data_A4H
#
_chem_comp.id A4H
_chem_comp.name
"(2~{Z},4~{E})-3-cyclopropyl-5-[(1~{S})-2,6,6-trimethyl-1-oxidanyl-4-oxidanylidene-cyclohex-2-en-1-yl]penta-2,4-dienoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H22 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 290.354
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A4H
_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 5OR2
_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
A4H C1 C1 C 0 1 N N N N N N 3.371 22.280 37.049 -3.176 -1.759 -0.113 C1 A4H 1
A4H C2 C2 C 0 1 N N N N N N 1.895 22.313 37.016 -3.515 -0.464 0.354 C2 A4H 2
A4H C3 C3 C 0 1 N N N N N N 1.058 22.425 35.957 -2.632 0.553 0.227 C3 A4H 3
A4H C5 C4 C 0 1 N N N N N N 0.843 22.667 33.427 -0.213 0.412 0.257 C5 A4H 4
A4H C6 C5 C 0 1 N N N N N N -0.427 22.440 36.222 -2.971 1.918 0.771 C6 A4H 5
A4H C13 C6 C 0 1 N N N N N N 1.594 20.258 31.336 1.395 2.595 -0.634 C13 A4H 6
A4H C15 C7 C 0 1 N N N N N N 1.199 25.387 32.234 1.813 -0.769 1.862 C15 A4H 7
A4H C24 C8 C 0 1 N N N N N N -1.352 21.421 35.669 -1.916 3.016 0.630 C24 A4H 8
A4H O11 O1 O 0 1 N N N N N N 4.169 22.347 36.137 -2.136 -1.934 -0.719 O11 A4H 9
A4H O12 O2 O 0 1 N N N N N N 3.781 22.156 38.321 -4.005 -2.798 0.119 O12 A4H 10
A4H C23 C9 C 0 1 N N N N N N -1.029 21.432 37.129 -3.175 3.050 -0.238 C23 A4H 11
A4H C4 C10 C 0 1 N N N N N N 1.545 22.547 34.575 -1.349 0.329 -0.438 C4 A4H 12
A4H C7 C11 C 0 1 N N S N N N 1.384 22.793 31.997 1.096 0.041 -0.390 C7 A4H 13
A4H O7 O3 O 0 1 N N N N N N 2.815 22.756 32.011 0.854 -0.363 -1.740 O7 A4H 14
A4H C12 C12 C 0 1 N N N N N N 0.949 24.167 31.317 1.722 -1.124 0.376 C12 A4H 15
A4H C14 C13 C 0 1 N N N N N N 1.768 24.483 30.032 0.859 -2.375 0.200 C14 A4H 16
A4H C8 C14 C 0 1 N N N N N N 0.870 21.574 31.208 2.001 1.237 -0.390 C8 A4H 17
A4H C9 C15 C 0 1 N N N N N N -0.217 21.636 30.411 3.310 1.157 -0.185 C9 A4H 18
A4H C10 C16 C 0 1 N N N N N N -0.989 22.892 30.228 3.950 -0.139 0.067 C10 A4H 19
A4H O10 O4 O 0 1 N N N N N N -1.964 22.885 29.483 5.097 -0.207 0.456 O10 A4H 20
A4H C11 C17 C 0 1 N N N N N N -0.554 24.149 30.958 3.130 -1.387 -0.176 C11 A4H 21
A4H H1 H1 H 0 1 N N N N N N 1.411 22.237 37.979 -4.478 -0.289 0.812 H1 A4H 22
A4H H2 H2 H 0 1 N N N N N N -0.232 22.675 33.529 -0.232 0.744 1.285 H2 A4H 23
A4H H3 H3 H 0 1 N N N N N N -0.858 23.448 36.310 -3.590 1.926 1.668 H3 A4H 24
A4H H4 H4 H 0 1 N N N N N N 2.450 20.375 32.016 1.098 3.036 0.317 H4 A4H 25
A4H H5 H5 H 0 1 N N N N N N 0.907 19.499 31.739 2.129 3.238 -1.120 H5 A4H 26
A4H H6 H6 H 0 1 N N N N N N 1.953 19.939 30.346 0.521 2.492 -1.276 H6 A4H 27
A4H H7 H7 H 0 1 N N N N N N 0.653 25.253 33.180 0.813 -0.575 2.250 H7 A4H 28
