data_Y3H
#
_chem_comp.id Y3H
_chem_comp.name "~{O}3-~{tert}-butyl ~{O}1-prop-2-ynyl (1~{S},3~{S})-1-methyl-4-oxidanylidene-cyclohexane-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 2023-11-16
_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 Y3H
_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 8R5F
_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
Y3H O O1 O 0 1 N N N N N N -21.146 -36.074 24.071 -3.954 0.185 0.056 O Y3H 1
Y3H C1 C1 C 0 1 N N N N N N -25.009 -35.124 21.107 0.874 -1.682 -0.188 C1 Y3H 2
Y3H C16 C2 C 0 1 N N N N N N -24.400 -32.764 21.653 2.249 0.340 0.146 C16 Y3H 3
Y3H C17 C3 C 0 1 N N N N N N -24.890 -31.001 19.879 4.627 0.467 0.061 C17 Y3H 4
Y3H C18 C4 C 0 1 N N N N N N -25.179 -32.032 18.786 4.641 0.679 -1.455 C18 Y3H 5
Y3H C19 C5 C 0 1 N N N N N N -24.175 -29.821 19.233 5.853 -0.350 0.473 C19 Y3H 6
Y3H C2 C6 C 0 1 N N S N N N -23.902 -34.117 21.208 0.954 -0.342 0.507 C2 Y3H 7
Y3H C20 C7 C 0 1 N N N N N N -26.195 -30.522 20.501 4.659 1.825 0.765 C20 Y3H 8
Y3H C21 C8 C 0 1 N N N N N N -21.156 -36.345 22.635 -2.699 0.641 -0.082 C21 Y3H 9
Y3H C22 C9 C 0 1 N N N N N N -20.008 -36.282 24.913 -5.028 1.088 -0.319 C22 Y3H 10
Y3H C23 C10 C 0 1 N N N N N N -18.760 -35.663 24.437 -6.324 0.425 -0.103 C23 Y3H 11
Y3H C24 C11 C 0 1 N N N N N N -17.659 -35.144 24.061 -7.358 -0.104 0.068 C24 Y3H 12
Y3H C3 C12 C 0 1 N N N N N N -22.822 -34.608 22.157 -0.227 0.519 0.046 C3 Y3H 13
Y3H C4 C13 C 0 1 N N S N N N -22.371 -36.011 21.807 -1.533 -0.239 0.288 C4 Y3H 14
Y3H C5 C14 C 0 1 N N N N N N -23.521 -36.983 22.057 -1.562 -1.507 -0.567 C5 Y3H 15
Y3H C6 C15 C 0 1 N N N N N N -24.771 -36.622 21.253 -0.432 -2.444 -0.129 C6 Y3H 16
Y3H C7 C16 C 0 1 N N N N N N -21.897 -36.094 20.365 -1.633 -0.621 1.766 C7 Y3H 17
Y3H O1 O2 O 0 1 N N N N N N -20.177 -36.828 22.086 -2.504 1.757 -0.501 O1 Y3H 18
Y3H O2 O3 O 0 1 N N N N N N -25.093 -32.670 22.653 2.232 1.413 -0.409 O2 Y3H 19
Y3H O3 O4 O 0 1 N N N N N N -24.063 -31.531 20.934 3.421 -0.246 0.439 O3 Y3H 20
Y3H O4 O5 O 0 1 N N N N N N -26.124 -34.701 20.869 1.826 -2.131 -0.780 O4 Y3H 21
Y3H H1 H1 H 0 1 N N N N N N -25.696 -32.898 19.225 5.547 1.215 -1.738 H1 Y3H 22
Y3H H2 H2 H 0 1 N N N N N N -25.816 -31.578 18.013 4.619 -0.288 -1.957 H2 Y3H 23
Y3H H3 H3 H 0 1 N N N N N N -24.232 -32.362 18.334 3.768 1.261 -1.748 H3 Y3H 24
Y3H H4 H4 H 0 1 N N N N N N -23.954 -29.062 19.998 5.843 -0.500 1.552 H4 Y3H 25
Y3H H5 H5 H 0 1 N N N N N N -23.235 -30.167 18.778 5.831 -1.317 -0.029 H5 Y3H 26
Y3H H6 H6 H 0 1 N N N N N N -24.819 -29.382 18.457 6.759 0.186 0.189 H6 Y3H 27
Y3H H7 H7 H 0 1 N N N N N N -23.450 -34.003 20.211 0.906 -0.486 1.587 H7 Y3H 28
Y3H H8 H8 H 0 1 N N N N N N -25.978 -29.782 21.285 4.649 1.674 1.845 H8 Y3H 29
Y3H H9 H9 H 0 1 N N N N N N -26.823 -30.061 19.725 5.565 2.361 0.481 H9 Y3H 30
Y3H H10 H10 H 0 1 N N N N N N -26.727 -31.378 20.942 3.785 2.407 0.472 H10 Y3H 31
Y3H H11 H11 H 0 1 N N N N N N -20.238 -35.867 25.906 -4.975 1.989 0.292 H11 Y3H 32
Y3H H12 H12 H 0 1 N N N N N N -19.840 -37.366 24.998 -4.927 1.356 -1.371 H12 Y3H 33
