data_VYA # _chem_comp.id VYA _chem_comp.name "2-[(4~{Z})-2-[(1~{S})-1-azanyl-3-methyl-butyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid" _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C17 H21 N3 O4" _chem_comp.mon_nstd_parent_comp_id "LEU, TYR, GLY" _chem_comp.pdbx_synonyms "PEPTIDE DERIVED CHROMOPHORE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-08-09 _chem_comp.pdbx_modified_date 2023-11-03 _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 331.366 _chem_comp.one_letter_code LYG _chem_comp.three_letter_code VYA _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 5OOZ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 VYA C12 C2 C 0 1 Y N N N N N 40.049 80.461 99.498 3.955 -1.288 -0.517 C2 VYA 1 VYA C4 C4 C 0 1 Y N N N N N 40.535 82.833 99.861 5.511 0.457 0.079 C4 VYA 2 VYA C5 C5 C 0 1 Y N N N N N 41.914 82.561 99.599 4.471 1.257 0.477 C5 VYA 3 VYA C6 C6 C 0 1 Y N N N N N 41.421 80.196 99.224 2.907 -0.495 -0.127 C6 VYA 4 VYA C8 C8 C 0 1 N N N N N N 43.742 80.859 99.005 2.037 1.641 0.796 C8 VYA 5 VYA C22 C3 C 0 1 N N N N N N 45.487 88.366 99.598 -3.021 -4.345 1.339 C3 VYA 6 VYA C21 C21 C 0 1 N N N N N N 46.227 87.415 98.631 -2.916 -3.289 0.237 C21 VYA 7 VYA C10 C10 C 0 1 N N N N N N 47.709 87.625 98.926 -4.307 -2.727 -0.066 C10 VYA 8 VYA C20 C20 C 0 1 N N N N N N 45.792 85.967 99.003 -1.999 -2.156 0.703 C20 VYA 9 VYA CA1 C16 C 0 1 N N S Y N N 46.645 84.804 98.381 -1.781 -1.170 -0.447 C16 VYA 10 VYA N1 N N 0 1 N N N Y Y N 46.813 84.985 96.950 -1.063 -1.842 -1.538 N VYA 11 VYA C1 C14 C 0 1 N N N Y N N 46.093 83.391 98.491 -0.969 0.001 0.043 C14 VYA 12 VYA N2 N15 N 0 1 N N N Y N N 44.828 83.056 98.767 0.326 0.021 0.098 N15 VYA 13 VYA N3 N13 N 0 1 N N N Y N N 46.864 82.281 98.378 -1.503 1.181 0.480 N13 VYA 14 VYA CA3 C17 C 0 1 N N N Y N N 48.158 82.202 97.607 -2.931 1.501 0.550 C17 VYA 15 VYA C3 C C 0 1 N N N Y N Y 49.207 81.449 98.453 -3.369 2.128 -0.748 C VYA 16 VYA O3 O19 O 0 1 N N N Y N Y 50.240 80.848 98.082 -2.571 2.291 -1.640 O19 VYA 17 VYA C2 C12 C 0 1 N N N Y N N 45.993 81.281 98.463 -0.491 1.999 0.840 C12 VYA 18 VYA O2 O25 O 0 1 N N N Y N N 46.401 80.008 98.371 -0.576 3.132 1.278 O25 VYA 19 VYA CA2 C9 C 0 1 N N N Y N N 44.768 81.708 98.792 0.739 1.229 0.587 C9 VYA 20 VYA C7 C7 C 0 1 Y N N N N N 42.373 81.246 99.276 3.153 0.790 0.377 C7 VYA 21 VYA C11 C1 C 0 1 Y N N N N N 39.618 81.770 99.788 5.261 -0.819 -0.415 C1 VYA 22 VYA O19 O3 O 0 1 N N N N N N 38.287 82.006 100.027 6.295 -1.610 -0.797 O3 VYA 23 VYA OXT OXT O 0 1 N Y N Y N Y 49.029 81.488 100.039 -4.647 2.507 -0.914 O1 VYA 24 VYA H1 H1 H 0 1 N N N N N N 39.334 79.652 99.483 3.767 -2.280 -0.901 H1 VYA 25 VYA H22 H2 H 0 1 N N N N N N 40.206 83.831 100.109 6.527 0.815 0.156 H2 VYA 26 VYA H3 H3 H 0 1 N N N N N N 42.628 83.370 99.646 4.667 2.244 0.869 H3 VYA 27 VYA H4 H4 H 0 1 N N N N N N 41.737 79.194 98.976 1.893 -0.860 -0.207 H4 VYA 28 VYA H5 H5 H 0 1 N N N N N N 43.960 79.802 98.971 2.232 2.593 1.269 H5 VYA 29 VYA H6 H6 H 0 1 N N N N N N 44.402 88.273 99.446 -3.603 -5.192 0.975 H6 VYA 30 VYA H7 H7 H 0 1 N N N N N N 45.736 88.100 100.636 -2.022 -4.682 1.616 H7 VYA 31 VYA H8 H8 H 0 1 N N N N N N 45.797 89.403 99.401 -3.514 -3.914 2.210 H8 VYA 32 VYA H9 H9 H 0 1 N N N N N N 45.986 87.644 97.582 -2.503 -3.743 -0.664 H9 VYA 33 VYA H10 H10 H 0 1 N N N N N N 47.995 88.652 98.657 -4.232 -1.975 -0.851 H10 VYA 34 VYA H11 H11 H 0 1 N N N N N N 47.896 87.462 99.998 -4.959 -3.535 -0.398 H11 VYA 35 VYA H12 H12 H 0 1 N N N N N N 48.305 86.912 98.337 -4.720 -2.273 0.835 H12 VYA 36 VYA H13 H13 H 0 1 N N N N N N 44.751 85.834 98.672 -2.461 -1.637 1.544 H13 VYA 37 VYA H14 H14 H 0 1 N N N N N N 45.843 85.872 100.098 -1.040 -2.569 1.014 H14 VYA 38 VYA HA1 H15 H 0 1 N N N Y N N 47.633 84.824 98.863 -2.746 -0.817 -0.810 H15 VYA 39 VYA H H16 H 0 1 N N N Y Y N 47.177 85.899 96.770 -0.208 -2.260 -1.204 H16 VYA 40 VYA H2 H17 H 0 1 N Y N Y Y N 47.449 84.297 96.600 -1.650 -2.529 -1.988 H17 VYA 41 VYA HA31 H19 H 0 1 N N N Y N N 47.991 81.663 96.663 -3.501 0.588 0.723 H19 VYA 42 VYA HA32 H20 H 0 1 N N N Y N N 48.520 83.218 97.391 -3.107 2.199 1.368 H20 VYA 43 VYA H21 H21 H 0 1 N N N N N N 38.156 82.930 100.206 6.541 -1.513 -1.727 H21 VYA 44 VYA HXT H22 H 0 1 N Y N Y N Y 49.756 81.036 100.451 -4.880 2.904 -1.764 H22 VYA 45 # 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 VYA N1 CA1 SING N N 1 VYA CA3 N3 SING N N 2 VYA CA3 C3 SING N N 3 VYA O3 C3 DOUB N N 4 VYA O2 C2 DOUB N N 5 VYA N3 C2 SING N N 6 VYA N3 C1 SING N N 7 VYA CA1 C1 SING N N 8 VYA CA1 C20 SING N N 9 VYA C2 CA2 SING N N 10 VYA C1 N2 DOUB N N 11 VYA C21 C10 SING N N 12 VYA C21 C20 SING N N 13 VYA C21 C22 SING N N 14 VYA N2 CA2 SING N N 15 VYA CA2 C8 DOUB N Z 16 VYA C8 C7 SING N N 17 VYA C6 C7 DOUB Y N 18 VYA C6 C12 SING Y N 19 VYA C7 C5 SING Y N 20 VYA C12 C11 DOUB Y N 21 VYA C5 C4 DOUB Y N 22 VYA C11 C4 SING Y N 23 VYA C11 O19 SING N N 24 VYA C3 OXT SING N N 25 VYA C12 H1 SING N N 26 VYA C4 H22 SING N N 27 VYA C5 H3 SING N N 28 VYA C6 H4 SING N N 29 VYA C8 H5 SING N N 30 VYA C22 H6 SING N N 31 VYA C22 H7 SING N N 32 VYA C22 H8 SING N N 33 VYA C21 H9 SING N N 34 VYA C10 H10 SING N N 35 VYA C10 H11 SING N N 36 VYA C10 H12 SING N N 37 VYA C20 H13 SING N N 38 VYA C20 H14 SING N N 39 VYA CA1 HA1 SING N N 40 VYA N1 H SING N N 41 VYA N1 H2 SING N N 42 VYA CA3 HA31 SING N N 43 VYA CA3 HA32 SING N N 44 VYA O19 H21 SING N N 45 VYA OXT HXT SING N N 46 # 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 VYA InChI InChI 1.03 "InChI=1S/C17H21N3O4/c1-10(2)7-13(18)16-19-14(17(24)20(16)9-15(22)23)8-11-3-5-12(21)6-4-11/h3-6,8,10,13,21H,7,9,18H2,1-2H3,(H,22,23)/b14-8-/t13-/m0/s1" VYA InChIKey InChI 1.03 ALXOAIZIOMYWBO-IAOKNECISA-N VYA SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](N)C1=N\C(=C/c2ccc(O)cc2)C(=O)N1CC(O)=O" VYA SMILES CACTVS 3.385 "CC(C)C[CH](N)C1=NC(=Cc2ccc(O)cc2)C(=O)N1CC(O)=O" VYA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC(C)C[C@@H](C1=N/C(=C\c2ccc(cc2)O)/C(=O)N1CC(=O)O)N" VYA SMILES "OpenEye OEToolkits" 2.0.6 "CC(C)CC(C1=NC(=Cc2ccc(cc2)O)C(=O)N1CC(=O)O)N" # _pdbx_chem_comp_identifier.comp_id VYA _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "2-[(4~{Z})-2-[(1~{S})-1-azanyl-3-methyl-butyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic 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 VYA "Create component" 2017-08-09 EBI VYA "Other modification" 2017-08-09 EBI VYA "Initial release" 2017-12-06 RCSB VYA "Other modification" 2018-10-20 EBI VYA "Modify synonyms" 2021-03-01 PDBE VYA "Modify backbone" 2023-11-03 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VYA _pdbx_chem_comp_synonyms.name "PEPTIDE DERIVED CHROMOPHORE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? #