data_38E
#
_chem_comp.id 38E
_chem_comp.name (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H10 F2 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-07-03
_chem_comp.pdbx_modified_date 2014-09-05
_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 252.217
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 38E
_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 4TS0
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
38E F1 F1 F 0 1 N N N N N N 25.981 22.726 16.723 -2.320 2.525 0.059 F1 38E 1
38E C2 C1 C 0 1 Y N N N N N 27.293 22.731 16.327 -2.207 1.179 0.049 C2 38E 2
38E C1 C2 C 0 1 Y N N N N N 27.955 21.452 16.089 -3.349 0.386 -0.017 C1 38E 3
38E O1 O1 O 0 1 N N N N N N 27.244 20.364 16.290 -4.575 0.968 -0.071 O1 38E 4
38E C3 C3 C 0 1 Y N N N N N 28.039 23.885 16.137 -0.960 0.593 0.098 C3 38E 5
38E C4 C4 C 0 1 Y N N N N N 29.379 23.808 15.745 -0.844 -0.804 0.087 C4 38E 6
38E C5 C5 C 0 1 Y N N N N N 30.020 22.578 15.524 -1.998 -1.598 0.025 C5 38E 7
38E C C6 C 0 1 Y N N N N N 29.371 21.387 15.681 -3.239 -1.002 -0.029 C 38E 8
38E F F2 F 0 1 N N N N N N 30.026 20.210 15.461 -4.352 -1.766 -0.088 F 38E 9
38E C6 C7 C 0 1 N N N N N N 30.239 25.032 15.537 0.478 -1.432 0.138 C6 38E 10
38E C7 C8 C 0 1 N N N N N N 29.803 26.421 15.782 1.614 -0.654 0.073 C7 38E 11
38E C9 C9 C 0 1 N N N N N N 30.595 27.638 15.622 3.009 -1.121 -0.001 C9 38E 12
38E O O2 O 0 1 N N N N N N 31.838 27.721 15.220 3.403 -2.273 -0.018 O 38E 13
38E N1 N1 N 0 1 N N N N N N 29.812 28.666 15.879 3.758 0.003 -0.047 N1 38E 14
38E C10 C10 C 0 1 N N N N N N 30.239 30.079 15.820 5.219 0.057 -0.128 C10 38E 15
38E C8 C11 C 0 1 N N N N N N 28.606 28.198 16.215 2.919 1.082 -0.007 C8 38E 16
38E N N2 N 0 1 N N N N N N 28.559 26.819 16.162 1.678 0.712 0.058 N 38E 17
38E C11 C12 C 0 1 N N N N N N 27.492 29.126 16.621 3.378 2.517 -0.039 C11 38E 18
38E H1 H1 H 0 1 N N N N N N 26.361 20.605 16.545 -4.886 1.147 -0.969 H1 38E 19
38E H2 H2 H 0 1 N N N N N N 27.581 24.851 16.293 -0.075 1.209 0.145 H2 38E 20
38E H3 H3 H 0 1 N N N N N N 31.057 22.574 15.221 -1.914 -2.675 0.016 H3 38E 21
38E H4 H4 H 0 1 N N N N N N 31.248 24.880 15.183 0.564 -2.505 0.228 H4 38E 22
38E H5 H5 H 0 1 N N N N N N 29.391 30.730 16.079 5.620 -0.957 -0.146 H5 38E 23
38E H6 H6 H 0 1 N N N N N N 31.060 30.244 16.534 5.514 0.579 -1.039 H6 38E 24
38E H7 H7 H 0 1 N N N N N N 30.585 30.315 14.803 5.612 0.588 0.739 H7 38E 25
38E H8 H8 H 0 1 N N N N N N 26.600 28.537 16.880 3.432 2.858 -1.073 H8 38E 26
38E H9 H9 H 0 1 N N N N N N 27.807 29.717 17.493 2.670 3.137 0.512 H9 38E 27
38E H10 H10 H 0 1 N N N N N N 27.255 29.802 15.786 4.363 2.594 0.422 H10 38E 28
#
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
38E O C9 DOUB N N 1
38E F C SING N N 2
38E C5 C DOUB Y N 3
38E C5 C4 SING Y N 4
38E C6 C4 SING N N 5
38E C6 C7 DOUB N Z 6
38E C9 C7 SING N N 7
38E C9 N1 SING N N 8
38E C C1 SING Y N 9
38E C4 C3 DOUB Y N 10
