data_WNT
# 
_chem_comp.id                                    WNT 
_chem_comp.name                                  "(4~{S},9~{S},10~{S},12~{E})-16-methoxy-4-methyl-9,10,18-tris(oxidanyl)-3-oxabicyclo[12.4.0]octadeca-1(18),12,14,16-tetraene-2,8-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H24 O7" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-10-09 
_chem_comp.pdbx_modified_date                    2025-01-17 
_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                        364.390 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     WNT 
_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        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
WNT C3   C1  C 0 1 Y N N N N N ? ? ? 2.948  -1.188 -0.131 C3   WNT 1  
WNT C5   C2  C 0 1 Y N N N N N ? ? ? 1.651  0.865  -0.238 C5   WNT 2  
WNT C6   C3  C 0 1 Y N N N N N ? ? ? 2.807  1.605  -0.105 C6   WNT 3  
WNT C9   C4  C 0 1 N N N N N N ? ? ? -1.346 3.259  -0.341 C9   WNT 4  
WNT C10  C5  C 0 1 N N S N N N ? ? ? -2.382 2.418  0.405  C10  WNT 5  
WNT C11  C6  C 0 1 N N S N N N ? ? ? -3.025 1.409  -0.547 C11  WNT 6  
WNT C8   C7  C 0 1 N N N N N N ? ? ? 0.038  2.717  -0.082 C8   WNT 7  
WNT C2   C8  C 0 1 Y N N N N N ? ? ? 4.103  -0.428 -0.021 C2   WNT 8  
WNT C7   C9  C 0 1 N N N N N N ? ? ? 0.331  1.483  -0.442 C7   WNT 9  
WNT C16  C10 C 0 1 N N S N N N ? ? ? -0.877 -3.298 -0.361 C16  WNT 10 
WNT C15  C11 C 0 1 N N N N N N ? ? ? -2.046 -2.461 -0.862 C15  WNT 11 
WNT C13  C12 C 0 1 N N N N N N ? ? ? -4.004 -1.009 -0.321 C13  WNT 12 
WNT C12  C13 C 0 1 N N N N N N ? ? ? -3.786 0.374  0.240  C12  WNT 13 
WNT C18  C14 C 0 1 N N N N N N ? ? ? 0.452  -1.308 -0.150 C18  WNT 14 
WNT C17  C15 C 0 1 N N N N N N ? ? ? -1.047 -3.704 1.102  C17  WNT 15 
WNT C    C16 C 0 1 N N N N N N ? ? ? 6.394  0.959  0.270  C    WNT 16 
WNT O    O1  O 0 1 N N N N N N ? ? ? 5.168  1.684  0.157  O    WNT 17 
WNT C1   C17 C 0 1 Y N N N N N ? ? ? 4.032  0.956  0.010  C1   WNT 18 
WNT C14  C18 C 0 1 N N N N N N ? ? ? -2.948 -1.961 0.259  C14  WNT 19 
WNT C4   C19 C 0 1 Y N N N N N ? ? ? 1.710  -0.551 -0.164 C4   WNT 20 
WNT O1   O2  O 0 1 N N N N N N ? ? ? 3.030  -2.542 -0.164 O1   WNT 21 
WNT O2   O3  O 0 1 N N N N N N ? ? ? -1.750 1.729  1.484  O2   WNT 22 
WNT O3   O4  O 0 1 N N N N N N ? ? ? -3.926 2.091  -1.425 O3   WNT 23 
WNT O4   O5  O 0 1 N N N N N N ? ? ? -4.233 0.654  1.326  O4   WNT 24 
WNT O5   O6  O 0 1 N N N N N N ? ? ? 0.374  -2.585 -0.537 O5   WNT 25 
WNT O6   O7  O 0 1 N N N N N N ? ? ? -0.543 -0.747 0.268  O6   WNT 26 
WNT H8   H1  H 0 1 N N N N N N ? ? ? 2.763  2.684  -0.091 H8   WNT 27 
WNT H11  H2  H 0 1 N N N N N N ? ? ? -1.551 3.224  -1.411 H11  WNT 28 
WNT H12  H3  H 0 1 N N N N N N ? ? ? -1.401 4.291  0.004  H12  WNT 29 
WNT H    H4  H 0 1 N N N N N N ? ? ? -3.156 3.077  0.805  H    WNT 30 
WNT H1   H5  H 0 1 N N N N N N ? ? ? -2.254 0.917  -1.139 H1   WNT 31 
WNT H10  H6  H 0 1 N N N N N N ? ? ? 0.778  3.337  0.398  H10  WNT 32 
WNT H6   H7  H 0 1 N N N N N N ? ? ? 5.062  -0.919 0.043  H6   WNT 33 
WNT H9   H8  H 0 1 N N N N N N ? ? ? -0.437 0.900  -0.947 H9   WNT 34 
WNT H2   H9  H 0 1 N N N N N N ? ? ? -0.830 -4.221 -0.964 H2   WNT 35 
WNT H18  H10 H 0 1 N N N N N N ? ? ? -1.666 -1.605 -1.429 H18  WNT 36 
WNT H17  H11 H 0 1 N N N N N N ? ? ? -2.647 -3.068 -1.551 H17  WNT 37 
WNT H15  H12 H 0 1 N N N N N N ? ? ? -4.997 -1.363 -0.040 H15  WNT 38 
WNT H131 H13 H 0 0 N N N N N N ? ? ? -3.915 -0.985 -1.405 H131 WNT 39 
WNT H21  H14 H 0 1 N N N N N N ? ? ? -1.958 -4.292 1.212  H21  WNT 40 
WNT H20  H15 H 0 1 N N N N N N ? ? ? -0.190 -4.299 1.416  H20  WNT 41 
WNT H19  H16 H 0 1 N N N N N N ? ? ? -1.115 -2.810 1.721  H19  WNT 42 
WNT H5   H17 H 0 1 N N N N N N ? ? ? 6.351  0.306  1.142  H5   WNT 43 
