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 ? #