Y3H H13 H13 H 0 1 N N N N N N -16.743 -34.712 23.748 -8.283 -0.577 0.222 H13 Y3H 34
Y3H H14 H14 H 0 1 N N N N N N -21.958 -33.930 22.097 -0.238 1.452 0.609 H14 Y3H 35
Y3H H15 H15 H 0 1 N N N N N N -23.220 -34.606 23.183 -0.124 0.737 -1.017 H15 Y3H 36
Y3H H16 H16 H 0 1 N N N N N N -23.772 -36.966 23.128 -2.521 -2.010 -0.439 H16 Y3H 37
Y3H H17 H17 H 0 1 N N N N N N -23.197 -37.995 21.772 -1.429 -1.242 -1.616 H17 Y3H 38
Y3H H18 H18 H 0 1 N N N N N N -25.644 -37.063 21.757 -0.386 -3.302 -0.799 H18 Y3H 39
Y3H H19 H19 H 0 1 N N N N N N -24.671 -37.055 20.247 -0.612 -2.782 0.891 H19 Y3H 40
Y3H H20 H20 H 0 1 N N N N N N -21.070 -35.386 20.209 -0.793 -1.260 2.034 H20 Y3H 41
Y3H H21 H21 H 0 1 N N N N N N -21.550 -37.116 20.151 -1.612 0.282 2.376 H21 Y3H 42
Y3H H22 H22 H 0 1 N N N N N N -22.728 -35.840 19.691 -2.567 -1.156 1.941 H22 Y3H 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
Y3H C18 C17 SING N N 1
Y3H C19 C17 SING N N 2
Y3H C17 C20 SING N N 3
Y3H C17 O3 SING N N 4
Y3H C7 C4 SING N N 5
Y3H O4 C1 DOUB N N 6
Y3H O3 C16 SING N N 7
Y3H C1 C2 SING N N 8
Y3H C1 C6 SING N N 9
Y3H C2 C16 SING N N 10
Y3H C2 C3 SING N N 11
Y3H C6 C5 SING N N 12
Y3H C16 O2 DOUB N N 13
Y3H C4 C5 SING N N 14
Y3H C4 C3 SING N N 15
Y3H C4 C21 SING N N 16
Y3H O1 C21 DOUB N N 17
Y3H C21 O SING N N 18
Y3H C24 C23 TRIP N N 19
Y3H O C22 SING N N 20
Y3H C23 C22 SING N N 21
Y3H C18 H1 SING N N 22
Y3H C18 H2 SING N N 23
Y3H C18 H3 SING N N 24
Y3H C19 H4 SING N N 25
Y3H C19 H5 SING N N 26
Y3H C19 H6 SING N N 27
Y3H C2 H7 SING N N 28
Y3H C20 H8 SING N N 29
Y3H C20 H9 SING N N 30
Y3H C20 H10 SING N N 31
Y3H C22 H11 SING N N 32
Y3H C22 H12 SING N N 33
Y3H C24 H13 SING N N 34
Y3H C3 H14 SING N N 35
Y3H C3 H15 SING N N 36
Y3H C5 H16 SING N N 37
Y3H C5 H17 SING N N 38
Y3H C6 H18 SING N N 39
Y3H C6 H19 SING N N 40
Y3H C7 H20 SING N N 41
Y3H C7 H21 SING N N 42
Y3H C7 H22 SING N N 43
#
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
Y3H InChI InChI 1.06 "InChI=1S/C16H22O5/c1-6-9-20-14(19)16(5)8-7-12(17)11(10-16)13(18)21-15(2,3)4/h1,11H,7-10H2,2-5H3/t11-,16-/m0/s1"
Y3H InChIKey InChI 1.06 VWWMPCGCVQSEOW-ZBEGNZNMSA-N
Y3H SMILES_CANONICAL CACTVS 3.385 "CC(C)(C)OC(=O)[C@H]1C[C@](C)(CCC1=O)C(=O)OCC#C"
Y3H SMILES CACTVS 3.385 "CC(C)(C)OC(=O)[CH]1C[C](C)(CCC1=O)C(=O)OCC#C"
Y3H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@]1(CCC(=O)[C@H](C1)C(=O)OC(C)(C)C)C(=O)OCC#C"
Y3H SMILES "OpenEye OEToolkits" 2.0.7 "CC1(CCC(=O)C(C1)C(=O)OC(C)(C)C)C(=O)OCC#C"
#
_pdbx_chem_comp_identifier.comp_id Y3H
_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-prop-2-ynyl (1~{S},3~{S})-1-methyl-4-oxidanylidene-cyclohexane-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
Y3H "Create component" 2023-11-16 PDBE
Y3H "Modify PCM" 2024-09-27 PDBE
Y3H "Initial release" 2024-11-27 RCSB
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 Y3H HIS None "Covalent chemical modification" "Amino-acid side chain" "Any position" C3 NE2 ? ?
2 Y3H CYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" C3 SG ? ?
#