data_A1BDE
# 
_chem_comp.id                                    A1BDE 
_chem_comp.name                                  N~6~-L-seryl-L-lysine 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C9 H19 N3 O4" 
_chem_comp.mon_nstd_parent_comp_id               LYS 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-10-15 
_chem_comp.pdbx_modified_date                    2025-05-30 
_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                        233.265 
_chem_comp.one_letter_code                       K 
_chem_comp.three_letter_code                     A1BDE 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        9DXV 
_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_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 
A1BDE C10 C1  C 0 1 N N N N N N -16.235 -15.963 15.569 -3.240 -0.592 -0.146 C10 A1BDE 1  
A1BDE C13 C2  C 0 1 N N N N N N -14.648 -14.085 16.114 -4.854 1.091  0.698  C13 A1BDE 2  
A1BDE CG  C3  C 0 1 N N N N N N -19.977 -13.622 15.391 1.682  -0.601 0.072  CG  A1BDE 3  
A1BDE CE  C4  C 0 1 N N N N N N -18.401 -15.458 14.437 -0.812 -0.731 0.009  CE  A1BDE 4  
A1BDE CD  C5  C 0 1 N N N N N N -19.330 -14.238 14.114 0.399  0.166  -0.255 CD  A1BDE 5  
A1BDE CB  C6  C 0 1 N N N N N N -20.461 -12.208 15.086 2.893  0.296  -0.192 CB  A1BDE 6  
A1BDE CA  C7  C 0 1 N N S N Y N -19.254 -11.206 14.945 4.176  -0.470 0.134  CA  A1BDE 7  
A1BDE C   C8  C 0 1 N N N N Y Y -19.679 -10.146 13.955 5.371  0.368  -0.241 C   A1BDE 8  
A1BDE C12 C9  C 0 1 N N S N N N -15.013 -15.568 16.383 -4.504 0.163  -0.467 C12 A1BDE 9  
A1BDE N   N1  N 0 1 N N N Y Y N -18.991 -10.581 16.203 4.218  -0.766 1.573  N   A1BDE 10 
A1BDE NZ  N2  N 0 1 N N N N N N -17.255 -14.973 15.242 -2.041 0.003  -0.303 NZ  A1BDE 11 
A1BDE N14 N3  N 0 1 N N N N N N -13.973 -16.446 15.936 -5.602 -0.789 -0.682 N14 A1BDE 12 
A1BDE O   O1  O 0 1 N N N N Y Y -20.159 -10.465 12.872 5.968  0.984  0.610  O   A1BDE 13 
A1BDE O11 O2  O 0 1 N N N N N N -16.352 -17.099 15.203 -3.302 -1.733 0.260  O11 A1BDE 14 
A1BDE O15 O3  O 0 1 N N N N N N -14.052 -13.982 14.836 -5.985 1.891  0.347  O15 A1BDE 15 
A1BDE H1  H1  H 0 1 N N N N N N -13.941 -13.735 16.880 -5.090 0.495  1.579  H1  A1BDE 16 
A1BDE H3  H2  H 0 1 N N N N N N -15.559 -13.469 16.147 -4.004 1.739  0.915  H3  A1BDE 17 
A1BDE HG2 H3  H 0 1 N N N N N N -20.830 -14.242 15.705 1.671  -0.897 1.121  HG2 A1BDE 18 
A1BDE HG3 H4  H 0 1 N N N N N N -19.232 -13.588 16.199 1.744  -1.489 -0.557 HG3 A1BDE 19 
A1BDE HE2 H5  H 0 1 N N N N N N -18.963 -16.212 15.007 -0.750 -1.619 -0.619 HE2 A1BDE 20 
A1BDE HE3 H6  H 0 1 N N N N N N -18.035 -15.904 13.501 -0.823 -1.028 1.058  HE3 A1BDE 21 
A1BDE HD2 H7  H 0 1 N N N N N N -18.732 -13.463 13.613 0.337  1.055  0.374  HD2 A1BDE 22 
A1BDE HD3 H8  H 0 1 N N N N N N -20.132 -14.575 13.440 0.410  0.463  -1.303 HD3 A1BDE 23 
A1BDE HB2 H9  H 0 1 N N N N N N -21.114 -11.869 15.904 2.904  0.593  -1.241 HB2 A1BDE 24 
A1BDE HB3 H10 H 0 1 N N N N N N -21.029 -12.219 14.144 2.831  1.185  0.436  HB3 A1BDE 25 
A1BDE HA  H11 H 0 1 N N N N Y N -18.372 -11.746 14.571 4.195  -1.403 -0.429 HA  A1BDE 26 
A1BDE H13 H13 H 0 1 N N N N N N -15.217 -15.707 17.455 -4.354 0.755  -1.370 H13 A1BDE 27 
A1BDE H   H14 H 0 1 N N N Y Y N -18.709 -11.273 16.867 5.024  -1.327 1.804  H   A1BDE 28 
A1BDE H2  H15 H 0 1 N N N Y Y N -18.261 -9.907  16.094 4.201  0.083  2.117  H2  A1BDE 29 