A4H H8 H8 H 0 1 N N N N N N 2.276 25.475 32.441 2.259 -1.600 2.407 H8 A4H 29
A4H H9 H9 H 0 1 N N N N N N 0.846 26.300 31.733 2.430 0.120 1.986 H9 A4H 30
A4H H10 H10 H 0 1 N N N N N N -2.354 21.716 35.324 -1.840 3.747 1.435 H10 A4H 31
A4H H11 H11 H 0 1 N N N N N N -0.965 20.617 35.025 -0.976 2.753 0.144 H11 A4H 32
A4H H12 H12 H 0 1 N N N N N N 4.730 22.135 38.348 -3.690 -3.640 -0.238 H12 A4H 33
A4H H13 H13 H 0 1 N N N N N N -1.793 21.735 37.860 -3.064 2.808 -1.295 H13 A4H 34
A4H H14 H14 H 0 1 N N N N N N -0.404 20.637 37.561 -3.928 3.803 -0.005 H14 A4H 35
A4H H15 H15 H 0 1 N N N N N N 2.619 22.540 34.461 -1.320 0.097 -1.493 H15 A4H 36
A4H H16 H16 H 0 1 N N N N N N 3.147 23.503 32.495 0.444 0.322 -2.287 H16 A4H 37
A4H H17 H17 H 0 1 N N N N N N 2.841 24.499 30.275 0.798 -2.628 -0.858 H17 A4H 38
A4H H18 H18 H 0 1 N N N N N N 1.575 23.709 29.275 1.306 -3.205 0.747 H18 A4H 39
A4H H19 H19 H 0 1 N N N N N N 1.467 25.465 29.638 -0.142 -2.183 0.586 H19 A4H 40
A4H H20 H20 H 0 1 N N N N N N -0.536 20.745 29.890 3.910 2.055 -0.204 H20 A4H 41
A4H H21 H21 H 0 1 N N N N N N -0.769 25.016 30.316 3.579 -2.233 0.345 H21 A4H 42
A4H H22 H22 H 0 1 N N N N N N -1.135 24.229 31.889 3.078 -1.594 -1.245 H22 A4H 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
A4H O10 C10 DOUB N N 1
A4H C14 C12 SING N N 2
A4H C10 C9 SING N N 3
A4H C10 C11 SING N N 4
A4H C9 C8 DOUB N N 5
A4H C11 C12 SING N N 6
A4H C8 C13 SING N N 7
A4H C8 C7 SING N N 8
A4H C12 C7 SING N N 9
A4H C12 C15 SING N N 10
A4H C7 O7 SING N N 11
A4H C7 C5 SING N N 12
A4H C5 C4 DOUB N E 13
A4H C4 C3 SING N N 14
A4H C24 C6 SING N N 15
A4H C24 C23 SING N N 16
A4H C3 C6 SING N N 17
A4H C3 C2 DOUB N Z 18
A4H O11 C1 DOUB N N 19
A4H C6 C23 SING N N 20
A4H C2 C1 SING N N 21
A4H C1 O12 SING N N 22
A4H C2 H1 SING N N 23
A4H C5 H2 SING N N 24
A4H C6 H3 SING N N 25
A4H C13 H4 SING N N 26
A4H C13 H5 SING N N 27
A4H C13 H6 SING N N 28
A4H C15 H7 SING N N 29
A4H C15 H8 SING N N 30
A4H C15 H9 SING N N 31
A4H C24 H10 SING N N 32
A4H C24 H11 SING N N 33
A4H O12 H12 SING N N 34
A4H C23 H13 SING N N 35
A4H C23 H14 SING N N 36
A4H C4 H15 SING N N 37
A4H O7 H16 SING N N 38
A4H C14 H17 SING N N 39
A4H C14 H18 SING N N 40
A4H C14 H19 SING N N 41
A4H C9 H20 SING N N 42
A4H C11 H21 SING N N 43
A4H C11 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
A4H InChI InChI 1.03 InChI=1S/C17H22O4/c1-11-8-14(18)10-16(2,3)17(11,21)7-6-13(9-15(19)20)12-4-5-12/h6-9,12,21H,4-5,10H2,1-3H3,(H,19,20)/b7-6+,13-9+/t17-/m1/s1
A4H InChIKey InChI 1.03 HKEUSUYMMUPOQP-PZUGTFMISA-N
A4H SMILES_CANONICAL CACTVS 3.385 CC1=CC(=O)CC(C)(C)[C@@]1(O)\C=C\C(=C/C(O)=O)C2CC2
A4H SMILES CACTVS 3.385 CC1=CC(=O)CC(C)(C)[C]1(O)C=CC(=CC(O)=O)C2CC2
