N N 147.033 123.423 104.894 -0.217 -0.124 -0.201 CB  A1D5B 3  
A1D5B CG  C3  C 0 1 N N N N N N 147.095 124.205 106.203 -1.556 0.324  0.387  CG  A1D5B 4  
A1D5B CD  C4  C 0 1 N N N N N N 146.074 123.721 107.240 -2.694 -0.436 -0.297 CD  A1D5B 5  
A1D5B CE  C5  C 0 1 N N N N N N 145.564 124.827 108.164 -4.034 0.012  0.291  CE  A1D5B 6  
A1D5B NZ  N2  N 0 1 N N N N N N 144.370 125.439 107.618 -5.126 -0.717 -0.366 NZ  A1D5B 7  
A1D5B C   C6  C 0 1 N N N N Y Y 148.656 122.409 103.378 2.244  0.108  -0.008 C   A1D5B 8  
A1D5B O   O1  O 0 1 N N N N Y Y 149.470 121.785 103.959 2.856  0.709  -0.859 O   A1D5B 9  
A1D5B OXT O2  O 0 1 N N N N N Y 148.144 121.916 102.182 2.743  -1.030 0.501  OXT A1D5B 10 
A1D5B C7  C7  C 0 1 N N N N N N 147.407 120.737 102.317 4.022  -1.479 -0.019 C7  A1D5B 11 
A1D5B H1  H1  H 0 1 N N N Y Y N 147.412 125.448 103.169 0.876  2.220  -0.830 H1  A1D5B 12 
A1D5B H2  H2  H 0 1 N N N Y Y N 148.494 124.714 102.190 -0.035 2.458  0.540  H2  A1D5B 13 
A1D5B H4  H4  H 0 1 N N N N Y N 148.995 124.228 104.481 0.852  0.498  1.562  H4  A1D5B 14 
A1D5B H5  H5  H 0 1 N N N N N N 146.084 123.662 104.392 -0.202 0.085  -1.271 H5  A1D5B 15 
A1D5B H6  H6  H 0 1 N N N N N N 147.063 122.349 105.130 -0.089 -1.194 -0.039 H6  A1D5B 16 
A1D5B H7  H7  H 0 1 N N N N N N 148.104 124.097 106.628 -1.572 0.115  1.457  H7  A1D5B 17 
A1D5B H8  H8  H 0 1 N N N N N N 146.899 125.266 105.987 -1.685 1.394  0.225  H8  A1D5B 18 
A1D5B H9  H9  H 0 1 N N N N N N 145.214 123.291 106.706 -2.679 -0.227 -1.367 H9  A1D5B 19 
A1D5B H10 H10 H 0 1 N N N N N N 146.548 122.944 107.858 -2.566 -1.506 -0.135 H10 A1D5B 20 
A1D5B H11 H11 H 0 1 N N N N N N 145.331 124.396 109.149 -4.049 -0.197 1.361  H11 A1D5B 21 
A1D5B H12 H12 H 0 1 N N N N N N 146.345 125.594 108.275 -4.162 1.082  0.128  H12 A1D5B 22 
A1D5B H13 H13 H 0 1 N N N N N N 144.052 126.159 108.235 -4.995 -1.714 -0.285 H13 A1D5B 23 
A1D5B H14 H14 H 0 1 N N N N N N 144.578 125.835 106.723 -6.022 -0.439 0.005  H14 A1D5B 24 
A1D5B H16 H16 H 0 1 N N N N N N 147.041 120.418 101.330 3.939  -1.650 -1.092 H16 A1D5B 25 
A1D5B H17 H17 H 0 1 N N N N N N 148.048 119.951 102.742 4.779  -0.717 0.170  H17 A1D5B 26 
A1D5B H18 H18 H 0 1 N N N N N N 146.552 120.914 102.986 4.310  -2.407 0.475  H18 A1D5B 27 
# 
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 
A1D5B OXT C7  SING N N 1  
A1D5B OXT C   SING N N 2  
A1D5B N   CA  SING N N 3  
A1D5B C   CA  SING N N 4  
A1D5B C   O   DOUB N N 5  
A1D5B CA  CB  SING N N 6  
A1D5B CB  CG  SING N N 7  
A1D5B CG  CD  SING N N 8  
A1D5B CD  CE  SING N N 9  
A1D5B NZ  CE  SING N N 10 
A1D5B N   H1  SING N N 11 
A1D5B N   H2  SING N N 12 
A1D5B CA  H4  SING N N 13 
A1D5B CB  H5  SING N N 14 
A1D5B CB  H6  SING N N 15 
A1D5B CG  H7  SING N N 16 
A1D5B CG  H8  SING N N 17 
A1D5B CD  H9  SING N N 18 
A1D5B CD  H10 SING N N 19 
A1D5B CE  H11 SING N N 20 
A1D5B CE  H12 SING N N 21 
A1D5B NZ  H13 SING N N 22 
A1D5B NZ  H14 SING N N 23 
A1D5B C7  H16 SING N N 24 
A1D5B C7  H17 SING N N 25 
A1D5B C7  H18 SING N N 26 
# 
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 
A1D5B InChI            InChI                1.06  "InChI=1S/C7H16N2O2/c1-11-7(10)6(9)4-2-3-5-8/h6H,2-5,8-9H2,1H3/t6-/m0/s1" 
A1D5B InChIKey         InChI                1.06  KPNBUPJZFJCCIQ-LURJTMIESA-N                                               
A1D5B SMILES_CANONICAL CACTVS               3.385 "COC(=O)[C@@H](N)CCCCN"                                                   
A1D5B SMILES           CACTVS               3.385 "COC(=O)[CH](N)CCCCN"                                                     
A1D5B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COC(=O)[C@H](CCCCN)N"                                                    
A1D5B SMILES           "OpenEye OEToolkits" 2.0.7 "COC(=O)C(CCCCN)N"                                                        
# 
_pdbx_chem_comp_identifier.comp_id           A1D5B 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "methyl (2~{S})-2,6-bis(azanyl)hexanoate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1D5B 
_pdbx_chem_comp_synonyms.name         "Methyl lysinate" 
_pdbx_chem_comp_synonyms.provenance   PUBCHEM 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1D5B "Create component" 2024-01-02 PDBC 
A1D5B "Initial release"  2024-07-03 RCSB 
A1D5B "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1D5B 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_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               C-terminal 
_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     PTM-0170 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
