data_A4K
#
_chem_comp.id A4K
_chem_comp.name
"(~{E})-3-(trifluoromethyl)-5-[(1~{S})-2,6,6-trimethyl-1-oxidanyl-4-oxidanylidene-cyclohex-2-en-1-yl]pent-2-en-4-ynoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H15 F3 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-08-15
_chem_comp.pdbx_modified_date 2018-06-22
_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 316.272
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A4K
_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 5OR6
_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
A4K C1 C1 C 0 1 N N N N N N 3.288 22.257 36.608 1.931 2.421 -0.107 C1 A4K 1
A4K C2 C2 C 0 1 N N N N N N 1.780 22.085 36.634 2.793 1.301 -0.227 C2 A4K 2
A4K C4 C3 C 0 1 N N N N N N 1.248 22.353 34.259 0.923 -0.140 0.269 C4 A4K 3
A4K C5 C4 C 0 1 N N N N N N 1.517 22.573 33.107 -0.212 -0.297 0.526 C5 A4K 4
A4K C6 C5 C 0 1 N N N N N N -0.575 21.930 35.875 3.222 -1.139 -0.174 C6 A4K 5
A4K C8 C6 C 0 1 N N N N N N 1.197 21.783 30.839 -2.313 0.843 0.916 C8 A4K 6
A4K C9 C7 C 0 1 N N N N N N 0.015 21.930 30.209 -3.018 1.351 -0.087 C9 A4K 7
A4K C10 C8 C 0 1 N N N N N N -0.766 23.193 30.303 -3.178 0.606 -1.340 C10 A4K 8
A4K C11 C9 C 0 1 N N N N N N -0.230 24.346 31.127 -2.311 -0.618 -1.549 C11 A4K 9
A4K C12 C10 C 0 1 N N N N N N 1.309 24.338 31.277 -2.272 -1.383 -0.218 C12 A4K 10
A4K C13 C11 C 0 1 N N N N N N 1.946 20.482 30.708 -2.193 1.644 2.187 C13 A4K 11
A4K C14 C12 C 0 1 N N N N N N 1.932 24.838 29.945 -3.696 -1.747 0.205 C14 A4K 12
A4K C15 C13 C 0 1 N N N N N N 1.697 25.411 32.314 -1.443 -2.658 -0.384 C15 A4K 13
A4K O11 O1 O 0 1 N N N N N N 3.842 22.452 35.498 0.757 2.259 0.165 O11 A4K 14
A4K O12 O2 O 0 1 N N N N N N 3.804 22.181 37.754 2.416 3.667 -0.288 O12 A4K 15
A4K C3 C14 C 0 1 N N N N N N 0.886 22.124 35.622 2.307 0.052 -0.046 C3 A4K 16
A4K F20 F1 F 0 1 N N N N N N -0.863 21.384 37.091 4.515 -0.702 -0.483 F20 A4K 17
A4K F21 F2 F 0 1 N N N N N N -1.174 21.138 34.944 3.244 -1.842 1.036 F21 A4K 18
A4K F22 F3 F 0 1 N N N N N N -1.229 23.117 35.831 2.757 -1.977 -1.192 F22 A4K 19
A4K C7 C15 C 0 1 N N S N N N 1.819 22.897 31.696 -1.634 -0.493 0.849 C7 A4K 20
A4K O7 O3 O 0 1 N N N N N N 3.244 22.842 31.569 -1.740 -1.137 2.120 O7 A4K 21
A4K O10 O4 O 0 1 N N N N N N -1.833 23.266 29.701 -3.980 0.957 -2.180 O10 A4K 22
A4K H1 H1 H 0 1 N N N N N N 1.357 21.904 37.611 3.836 1.446 -0.464 H1 A4K 23
A4K H2 H2 H 0 1 N N N N N N -0.375 21.112 29.622 -3.477 2.322 0.021 H2 A4K 24