38E C7 N SING N N 11
38E C10 N1 SING N N 12
38E N1 C8 SING N N 13
38E C1 O1 SING N N 14
38E C1 C2 DOUB Y N 15
38E C3 C2 SING Y N 16
38E N C8 DOUB N N 17
38E C8 C11 SING N N 18
38E C2 F1 SING N N 19
38E O1 H1 SING N N 20
38E C3 H2 SING N N 21
38E C5 H3 SING N N 22
38E C6 H4 SING N N 23
38E C10 H5 SING N N 24
38E C10 H6 SING N N 25
38E C10 H7 SING N N 26
38E C11 H8 SING N N 27
38E C11 H9 SING N N 28
38E C11 H10 SING N N 29
#
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
38E SMILES ACDLabs 12.01 O=C1C(\N=C(N1C)C)=C\c2cc(F)c(O)c(F)c2
38E InChI InChI 1.03 InChI=1S/C12H10F2N2O2/c1-6-15-10(12(18)16(6)2)5-7-3-8(13)11(17)9(14)4-7/h3-5,17H,1-2H3/b10-5-
38E InChIKey InChI 1.03 ZDDIJYXDUBFLID-YHYXMXQVSA-N
38E SMILES_CANONICAL CACTVS 3.385 CN1C(=NC(=C/c2cc(F)c(O)c(F)c2)\C1=O)C
38E SMILES CACTVS 3.385 CN1C(=NC(=Cc2cc(F)c(O)c(F)c2)C1=O)C
38E SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 CC1=N/C(=C\c2cc(c(c(c2)F)O)F)/C(=O)N1C
38E SMILES "OpenEye OEToolkits" 1.9.2 CC1=NC(=Cc2cc(c(c(c2)F)O)F)C(=O)N1C
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
38E "SYSTEMATIC NAME" ACDLabs 12.01 (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one
38E "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 (5Z)-5-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]methylidene]-2,3-dimethyl-imidazol-4-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
38E 'Create component' 2014-07-03 RCSB
38E 'Initial release' 2014-07-23 RCSB
38E 'Modify descriptor' 2014-09-05 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
38E F1 F 8.196 -3.229 1
38E C2 C 6.897 -2.479 2
38E C1 C 5.598 -3.229 3
38E O1 O 5.598 -4.729 4
38E C3 C 6.897 -0.980 5
38E C4 C 5.598 -0.230 6
38E C5 C 4.299 -0.980 7
38E C C 4.299 -2.479 8
38E F F 3.000 -3.229 9
38E C6 C 5.598 1.270 10
38E C7 C 6.897 2.021 11
38E C9 C 7.054 3.512 12
38E O O 5.939 4.516 13
38E N1 N 8.521 3.824 14
38E C10 C 9.131 5.194 15
38E C8 C 9.271 2.525 16
38E N N 8.267 1.410 17
38E C11 C 10.763 2.368 18
#
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
38E O C9 DOUBLE NONE 1
38E F C SINGLE NONE 2
38E C5 C DOUBLE NONE 3
38E C5 C4 SINGLE NONE 4
38E C6 C4 SINGLE ENDDOWNRIGHT 5
38E C6 C7 DOUBLE NONE 6
38E C9 C7 SINGLE ENDDOWNRIGHT 7
38E C9 N1 SINGLE NONE 8
38E C C1 SINGLE NONE 9
38E C4 C3 DOUBLE NONE 10
38E C7 N SINGLE ENDDOWNRIGHT 11
38E C10 N1 SINGLE NONE 12
38E N1 C8 SINGLE NONE 13
38E C1 O1 SINGLE NONE 14
38E C1 C2 DOUBLE NONE 15
38E C3 C2 SINGLE NONE 16
38E N C8 DOUBLE NONE 17
38E C8 C11 SINGLE NONE 18
38E C2 F1 SINGLE NONE 19
#
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
38E MurckoScaffold S1 scaffold O=C1NC=N/C1=C\c1ccccc1 InChI=1S/C10H8N2O/c13-10-9(11-7-12-10)6-8-4-2-1-3-5-8/h1-7H,(H,11,12,13)/b9-6- CQGIJPFYWRPMRO-TWGQIWQCSA-N
38E amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
38E peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