A1BDE HZ1 H17 H 0 1 N N N N N N -17.185 -14.022 15.543 -1.992 0.917  -0.624 HZ1 A1BDE 30 
A1BDE H18 H18 H 0 1 N N N N N N -13.129 -16.243 16.432 -5.424 -1.371 -1.486 H18 A1BDE 31 
A1BDE H19 H19 H 0 1 N N N N N N -14.241 -17.394 16.107 -5.761 -1.349 0.142  H19 A1BDE 32 
A1BDE H21 H21 H 0 1 N N N N N N -13.825 -13.076 14.664 -6.263 2.505  1.040  H21 A1BDE 33 
A1BDE OXT OXT O 0 1 N Y N N Y Y ?       ?       ?      5.773  0.429  -1.520 OXT A1BDE 34 
A1BDE H4  H20 H 0 1 N N N N N N ?       ?       ?      6.545  0.980  -1.712 H4  A1BDE 35 
# 
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 
A1BDE O   C   DOUB N N 1  
A1BDE C   CA  SING N N 2  
A1BDE CD  CE  SING N N 3  
A1BDE CD  CG  SING N N 4  
A1BDE CE  NZ  SING N N 5  
A1BDE O15 C13 SING N N 6  
A1BDE CA  CB  SING N N 7  
A1BDE CA  N   SING N N 8  
A1BDE CB  CG  SING N N 9  
A1BDE O11 C10 DOUB N N 10 
A1BDE NZ  C10 SING N N 11 
A1BDE C10 C12 SING N N 12 
A1BDE N14 C12 SING N N 13 
A1BDE C13 C12 SING N N 14 
A1BDE C13 H1  SING N N 15 
A1BDE C13 H3  SING N N 16 
A1BDE CG  HG2 SING N N 17 
A1BDE CG  HG3 SING N N 18 
A1BDE CE  HE2 SING N N 19 
A1BDE CE  HE3 SING N N 20 
A1BDE CD  HD2 SING N N 21 
A1BDE CD  HD3 SING N N 22 
A1BDE CB  HB2 SING N N 23 
A1BDE CB  HB3 SING N N 24 
A1BDE CA  HA  SING N N 25 
A1BDE C12 H13 SING N N 26 
A1BDE N   H   SING N N 27 
A1BDE N   H2  SING N N 28 
A1BDE NZ  HZ1 SING N N 29 
A1BDE N14 H18 SING N N 30 
A1BDE N14 H19 SING N N 31 
A1BDE O15 H21 SING N N 32 
A1BDE C   OXT SING N N 33 
A1BDE OXT H4  SING N N 34 
# 
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 
A1BDE SMILES           ACDLabs              14.52   "O=C(NCCCCC(N)C(=O)O)C(N)CO"                                                                                      
A1BDE InChI            InChI                1.06    "InChI=1S/C9H19N3O4/c10-6(9(15)16)3-1-2-4-12-8(14)7(11)5-13/h6-7,13H,1-5,10-11H2,(H,12,14)(H,15,16)/t6-,7-/m0/s1" 
A1BDE InChIKey         InChI                1.06    XMXRWVAGRXQGGI-BQBZGAKWSA-N                                                                                       
A1BDE SMILES_CANONICAL CACTVS               3.385   "N[C@@H](CO)C(=O)NCCCC[C@H](N)C(O)=O"                                                                             
A1BDE SMILES           CACTVS               3.385   "N[CH](CO)C(=O)NCCCC[CH](N)C(O)=O"                                                                                
A1BDE SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C(CCNC(=O)[C@H](CO)N)C[C@@H](C(=O)O)N"                                                                           
A1BDE SMILES           "OpenEye OEToolkits" 3.1.0.0 "C(CCNC(=O)C(CO)N)CC(C(=O)O)N"                                                                                    
# 
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 
A1BDE "SYSTEMATIC NAME" ACDLabs              14.52   N~6~-L-seryl-L-lysine                                                            
A1BDE "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(2~{S})-2-azanyl-6-[[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]amino]hexanoic 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 
A1BDE "Create component" 2024-10-15 RCSB 
A1BDE "Modify atom id"   2025-05-29 RCSB 
A1BDE "Initial release"  2025-06-04 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1BDE 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_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      ? 
# 