A4K H3 H3 H 0 1 N N N N N N -0.527 25.288 30.642 -2.741 -1.249 -2.326 H3 A4K 25
A4K H4 H4 H 0 1 N N N N N N -0.677 24.294 32.131 -1.303 -0.314 -1.831 H4 A4K 26
A4K H5 H5 H 0 1 N N N N N N 2.882 20.538 31.283 -1.315 2.287 2.130 H5 A4K 27
A4K H6 H6 H 0 1 N N N N N N 1.326 19.661 31.097 -3.085 2.258 2.315 H6 A4K 28
A4K H7 H7 H 0 1 N N N N N N 2.177 20.297 29.649 -2.094 0.967 3.036 H7 A4K 29
A4K H8 H8 H 0 1 N N N N N N 3.029 24.840 30.031 -4.153 -2.375 -0.561 H8 A4K 30
A4K H9 H9 H 0 1 N N N N N N 1.630 24.170 29.125 -3.668 -2.290 1.150 H9 A4K 31
A4K H10 H10 H 0 1 N N N N N N 1.579 25.858 29.735 -4.284 -0.837 0.326 H10 A4K 32
A4K H11 H11 H 0 1 N N N N N N 1.292 25.134 33.298 -0.427 -2.395 -0.681 H11 A4K 33
A4K H12 H12 H 0 1 N N N N N N 2.793 25.482 32.376 -1.416 -3.199 0.562 H12 A4K 34
A4K H13 H13 H 0 1 N N N N N N 1.283 26.383 32.008 -1.894 -3.287 -1.150 H13 A4K 35
A4K H14 H14 H 0 1 N N N N N N 4.744 22.297 37.687 1.755 4.365 -0.186 H14 A4K 36
A4K H15 H15 H 0 1 N N N N N N 3.636 23.528 32.096 -1.334 -0.644 2.846 H15 A4K 37
#
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
A4K O10 C10 DOUB N N 1
A4K C14 C12 SING N N 2
A4K C9 C10 SING N N 3
A4K C9 C8 DOUB N N 4
A4K C10 C11 SING N N 5
A4K C13 C8 SING N N 6
A4K C8 C7 SING N N 7
A4K C11 C12 SING N N 8
A4K C12 C7 SING N N 9
A4K C12 C15 SING N N 10
A4K O7 C7 SING N N 11
A4K C7 C5 SING N N 12
A4K C5 C4 TRIP N N 13
A4K C4 C3 SING N N 14
A4K F21 C6 SING N N 15
A4K O11 C1 DOUB N N 16
A4K C3 C6 SING N N 17
A4K C3 C2 DOUB N E 18
A4K F22 C6 SING N N 19
A4K C6 F20 SING N N 20
A4K C1 C2 SING N N 21
A4K C1 O12 SING N N 22
A4K C2 H1 SING N N 23
A4K C9 H2 SING N N 24
A4K C11 H3 SING N N 25
A4K C11 H4 SING N N 26
A4K C13 H5 SING N N 27
A4K C13 H6 SING N N 28
A4K C13 H7 SING N N 29
A4K C14 H8 SING N N 30
A4K C14 H9 SING N N 31
A4K C14 H10 SING N N 32
A4K C15 H11 SING N N 33
A4K C15 H12 SING N N 34
A4K C15 H13 SING N N 35
A4K O12 H14 SING N N 36
A4K O7 H15 SING N N 37
#
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
A4K InChI InChI 1.03 InChI=1S/C15H15F3O4/c1-9-6-11(19)8-13(2,3)14(9,22)5-4-10(7-12(20)21)15(16,17)18/h6-7,22H,8H2,1-3H3,(H,20,21)/b10-7+/t14-/m1/s1
A4K InChIKey InChI 1.03 CQNKVZZCXKPIPC-DNGMOHDESA-N
A4K SMILES_CANONICAL CACTVS 3.385 "CC1=CC(=O)CC(C)(C)[C@@]1(O)C#C\C(=C/C(O)=O)C(F)(F)F"
A4K SMILES CACTVS 3.385 "CC1=CC(=O)CC(C)(C)[C]1(O)C#CC(=CC(O)=O)C(F)(F)F"