A4H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CC1=CC(=O)CC([C@]1(/C=C/C(=C\C(=O)O)/C2CC2)O)(C)C
A4H SMILES "OpenEye OEToolkits" 2.0.6 CC1=CC(=O)CC(C1(C=CC(=CC(=O)O)C2CC2)O)(C)C
#
_pdbx_chem_comp_identifier.comp_id A4H
_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
"(2~{Z},4~{E})-3-cyclopropyl-5-[(1~{S})-2,6,6-trimethyl-1-oxidanyl-4-oxidanylidene-cyclohex-2-en-1-yl]penta-2,4-dienoic 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
A4H 'Create component' 2017-08-15 EBI
A4H '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
A4H C1 C 9.198 1.835 1
A4H C2 C 8.049 2.799 2
A4H C3 C 6.549 2.799 3
A4H C5 C 6.549 0.201 4
A4H C6 C 5.799 4.098 5
A4H C13 C 8.397 -1.098 6
A4H C15 C 3.351 -0.884 7
A4H C24 C 5.799 5.598 8
A4H O11 O 10.608 2.348 9
A4H O12 O 8.938 0.358 10
A4H C23 C 4.500 4.848 11
A4H C4 C 5.799 1.500 12
A4H C7 C 5.799 -1.098 13
A4H O7 O 5.049 0.201 14
A4H C12 C 4.500 -1.848 15
A4H C14 C 3.000 -1.848 16
A4H C8 C 7.098 -1.848 17
A4H C9 C 7.098 -3.348 18
A4H C10 C 5.799 -4.098 19
A4H O10 O 5.799 -5.598 20
A4H C11 C 4.500 -3.348 21
#
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
A4H O10 C10 DOUBLE NONE 1
A4H C14 C12 SINGLE NONE 2
A4H C10 C9 SINGLE NONE 3
A4H C10 C11 SINGLE NONE 4
A4H C9 C8 DOUBLE NONE 5
A4H C11 C12 SINGLE NONE 6
A4H C8 C13 SINGLE NONE 7
A4H C8 C7 SINGLE NONE 8
A4H C12 C7 SINGLE NONE 9
A4H C12 C15 SINGLE NONE 10
A4H C7 O7 SINGLE BEGINDASH 11
A4H C7 C5 SINGLE ENDUPRIGHT 12
A4H C5 C4 DOUBLE NONE 13
A4H C4 C3 SINGLE ENDUPRIGHT 14
A4H C24 C6 SINGLE NONE 15
A4H C24 C23 SINGLE NONE 16
A4H C3 C6 SINGLE ENDUPRIGHT 17
A4H C3 C2 DOUBLE NONE 18
A4H O11 C1 DOUBLE NONE 19
A4H C6 C23 SINGLE NONE 20
A4H C2 C1 SINGLE ENDDOWNRIGHT 21
A4H C1 O12 SINGLE NONE 22
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
A4H MurckoScaffold S1 scaffold C=C(/C=C/C1C=CC(=O)CC1)C1CC1 InChI=1S/C13H16O/c1-10(12-6-7-12)2-3-11-4-8-13(14)9-5-11/h2-4,8,11-12H,1,5-7,9H2/b3-2+/t11-/m0/s1 SNKMKVMJUJDFMA-VUDBWIFFSA-N
A4H cyclopropane F1 fragment C1CC1 InChI=1S/C3H6/c1-2-3-1/h1-3H2 LVZWSLJZHVFIQJ-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
A4H C2 S1 1
A4H C3 S1 1
A4H C5 S1 1
A4H C6 S1 1
A4H C24 S1 1
A4H C23 S1 1
A4H C4 S1 1
A4H C7 S1 1
A4H C12 S1 1
A4H C8 S1 1
A4H C9 S1 1
A4H C10 S1 1
A4H O10 S1 1
A4H C11 S1 1
A4H C6 F1 1
A4H C24 F1 1
A4H C23 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id A4H
_pdbe_chem_comp_rdkit_properties.exactmw 290.152
_pdbe_chem_comp_rdkit_properties.amw 290.359
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 43
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.529
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_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 155.492
