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         ? 
# 