A4K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CC(=O)CC([C@]1(C#C/C(=C\C(=O)O)/C(F)(F)F)O)(C)C"
A4K SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CC(=O)CC(C1(C#CC(=CC(=O)O)C(F)(F)F)O)(C)C"
#
_pdbx_chem_comp_identifier.comp_id A4K
_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
"(~{E})-3-(trifluoromethyl)-5-[(1~{S})-2,6,6-trimethyl-1-oxidanyl-4-oxidanylidene-cyclohex-2-en-1-yl]pent-2-en-4-ynoic 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
A4K 'Create component' 2017-08-15 EBI
A4K 'Initial release' 2018-06-27 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
A4K C1 C 5.799 4.199 1
A4K C2 C 7.299 4.199 2
A4K C4 C 7.299 1.601 3
A4K C5 C 6.549 0.301 4
A4K C6 C 9.549 2.900 5
A4K C8 C 7.098 -1.748 6
A4K C9 C 7.098 -3.248 7
A4K C10 C 5.799 -3.998 8
A4K C11 C 4.500 -3.248 9
A4K C12 C 4.500 -1.748 10
A4K C13 C 8.397 -0.998 11
A4K C14 C 3.000 -1.748 12
A4K C15 C 3.750 -0.449 13
A4K O11 O 5.049 5.498 14
A4K O12 O 5.049 2.900 15
A4K C3 C 8.049 2.900 16
A4K F20 F 11.049 2.900 17
A4K F21 F 9.549 4.399 18
A4K F22 F 9.549 1.399 19
A4K C7 C 5.799 -0.998 20
A4K O7 O 5.049 0.301 21
A4K O10 O 5.799 -5.498 22
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
A4K O10 C10 DOUBLE NONE 1
A4K C14 C12 SINGLE NONE 2
A4K C9 C10 SINGLE NONE 3
A4K C9 C8 DOUBLE NONE 4
A4K C10 C11 SINGLE NONE 5
A4K C13 C8 SINGLE NONE 6
A4K C8 C7 SINGLE NONE 7
A4K C11 C12 SINGLE NONE 8
A4K C12 C7 SINGLE NONE 9
A4K C12 C15 SINGLE NONE 10
A4K C7 O7 SINGLE BEGINDASH 11
A4K C7 C5 SINGLE NONE 12
A4K C5 C4 TRIPLE NONE 13
A4K C4 C3 SINGLE ENDUPRIGHT 14
A4K F21 C6 SINGLE NONE 15
A4K O11 C1 DOUBLE NONE 16
A4K C3 C6 SINGLE ENDUPRIGHT 17
A4K C3 C2 DOUBLE NONE 18
A4K F22 C6 SINGLE NONE 19
A4K C6 F20 SINGLE NONE 20
A4K C1 C2 SINGLE ENDUPRIGHT 21
A4K C1 O12 SINGLE NONE 22
#
_pdbe_chem_comp_substructure.comp_id A4K
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles O=C1C=CCCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C6H8O/c7-6-4-2-1-3-5-6/h2,4H,1,3,5H2
_pdbe_chem_comp_substructure.substructure_inchikeys FWFSEYBSWVRWGL-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
A4K C8 S1 1
A4K C9 S1 1
A4K C10 S1 1
A4K C11 S1 1
A4K C12 S1 1
A4K C7 S1 1
A4K O10 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id A4K
_pdbe_chem_comp_rdkit_properties.exactmw 316.092
_pdbe_chem_comp_rdkit_properties.amw 316.275
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.467
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 146.119
