data_DYL # _chem_comp.id DYL _chem_comp.name "(2R)-2-aminopent-4-enoic acid" _chem_comp.type "D-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C5 H9 N O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-12-20 _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 115.130 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DYL _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 4NR1 _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 DYL N N N 0 1 N N N Y Y N -26.313 25.803 -3.969 -0.119 1.753 0.400 N DYL 1 DYL CA CA C 0 1 N N R Y N N -26.038 24.485 -3.391 -0.119 0.284 0.422 CA DYL 2 DYL C C C 0 1 N N N Y N Y -26.299 24.396 -1.882 -1.485 -0.223 0.038 C DYL 3 DYL O O O 0 1 N N N Y N Y -27.112 25.152 -1.331 -2.249 0.494 -0.564 O DYL 4 DYL CB CB C 0 1 N N N N N N -26.790 23.382 -4.151 0.918 -0.241 -0.573 CB DYL 5 DYL CG CG C 0 1 N N N N N N -25.782 22.455 -4.736 2.298 0.164 -0.121 CG DYL 6 DYL CD CD C 0 1 N N N N N N -25.712 21.197 -4.333 3.225 -0.745 0.047 CD DYL 7 DYL OXT O1 O 0 1 N Y N Y N Y -25.578 23.464 -1.250 -1.853 -1.472 0.364 O1 DYL 8 DYL H H1 H 0 1 N N N Y Y N -25.813 26.502 -3.458 0.767 2.119 0.716 H1 DYL 9 DYL H2 H2 H 0 1 N Y N Y Y N -26.020 25.815 -4.925 -0.347 2.101 -0.519 H2 DYL 10 DYL HA H4 H 0 1 N N N Y N N -24.966 24.284 -3.533 0.130 -0.064 1.424 H4 DYL 11 DYL H5 H5 H 0 1 N N N N N N -27.396 23.828 -4.953 0.857 -1.328 -0.622 H5 DYL 12 DYL H6 H6 H 0 1 N N N N N N -27.445 22.832 -3.459 0.721 0.180 -1.559 H6 DYL 13 DYL H7 H7 H 0 1 N N N N N N -25.103 22.813 -5.495 2.521 1.204 0.065 H7 DYL 14 DYL H8 H8 H 0 1 N N N N N N -24.978 20.532 -4.763 3.001 -1.785 -0.139 H8 DYL 15 DYL H9 H9 H 0 1 N N N N N N -26.389 20.835 -3.574 4.214 -0.455 0.371 H9 DYL 16 DYL HXT H10 H 0 1 N Y N Y N Y -25.787 23.475 -0.323 -2.739 -1.753 0.097 H10 DYL 17 # 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 DYL CG CD DOUB N N 1 DYL CG CB SING N N 2 DYL CB CA SING N N 3 DYL N CA SING N N 4 DYL CA C SING N N 5 DYL C O DOUB N N 6 DYL C OXT SING N N 7 DYL N H SING N N 8 DYL N H2 SING N N 9 DYL CA HA SING N N 10 DYL CB H5 SING N N 11 DYL CB H6 SING N N 12 DYL CG H7 SING N N 13 DYL CD H8 SING N N 14 DYL CD H9 SING N N 15 DYL OXT HXT SING N N 16 # 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 DYL SMILES ACDLabs 12.01 "O=C(O)C(N)C/C=C" DYL InChI InChI 1.03 "InChI=1S/C5H9NO2/c1-2-3-4(6)5(7)8/h2,4H,1,3,6H2,(H,7,8)/t4-/m1/s1" DYL InChIKey InChI 1.03 WNNNWFKQCKFSDK-SCSAIBSYSA-N DYL SMILES_CANONICAL CACTVS 3.385 "N[C@H](CC=C)C(O)=O" DYL SMILES CACTVS 3.385 "N[CH](CC=C)C(O)=O" DYL SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C=CC[C@H](C(=O)O)N" DYL SMILES "OpenEye OEToolkits" 1.7.6 "C=CCC(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 DYL "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2-aminopent-4-enoic acid" DYL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-2-azanylpent-4-enoic 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 DYL "Create component" 2013-12-20 RCSB DYL "Initial release" 2015-01-21 RCSB DYL "Modify backbone" 2023-11-03 PDBE DYL "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id DYL _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 ? #