_pdbe_chem_comp_rdkit_properties.tpsa 74.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.640
_pdbe_chem_comp_rdkit_properties.CrippenMR 79.695
_pdbe_chem_comp_rdkit_properties.chi0v 10.133
_pdbe_chem_comp_rdkit_properties.chi1v 5.316
_pdbe_chem_comp_rdkit_properties.chi2v 2.510
_pdbe_chem_comp_rdkit_properties.chi3v 2.510
_pdbe_chem_comp_rdkit_properties.chi4v 1.400
_pdbe_chem_comp_rdkit_properties.chi0n 32.133
_pdbe_chem_comp_rdkit_properties.chi1n 16.133
_pdbe_chem_comp_rdkit_properties.chi2n 2.510
_pdbe_chem_comp_rdkit_properties.chi3n 2.510
_pdbe_chem_comp_rdkit_properties.chi4n 1.400
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.680
_pdbe_chem_comp_rdkit_properties.kappa1 3.620
_pdbe_chem_comp_rdkit_properties.kappa2 5.261
_pdbe_chem_comp_rdkit_properties.kappa3 3.156
_pdbe_chem_comp_rdkit_properties.Phi 0.907
#
_pdbe_chem_comp_external_mappings.comp_id A4H
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 134611692
#
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
A4H C1 3.560 0.762 -2.415 ETKDGv3 1
A4H C2 3.303 -0.535 -1.755 ETKDGv3 2
A4H C3 2.232 -0.844 -0.995 ETKDGv3 3
A4H C5 -0.097 -0.180 -0.486 ETKDGv3 4
A4H C6 2.080 -2.271 -0.518 ETKDGv3 5
A4H C13 -2.528 -0.075 -2.196 ETKDGv3 6
A4H C15 -0.082 1.406 2.175 ETKDGv3 7
A4H C24 1.890 -2.433 0.985 ETKDGv3 8
A4H O11 2.642 1.605 -2.600 ETKDGv3 9
A4H O12 4.838 1.028 -2.895 ETKDGv3 10
A4H C23 3.217 -2.798 0.350 ETKDGv3 11
A4H C4 1.191 0.156 -0.645 ETKDGv3 12
A4H C7 -1.180 0.822 -0.092 ETKDGv3 13
A4H O7 -0.825 2.120 -0.521 ETKDGv3 14
A4H C12 -1.346 0.838 1.482 ETKDGv3 15
A4H C14 -1.597 -0.587 2.049 ETKDGv3 16
A4H C8 -2.507 0.454 -0.782 ETKDGv3 17
A4H C9 -3.690 0.742 -0.212 ETKDGv3 18
A4H C10 -3.782 1.362 1.116 ETKDGv3 19
A4H O10 -4.913 1.612 1.610 ETKDGv3 20
A4H C11 -2.542 1.751 1.860 ETKDGv3 21
A4H H1 4.049 -1.302 -1.929 ETKDGv3 22
A4H H2 -0.392 -1.215 -0.613 ETKDGv3 23
A4H H3 1.564 -3.021 -1.154 ETKDGv3 24
A4H H4 -1.517 -0.085 -2.654 ETKDGv3 25
A4H H5 -3.171 0.569 -2.834 ETKDGv3 26
A4H H6 -2.932 -1.109 -2.201 ETKDGv3 27
A4H H7 0.161 2.423 1.800 ETKDGv3 28
A4H H8 0.798 0.751 2.009 ETKDGv3 29
A4H H9 -0.240 1.478 3.273 ETKDGv3 30
A4H H10 1.276 -3.310 1.280 ETKDGv3 31
A4H H11 1.933 -1.505 1.594 ETKDGv3 32
A4H H12 5.045 1.899 -3.371 ETKDGv3 33
A4H H13 3.390 -3.892 0.269 ETKDGv3 34
A4H H14 4.033 -2.081 0.585 ETKDGv3 35
A4H H15 1.492 1.184 -0.494 ETKDGv3 36
A4H H16 -0.717 2.103 -1.508 ETKDGv3 37
A4H H17 -0.708 -1.236 1.913 ETKDGv3 38
A4H H18 -1.810 -0.542 3.139 ETKDGv3 39
A4H H19 -2.459 -1.079 1.552 ETKDGv3 40
A4H H20 -4.612 0.518 -0.737 ETKDGv3 41
A4H H21 -2.311 2.809 1.608 ETKDGv3 42
A4H H22 -2.736 1.704 2.954 ETKDGv3 43
#