_pdbe_chem_comp_rdkit_properties.tpsa 74.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.240
_pdbe_chem_comp_rdkit_properties.CrippenMR 71.662
_pdbe_chem_comp_rdkit_properties.chi0v 10.267
_pdbe_chem_comp_rdkit_properties.chi1v 5.133
_pdbe_chem_comp_rdkit_properties.chi2v 2.294
_pdbe_chem_comp_rdkit_properties.chi3v 2.294
_pdbe_chem_comp_rdkit_properties.chi4v 1.260
_pdbe_chem_comp_rdkit_properties.chi0n 25.267
_pdbe_chem_comp_rdkit_properties.chi1n 12.450
_pdbe_chem_comp_rdkit_properties.chi2n 2.294
_pdbe_chem_comp_rdkit_properties.chi3n 2.294
_pdbe_chem_comp_rdkit_properties.chi4n 1.260
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.070
_pdbe_chem_comp_rdkit_properties.kappa1 5.853
_pdbe_chem_comp_rdkit_properties.kappa2 5.612
_pdbe_chem_comp_rdkit_properties.kappa3 3.572
_pdbe_chem_comp_rdkit_properties.Phi 1.493
#
_pdbe_chem_comp_external_mappings.comp_id A4K
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 134611693
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
A4K C1 2.594 0.747 -2.958 ETKDGv3 1
A4K C2 3.156 1.508 -1.823 ETKDGv3 2
A4K C4 1.607 0.585 -0.186 ETKDGv3 3
A4K C5 0.662 -0.100 0.114 ETKDGv3 4
A4K C6 3.403 2.242 0.517 ETKDGv3 5
A4K C8 -0.835 -0.645 1.942 ETKDGv3 6
A4K C9 -1.695 0.335 2.272 ETKDGv3 7
A4K C10 -2.425 1.106 1.254 ETKDGv3 8
A4K C11 -2.216 0.839 -0.208 ETKDGv3 9
A4K C12 -1.733 -0.614 -0.458 ETKDGv3 10
A4K C13 -0.113 -1.350 3.063 ETKDGv3 11
A4K C14 -2.904 -1.596 -0.184 ETKDGv3 12
A4K C15 -1.350 -0.758 -1.953 ETKDGv3 13
A4K O11 2.506 1.307 -4.082 ETKDGv3 14
A4K O12 2.219 -0.590 -2.840 ETKDGv3 15
A4K C3 2.737 1.410 -0.548 ETKDGv3 16
A4K F20 3.274 3.584 0.210 ETKDGv3 17
A4K F21 4.747 1.920 0.585 ETKDGv3 18
A4K F22 2.832 2.015 1.758 ETKDGv3 19
A4K C7 -0.506 -0.944 0.477 ETKDGv3 20
A4K O7 -0.190 -2.314 0.320 ETKDGv3 21
A4K O10 -3.205 2.027 1.614 ETKDGv3 22
A4K H1 3.928 2.231 -2.062 ETKDGv3 23
A4K H2 -1.880 0.563 3.316 ETKDGv3 24
A4K H3 -3.162 1.032 -0.760 ETKDGv3 25
A4K H4 -1.462 1.566 -0.582 ETKDGv3 26
A4K H5 -0.840 -1.940 3.660 ETKDGv3 27
A4K H6 0.377 -0.604 3.725 ETKDGv3 28
A4K H7 0.677 -2.033 2.696 ETKDGv3 29
A4K H8 -3.220 -1.571 0.880 ETKDGv3 30
A4K H9 -2.614 -2.640 -0.430 ETKDGv3 31
A4K H10 -3.788 -1.337 -0.806 ETKDGv3 32
A4K H11 -2.236 -0.588 -2.602 ETKDGv3 33
A4K H12 -0.576 -0.019 -2.248 ETKDGv3 34
A4K H13 -0.957 -1.776 -2.163 ETKDGv3 35
A4K H14 2.414 -1.131 -2.007 ETKDGv3 36
A4K H15 0.776 -2.465 0.499 ETKDGv3 37
#