data_XYC
# 
_chem_comp.id                                    XYC 
_chem_comp.name                                  "(2~{S})-2-azanyl-3-cyclopentyl-propanoic acid" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C8 H15 N O2" 
_chem_comp.mon_nstd_parent_comp_id               ALA 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2016-06-10 
_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                        157.210 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XYC 
_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        5B6G 
_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 
XYC O   O1  O 0 1 N N N Y N Y 0.671  20.930 103.310 2.978  -0.619 -0.693 O   XYC 1  
XYC C   C1  C 0 1 N N N Y N Y 1.212  21.760 104.014 1.972  -0.652 -0.025 C   XYC 2  
XYC CA  C2  C 0 1 N N S Y N N 2.587  22.277 103.627 1.368  0.628  0.492  CA  XYC 3  
XYC N   N1  N 0 1 N N N Y Y N 3.211  21.411 102.608 2.385  1.688  0.481  N   XYC 4  
XYC CB  C3  C 0 1 N N N N N N 2.354  23.695 103.108 0.195  1.036  -0.401 CB  XYC 5  
XYC C04 C4  C 0 1 N N N N N N 3.634  24.477 102.795 -0.927 0.004  -0.272 C04 XYC 6  
XYC C08 C5  C 0 1 N N N N N N 3.290  25.821 102.141 -1.595 0.101  1.122  C08 XYC 7  
XYC C07 C6  C 0 1 N N N N N N 3.299  26.868 103.242 -2.997 -0.509 0.873  C07 XYC 8  
XYC C06 C7  C 0 1 N N N N N N 3.735  26.135 104.512 -3.384 -0.005 -0.533 C06 XYC 9  
XYC C05 C8  C 0 1 N N N N N N 4.385  24.836 104.073 -2.068 0.321  -1.261 C05 XYC 10 
XYC HA  H2  H 0 1 N N N Y N N 3.224  22.320 104.522 1.013  0.476  1.512  HA  XYC 11 
XYC H   H3  H 0 1 N N N Y Y N 3.346  20.495 102.986 2.786  1.795  -0.439 H   XYC 12 
XYC H2  H4  H 0 1 N Y N Y Y N 2.615  21.356 101.807 2.001  2.561  0.811  H2  XYC 13 
XYC H6  H6  H 0 1 N N N N N N 1.790  24.251 103.871 -0.173 2.014  -0.092 H6  XYC 14 
XYC H7  H7  H 0 1 N N N N N N 1.758  23.629 102.186 0.528  1.084  -1.438 H7  XYC 15 
XYC H8  H8  H 0 1 N N N N N N 4.281  23.889 102.128 -0.541 -1.001 -0.444 H8  XYC 16 
XYC H9  H9  H 0 1 N N N N N N 4.040  26.071 101.376 -1.043 -0.486 1.856  H9  XYC 17 
XYC H10 H10 H 0 1 N N N N N N 2.294  25.771 101.676 -1.677 1.140  1.440  H10 XYC 18 
XYC H11 H11 H 0 1 N N N N N N 4.010  27.672 103.000 -2.947 -1.598 0.887  H11 XYC 19 
XYC H12 H12 H 0 1 N N N N N N 2.294  27.295 103.372 -3.707 -0.149 1.616  H12 XYC 20 
XYC H13 H13 H 0 1 N N N N N N 4.456  26.748 105.073 -3.926 -0.783 -1.072 H13 XYC 21 
XYC H14 H14 H 0 1 N N N N N N 2.861  25.925 105.146 -3.999 0.891  -0.452 H14 XYC 22 
XYC H15 H15 H 0 1 N N N N N N 4.258  24.055 104.837 -2.044 1.376  -1.533 H15 XYC 23 
XYC H16 H16 H 0 1 N N N N N N 5.457  24.981 103.872 -1.971 -0.298 -2.153 H16 XYC 24 
XYC OXT O2  O 0 1 N Y N Y N Y 0.643  22.224 105.132 1.389  -1.829 0.251  OXT XYC 25 
XYC HXT H1  H 0 1 N Y N Y N Y -0.202 21.807 105.255 1.810  -2.623 -0.106 HXT XYC 26 
# 
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 
XYC C08 C04 SING N N 1  
XYC C08 C07 SING N N 2  
XYC N   CA  SING N N 3  
XYC C04 CB  SING N N 4  
XYC C04 C05 SING N N 5  
XYC CB  CA  SING N N 6  
XYC C07 C06 SING N N 7  
XYC O   C   DOUB N N 8  
XYC CA  C   SING N N 9  
XYC C05 C06 SING N N 10 
XYC CA  HA  SING N N 11 
XYC N   H   SING N N 12 
XYC N   H2  SING N N 13 
XYC CB  H6  SING N N 14 
XYC CB  H7  SING N N 15 
XYC C04 H8  SING N N 16 
XYC C08 H9  SING N N 17 
XYC C08 H10 SING N N 18 
XYC C07 H11 SING N N 19 
XYC C07 H12 SING N N 20 
XYC C06 H13 SING N N 21 
XYC C06 H14 SING N N 22 
XYC C05 H15 SING N N 23 
XYC C05 H16 SING N N 24 
XYC C   OXT SING N N 25 
XYC OXT HXT 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 
XYC InChI            InChI                1.03  "InChI=1S/C8H15NO2/c9-7(8(10)11)5-6-3-1-2-4-6/h6-7H,1-5,9H2,(H,10,11)/t7-/m0/s1" 
XYC InChIKey         InChI                1.03  KDYAKYRBGLKMAK-ZETCQYMHSA-N                                                      
XYC SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CC1CCCC1)C(O)=O"                                                        
XYC SMILES           CACTVS               3.385 "N[CH](CC1CCCC1)C(O)=O"                                                          
XYC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "C1CCC(C1)C[C@@H](C(=O)O)N"                                                      
XYC SMILES           "OpenEye OEToolkits" 2.0.5 "C1CCC(C1)CC(C(=O)O)N"                                                           
# 
_pdbx_chem_comp_identifier.comp_id           XYC 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.5 
_pdbx_chem_comp_identifier.identifier        "(2~{S})-2-azanyl-3-cyclopentyl-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 
XYC "Create component" 2016-06-10 PDBJ 
XYC "Initial release"  2017-05-31 RCSB 
XYC "Modify backbone"  2023-11-03 PDBE 
XYC "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            XYC 
_pdbx_chem_comp_pcm.modified_residue_id                ? 
_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      ? 
# 
