data_W40
#
_chem_comp.id W40
_chem_comp.name 5-[3,5-bis(fluoranyl)phenyl]-1-[(1S)-1-phenylethyl]pyrimidine-2,4-dione
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C18 H14 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 2023-04-26
_chem_comp.pdbx_modified_date 2023-06-30
_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 328.313
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W40
_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 8OW3
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
W40 C1 C1 C 0 1 N N S N N N -13.721 5.674 1.503 2.758 -0.816 -0.981 C1 W40 1
W40 C2 C2 C 0 1 Y N N N N N -13.771 5.873 3.012 3.218 0.489 -0.383 C2 W40 2
W40 C3 C3 C 0 1 Y N N N N N -14.143 7.095 3.565 2.985 0.757 0.953 C3 W40 3
W40 C7 C4 C 0 1 Y N N N N N -13.447 4.833 3.869 3.879 1.415 -1.168 C7 W40 4
W40 C8 C5 C 0 1 N N N N N N -13.878 7.893 0.386 0.396 -0.474 -0.461 C8 W40 5
W40 C9 C6 C 0 1 N N N N N N -14.524 8.901 -0.242 -0.762 -0.869 0.140 C9 W40 6
W40 C10 C7 C 0 1 N N N N N N -15.959 8.754 -0.484 -0.755 -2.118 0.913 C10 W40 7
W40 C11 C8 C 0 1 N N N N N N -15.844 6.532 0.611 1.507 -2.378 0.386 C11 W40 8
W40 C12 C9 C 0 1 Y N N N N N -13.789 10.120 -0.660 -1.998 -0.059 0.017 C12 W40 9
W40 C13 C10 C 0 1 Y N N N N N -14.294 11.384 -0.363 -3.107 -0.573 -0.653 C13 W40 10
W40 C14 C11 C 0 1 Y N N N N N -13.577 12.486 -0.762 -4.257 0.186 -0.765 C14 W40 11
W40 C15 C12 C 0 1 Y N N N N N -12.384 12.415 -1.433 -4.308 1.456 -0.214 C15 W40 12
W40 C16 C13 C 0 1 Y N N N N N -11.920 11.154 -1.700 -3.208 1.971 0.452 C16 W40 13
W40 N N1 N 0 1 N N N N N N -14.495 6.735 0.807 1.517 -1.241 -0.329 N W40 14
W40 C C14 C 0 1 N N N N N N -12.289 5.593 0.979 2.509 -0.630 -2.479 C W40 15
W40 O O1 O 0 1 N N N N N N -16.679 9.585 -1.041 -1.765 -2.512 1.467 O W40 16
W40 N1 N2 N 0 1 N N N N N N -16.499 7.561 -0.029 0.394 -2.821 0.997 N1 W40 17
W40 O1 O2 O 0 1 N N N N N N -16.426 5.518 0.973 2.529 -3.030 0.475 O1 W40 18
W40 C4 C15 C 0 1 Y N N N N N -14.186 7.266 4.936 3.407 1.953 1.502 C4 W40 19
W40 C5 C16 C 0 1 Y N N N N N -13.861 6.224 5.775 4.063 2.882 0.715 C5 W40 20
W40 C6 C17 C 0 1 Y N N N N N -13.493 5.009 5.242 4.301 2.611 -0.620 C6 W40 21
W40 C17 C18 C 0 1 Y N N N N N -12.578 10.004 -1.335 -2.056 1.217 0.575 C17 W40 22
W40 F F1 F 0 1 N N N N N N -10.742 11.038 -2.363 -3.263 3.211 0.987 F W40 23
W40 F1 F2 F 0 1 N N N N N N -14.072 13.719 -0.477 -5.333 -0.311 -1.414 F1 W40 24
W40 H1 H1 H 0 1 N N N N N N -14.203 4.710 1.284 3.526 -1.575 -0.832 H1 W40 25
W40 H2 H2 H 0 1 N N N N N N -14.401 7.919 2.916 2.473 0.032 1.568 H2 W40 26
W40 H3 H3 H 0 1 N N N N N N -13.156 3.876 3.462 4.065 1.204 -2.211 H3 W40 27
W40 H4 H4 H 0 1 N N N N N N -12.819 8.001 0.568 0.424 0.437 -1.041 H4 W40 28
