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 ?
#