data_Y6K
# 
_chem_comp.id                                    Y6K 
_chem_comp.name                                  "~{O}3-~{tert}-butyl ~{O}1-methyl (1~{S},3~{R},5~{R})-6-methylidene-4-oxidanylidene-bicyclo[3.2.1]octane-1,3-dicarboxylate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H22 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-23 
_chem_comp.pdbx_modified_date                    2024-11-22 
_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                        294.343 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y6K 
_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        8R5E 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
Y6K C1  C1  C 0 1 N N N N N N -4.145 -11.833 5.612 -0.001 -2.391 0.744  C1  Y6K 1  
Y6K C2  C2  C 0 1 N N R N N N -2.689 -12.059 5.231 -0.320 -1.062 1.396  C2  Y6K 2  
Y6K C3  C3  C 0 1 N N N N N N -2.176 -13.482 5.273 0.946  -0.202 1.442  C3  Y6K 3  
Y6K C8  C4  C 0 1 N N N N N N -5.399 -13.812 4.924 0.037  -1.319 -1.440 C8  Y6K 4  
Y6K C14 C5  C 0 1 N N N N N N -2.391 -15.867 5.743 2.722  0.833  -0.018 C14 Y6K 5  
Y6K C15 C6  C 0 1 N N N N N N -1.742 -17.477 7.295 3.569  3.056  0.105  C15 Y6K 6  
Y6K C16 C7  C 0 1 N N N N N N -2.136 -10.960 4.366 -1.382 -0.352 0.597  C16 Y6K 7  
Y6K C17 C8  C 0 1 N N N N N N -0.018 -10.396 3.140 -2.691 1.562  0.046  C17 Y6K 8  
Y6K C19 C9  C 0 1 N N N N N N 0.445  -9.363  4.132 -3.989 0.863  0.456  C19 Y6K 9  
Y6K C20 C10 C 0 1 N N N N N N 1.175  -11.210 2.687 -2.478 1.401  -1.460 C20 Y6K 10 
Y6K C18 C11 C 0 1 N N N N N N -0.757 -9.752  1.972 -2.782 3.049  0.393  C18 Y6K 11 
Y6K C7  C12 C 0 1 N N N N N N -4.269 -14.684 4.418 0.529  0.048  -1.010 C7  Y6K 12 
Y6K C5  C13 C 0 1 N N N N N N -3.920 -14.047 6.740 2.108  -1.628 -0.234 C5  Y6K 13 
Y6K C6  C14 C 0 1 N N R N N N -4.906 -13.043 6.130 0.768  -2.339 -0.573 C6  Y6K 14 
Y6K C9  C15 C 0 1 N N N N N N -6.618 -13.727 4.432 -0.846 -1.575 -2.373 C9  Y6K 15 
Y6K C4  C16 C 0 1 N N S N N N -3.164 -14.585 5.492 1.615  -0.187 0.062  C4  Y6K 16 
Y6K O4  O1  O 0 1 N N N N N N -4.642 -10.715 5.591 -0.333 -3.439 1.244  O4  Y6K 17 
Y6K O3  O2  O 0 1 N N N N N N -0.964 -11.323 3.827 -1.576 0.966  0.759  O3  Y6K 18 
Y6K O2  O3  O 0 1 N N N N N N -2.616 -9.863  4.398 -2.059 -0.969 -0.191 O2  Y6K 19 
Y6K O   O4  O 0 1 N N N N N N -2.498 -16.279 6.991 2.455  2.130  0.199  O   Y6K 20 
Y6K O1  O5  O 0 1 N N N N N N -1.675 -16.395 4.947 3.849  0.482  -0.278 O1  Y6K 21 
Y6K H1  H1  H 0 1 N N N N N N -2.245 -11.725 6.180 -0.681 -1.232 2.411  H1  Y6K 22 
Y6K H2  H2  H 0 1 N N N N N N -1.677 -13.677 4.312 0.682  0.816  1.728  H2  Y6K 23 
Y6K H3  H3  H 0 1 N N N N N N -1.438 -13.539 6.087 1.638  -0.615 2.176  H3  Y6K 24 
Y6K H4  H4  H 0 1 N N N N N N -1.889 -17.746 8.351 3.218  4.069  0.302  H4  Y6K 25 
Y6K H5  H5  H 0 1 N N N N N N -2.089 -18.302 6.655 4.329  2.787  0.839  H5  Y6K 26 
Y6K H6  H6  H 0 1 N N N N N N -0.674 -17.293 7.109 3.999  3.009  -0.896 H6  Y6K 27 
Y6K H7  H7  H 0 1 N N N N N N 0.973  -9.859  4.960 -4.177 1.036  1.515  H7  Y6K 28 
Y6K H8  H8  H 0 1 N N N N N N 1.126  -8.656  3.635 -4.817 1.262  -0.131 H8  Y6K 29 
Y6K H9  H9  H 0 1 N N N N N N -0.425 -8.818  4.527 -3.898 -0.208 0.273  H9  Y6K 30 
Y6K H10 H10 H 0 1 N N N N N N 1.672  -11.652 3.563 -2.414 0.341  -1.707 H10 Y6K 31 
Y6K H11 H11 H 0 1 N N N N N N 0.837  -12.012 2.014 -3.316 1.848  -1.995 H11 Y6K 32 
Y6K H12 H12 H 0 1 N N N N N N 1.883  -10.558 2.154 -1.554 1.899  -1.752 H12 Y6K 33 
Y6K H13 H13 H 0 1 N N N N N N -1.612 -9.174  2.352 -1.858 3.548  0.101  H13 Y6K 34 