38E phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
38E C2 S1 1
38E C1 S1 1
38E C3 S1 1
38E C4 S1 1
38E C5 S1 1
38E C S1 1
38E C6 S1 1
38E C7 S1 1
38E C9 S1 1
38E O S1 1
38E N1 S1 1
38E C8 S1 1
38E N S1 1
38E N1 F1 1
38E C9 F1 1
38E O F1 1
38E C7 F1 1
38E O F2 1
38E C9 F2 1
38E C7 F2 1
38E N F2 1
38E C2 F3 1
38E C1 F3 1
38E C F3 1
38E C5 F3 1
38E C4 F3 1
38E C3 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 38E
_pdbe_chem_comp_rdkit_properties.exactmw 252.071
_pdbe_chem_comp_rdkit_properties.amw 252.220
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.167
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 116.004
_pdbe_chem_comp_rdkit_properties.tpsa 52.900
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.385
_pdbe_chem_comp_rdkit_properties.CrippenMR 61.003
_pdbe_chem_comp_rdkit_properties.chi0v 8.467
_pdbe_chem_comp_rdkit_properties.chi1v 4.404
_pdbe_chem_comp_rdkit_properties.chi2v 1.947
_pdbe_chem_comp_rdkit_properties.chi3v 1.947
_pdbe_chem_comp_rdkit_properties.chi4v 1.129
_pdbe_chem_comp_rdkit_properties.chi0n 18.467
_pdbe_chem_comp_rdkit_properties.chi1n 9.312
_pdbe_chem_comp_rdkit_properties.chi2n 1.947
_pdbe_chem_comp_rdkit_properties.chi3n 1.947
_pdbe_chem_comp_rdkit_properties.chi4n 1.129
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.240
_pdbe_chem_comp_rdkit_properties.kappa1 4.795
_pdbe_chem_comp_rdkit_properties.kappa2 4.211
_pdbe_chem_comp_rdkit_properties.kappa3 1.966
_pdbe_chem_comp_rdkit_properties.Phi 1.122
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
38E UniChem PDBe 38E
38E UniChem ZINC ZINC000098208407
38E UniChem SureChEMBL SCHEMBL12960487
38E UniChem PubChem 70808995
38E UniChem Nikkaji J3.217.868E
38E UniChem Nikkaji J3.362.740H
38E UniChem MedChemExpress HY-110250
38E UniChem 'Probes And Drugs' PD069438
#
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
38E F1 3.582 -2.354 -0.025 ETKDGv3 1
38E C2 3.304 -1.054 -0.292 ETKDGv3 2
38E C1 4.272 -0.129 -0.224 ETKDGv3 3
38E O1 5.566 -0.507 0.127 ETKDGv3 4
38E C3 1.927 -0.665 -0.664 ETKDGv3 5
38E C4 1.627 0.625 -0.915 ETKDGv3 6
38E C5 2.707 1.640 -0.860 ETKDGv3 7
38E C 3.956 1.287 -0.528 ETKDGv3 8
38E F 4.929 2.230 -0.476 ETKDGv3 9
38E C6 0.272 1.060 -1.321 ETKDGv3 10
38E C7 -0.864 0.545 -0.832 ETKDGv3 11
38E C9 -2.210 0.942 -1.173 ETKDGv3 12
38E O -2.555 1.768 -2.060 ETKDGv3 13
38E N1 -3.103 0.207 -0.356 ETKDGv3 14
38E C10 -4.508 -0.047 -0.650 ETKDGv3 15
38E C8 -2.230 -0.637 0.411 ETKDGv3 16
38E N -0.962 -0.460 0.176 ETKDGv3 17
38E C11 -2.723 -1.660 1.383 ETKDGv3 18
38E H1 6.317 0.170 0.185 ETKDGv3 19
38E H2 1.182 -1.443 -0.761 ETKDGv3 20
38E H3 2.485 2.676 -1.082 ETKDGv3 21
38E H4 0.200 1.893 -2.010 ETKDGv3 22
38E H5 -4.984 0.873 -1.051 ETKDGv3 23
38E H6 -4.591 -0.861 -1.401 ETKDGv3 24
38E H7 -5.042 -0.345 0.276 ETKDGv3 25
38E H8 -3.406 -1.180 2.114 ETKDGv3 26
38E H9 -3.271 -2.456 0.837 ETKDGv3 27
38E H10 -1.873 -2.117 1.933 ETKDGv3 28
#