WNT H4   H18 H 0 1 N N N N N N ? ? ? 6.545  0.358  -0.627 H4   WNT 44 
WNT H3   H19 H 0 1 N N N N N N ? ? ? 7.222  1.660  0.382  H3   WNT 45 
WNT H16  H20 H 0 1 N N N N N N ? ? ? -3.469 -2.800 0.724  H16  WNT 46 
WNT H141 H21 H 0 0 N N N N N N ? ? ? -2.373 -1.421 1.007  H141 WNT 47 
WNT H7   H22 H 0 1 N N N N N N ? ? ? 2.986  -2.960 0.706  H7   WNT 48 
WNT H13  H23 H 0 1 N N N N N N ? ? ? -1.335 2.313  2.134  H13  WNT 49 
WNT H14  H24 H 0 1 N N N N N N ? ? ? -4.372 1.512  -2.059 H14  WNT 50 
# 
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 
WNT O6  C18  DOUB N N 1  
WNT C18 C4   SING N N 2  
WNT C18 O5   SING N N 3  
WNT C4  C3   DOUB Y N 4  
WNT C4  C5   SING Y N 5  
WNT C3  O1   SING N N 6  
WNT C3  C2   SING Y N 7  
WNT C2  C1   DOUB Y N 8  
WNT O5  C16  SING N N 9  
WNT C16 C17  SING N N 10 
WNT C16 C15  SING N N 11 
WNT C15 C14  SING N N 12 
WNT C14 C13  SING N N 13 
WNT C13 C12  SING N N 14 
WNT C12 O4   DOUB N N 15 
WNT C12 C11  SING N N 16 
WNT C11 O3   SING N N 17 
WNT C11 C10  SING N N 18 
WNT C10 O2   SING N N 19 
WNT C10 C9   SING N N 20 
WNT C9  C8   SING N N 21 
WNT C8  C7   DOUB N E 22 
WNT C7  C5   SING N N 23 
WNT C5  C6   DOUB Y N 24 
WNT C6  C1   SING Y N 25 
WNT C1  O    SING N N 26 
WNT O   C    SING N N 27 
WNT C6  H8   SING N N 28 
WNT C9  H11  SING N N 29 
WNT C9  H12  SING N N 30 
WNT C10 H    SING N N 31 
WNT C11 H1   SING N N 32 
WNT C8  H10  SING N N 33 
WNT C2  H6   SING N N 34 
WNT C7  H9   SING N N 35 
WNT C16 H2   SING N N 36 
WNT C15 H18  SING N N 37 
WNT C15 H17  SING N N 38 
WNT C13 H15  SING N N 39 
WNT C13 H131 SING N N 40 
WNT C17 H21  SING N N 41 
WNT C17 H20  SING N N 42 
WNT C17 H19  SING N N 43 
WNT C   H5   SING N N 44 
WNT C   H4   SING N N 45 
WNT C   H3   SING N N 46 
WNT C14 H16  SING N N 47 
WNT C14 H141 SING N N 48 
WNT O1  H7   SING N N 49 
WNT O2  H13  SING N N 50 
WNT O3  H14  SING N N 51 
# 
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 
WNT InChI            InChI                1.06  "InChI=1S/C19H24O7/c1-11-5-3-7-14(20)18(23)15(21)8-4-6-12-9-13(25-2)10-16(22)17(12)19(24)26-11/h4,6,9-11,15,18,21-23H,3,5,7-8H2,1-2H3/t11-,15?,18-/m0/s1" 
WNT InChIKey         InChI                1.06  WFIUAGOQGGAREU-DQMVDXCWSA-N                                                                                                                               
WNT SMILES_CANONICAL CACTVS               3.385 "COc1cc(O)c2C(=O)O[C@@H](C)CCCC(=O)[C@@H](O)[C@@H](O)C\C=C\c2c1"                                                                                          
WNT SMILES           CACTVS               3.385 "COc1cc(O)c2C(=O)O[CH](C)CCCC(=O)[CH](O)[CH](O)CC=Cc2c1"                                                                                                  
WNT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]1CCCC(=O)[C@H]([C@H](C/C=C/c2cc(cc(c2C(=O)O1)O)OC)O)O"                                                                                             
WNT SMILES           "OpenEye OEToolkits" 2.0.7 "CC1CCCC(=O)C(C(CC=Cc2cc(cc(c2C(=O)O1)O)OC)O)O"                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           WNT 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(4~{S},9~{S},10~{S},12~{E})-16-methoxy-4-methyl-9,10,18-tris(oxidanyl)-3-oxabicyclo[12.4.0]octadeca-1(18),12,14,16-tetraene-2,8-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
WNT "Create component" 2023-10-09 PDBE 
WNT "Modify PCM"       2024-09-27 PDBE 
WNT "Initial release"  2025-01-22 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            WNT 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_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               C14 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