Y6K H14 H14 H 0 1 N N N N N N -0.073 -9.082  1.430 -3.620 3.497  -0.143 H14 Y6K 35 
Y6K H15 H15 H 0 1 N N N N N N -1.119 -10.536 1.290 -2.934 3.164  1.466  H15 Y6K 36 
Y6K H16 H16 H 0 1 N N N N N N -4.606 -15.725 4.307 0.955  0.576  -1.863 H16 Y6K 37 
Y6K H17 H17 H 0 1 N N N N N N -3.900 -14.313 3.450 -0.293 0.625  -0.587 H17 Y6K 38 
Y6K H18 H18 H 0 1 N N N N N N -4.451 -14.857 7.262 2.576  -2.071 0.645  H18 Y6K 39 
Y6K H19 H19 H 0 1 N N N N N N -3.230 -13.551 7.438 2.787  -1.644 -1.087 H19 Y6K 40 
Y6K H20 H20 H 0 1 N N N N N N -5.715 -12.772 6.824 0.882  -3.313 -1.048 H20 Y6K 41 
Y6K H21 H21 H 0 1 N N N N N N -7.343 -13.074 4.895 -1.184 -2.588 -2.534 H21 Y6K 42 
Y6K H22 H22 H 0 1 N N N N N N -6.893 -14.311 3.566 -1.237 -0.772 -2.981 H22 Y6K 43 
# 
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 
Y6K C18 C17 SING N N 1  
Y6K C20 C17 SING N N 2  
Y6K C17 O3  SING N N 3  
Y6K C17 C19 SING N N 4  
Y6K O3  C16 SING N N 5  
Y6K C16 O2  DOUB N N 6  
Y6K C16 C2  SING N N 7  
Y6K C7  C8  SING N N 8  
Y6K C7  C4  SING N N 9  
Y6K C9  C8  DOUB N N 10 
Y6K C8  C6  SING N N 11 
Y6K O1  C14 DOUB N N 12 
Y6K C2  C3  SING N N 13 
Y6K C2  C1  SING N N 14 
Y6K C3  C4  SING N N 15 
Y6K C4  C14 SING N N 16 
Y6K C4  C5  SING N N 17 
Y6K O4  C1  DOUB N N 18 
Y6K C1  C6  SING N N 19 
Y6K C14 O   SING N N 20 
Y6K C6  C5  SING N N 21 
Y6K O   C15 SING N N 22 
Y6K C2  H1  SING N N 23 
Y6K C3  H2  SING N N 24 
Y6K C3  H3  SING N N 25 
Y6K C15 H4  SING N N 26 
Y6K C15 H5  SING N N 27 
Y6K C15 H6  SING N N 28 
Y6K C19 H7  SING N N 29 
Y6K C19 H8  SING N N 30 
Y6K C19 H9  SING N N 31 
Y6K C20 H10 SING N N 32 
Y6K C20 H11 SING N N 33 
Y6K C20 H12 SING N N 34 
Y6K C18 H13 SING N N 35 
Y6K C18 H14 SING N N 36 
Y6K C18 H15 SING N N 37 
Y6K C7  H16 SING N N 38 
Y6K C7  H17 SING N N 39 
Y6K C5  H18 SING N N 40 
Y6K C5  H19 SING N N 41 
Y6K C6  H20 SING N N 42 
Y6K C9  H21 SING N N 43 
Y6K C9  H22 SING N N 44 
# 
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 
Y6K InChI            InChI                1.06  "InChI=1S/C16H22O5/c1-9-6-16(14(19)20-5)7-10(9)12(17)11(8-16)13(18)21-15(2,3)4/h10-11H,1,6-8H2,2-5H3/t10-,11-,16+/m1/s1" 
Y6K InChIKey         InChI                1.06  ILHZGEBKECHEND-UVWXRNBGSA-N                                                                                              
Y6K SMILES_CANONICAL CACTVS               3.385 "COC(=O)[C@]12C[C@H](C(=C)C1)C(=O)[C@@H](C2)C(=O)OC(C)(C)C"                                                              
Y6K SMILES           CACTVS               3.385 "COC(=O)[C]12C[CH](C(=C)C1)C(=O)[CH](C2)C(=O)OC(C)(C)C"                                                                  
Y6K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)[C@@H]1C[C@]2(C[C@@H](C1=O)C(=C)C2)C(=O)OC"                                                               
Y6K SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)C1CC2(CC(C1=O)C(=C)C2)C(=O)OC"                                                                            
# 
_pdbx_chem_comp_identifier.comp_id           Y6K 
_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        "~{O}3-~{tert}-butyl ~{O}1-methyl (1~{S},3~{R},5~{R})-6-methylidene-4-oxidanylidene-bicyclo[3.2.1]octane-1,3-dicarboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y6K "Create component" 2023-11-23 PDBE 
Y6K "Modify PCM"       2024-09-27 PDBE 
Y6K "Initial release"  2024-11-27 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y6K 
_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               C3 
_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      ? 
# 