W40 H5 H5 H 0 1 N N N N N N -15.228 11.495 0.169 -3.068 -1.562 -1.084 H5 W40 29
W40 H6 H6 H 0 1 N N N N N N -11.842 13.300 -1.733 -5.208 2.047 -0.304 H6 W40 30
W40 H7 H7 H 0 1 N N N N N N -11.746 4.800 1.514 2.177 -1.573 -2.912 H7 W40 31
W40 H8 H8 H 0 1 N N N N N N -12.305 5.364 -0.097 1.742 0.129 -2.629 H8 W40 32
W40 H9 H9 H 0 1 N N N N N N -11.784 6.557 1.142 3.433 -0.313 -2.964 H9 W40 33
W40 H10 H10 H 0 1 N N N N N N -17.479 7.432 -0.183 0.418 -3.648 1.503 H10 W40 34
W40 H11 H11 H 0 1 N N N N N N -14.476 8.220 5.350 3.224 2.163 2.546 H11 W40 35
W40 H12 H12 H 0 1 N N N N N N -13.895 6.359 6.846 4.392 3.816 1.144 H12 W40 36
W40 H13 H13 H 0 1 N N N N N N -13.239 4.189 5.898 4.817 3.335 -1.233 H13 W40 37
W40 H14 H14 H 0 1 N N N N N N -12.165 9.033 -1.567 -1.199 1.619 1.095 H14 W40 38
#
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
W40 F C16 SING N N 1
W40 C16 C15 DOUB Y N 2
W40 C16 C17 SING Y N 3
W40 C15 C14 SING Y N 4
W40 C17 C12 DOUB Y N 5
W40 O C10 DOUB N N 6
W40 C14 F1 SING N N 7
W40 C14 C13 DOUB Y N 8
W40 C12 C13 SING Y N 9
W40 C12 C9 SING N N 10
W40 C10 C9 SING N N 11
W40 C10 N1 SING N N 12
W40 C9 C8 DOUB N N 13
W40 N1 C11 SING N N 14
W40 C8 N SING N N 15
W40 C11 N SING N N 16
W40 C11 O1 DOUB N N 17
W40 N C1 SING N N 18
W40 C C1 SING N N 19
W40 C1 C2 SING N N 20
W40 C2 C3 DOUB Y N 21
W40 C2 C7 SING Y N 22
W40 C3 C4 SING Y N 23
W40 C7 C6 DOUB Y N 24
W40 C4 C5 DOUB Y N 25
W40 C6 C5 SING Y N 26
W40 C1 H1 SING N N 27
W40 C3 H2 SING N N 28
W40 C7 H3 SING N N 29
W40 C8 H4 SING N N 30
W40 C13 H5 SING N N 31
W40 C15 H6 SING N N 32
W40 C H7 SING N N 33
W40 C H8 SING N N 34
W40 C H9 SING N N 35
W40 N1 H10 SING N N 36
W40 C4 H11 SING N N 37
W40 C5 H12 SING N N 38
W40 C6 H13 SING N N 39
W40 C17 H14 SING N N 40
#
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
W40 InChI InChI 1.06 InChI=1S/C18H14F2N2O2/c1-11(12-5-3-2-4-6-12)22-10-16(17(23)21-18(22)24)13-7-14(19)9-15(20)8-13/h2-11H,1H3,(H,21,23,24)/t11-/m0/s1
W40 InChIKey InChI 1.06 PDFBJEYJDVRNBX-NSHDSACASA-N
W40 SMILES_CANONICAL CACTVS 3.385 C[C@H](N1C=C(C(=O)NC1=O)c2cc(F)cc(F)c2)c3ccccc3
W40 SMILES CACTVS 3.385 C[CH](N1C=C(C(=O)NC1=O)c2cc(F)cc(F)c2)c3ccccc3
W40 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@@H](c1ccccc1)N2C=C(C(=O)NC2=O)c3cc(cc(c3)F)F
W40 SMILES "OpenEye OEToolkits" 2.0.7 CC(c1ccccc1)N2C=C(C(=O)NC2=O)c3cc(cc(c3)F)F
#
_pdbx_chem_comp_identifier.comp_id W40
_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 5-[3,5-bis(fluoranyl)phenyl]-1-[(1~{S})-1-phenylethyl]pyrimidine-2,4-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W40 'Create component' 2023-04-26 PDBE
W40 'Initial release' 2023-07-05 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
W40 C1 C 9.495 -2.625 1
W40 C2 C 8.196 -3.375 2
W40 C3 C 8.196 -4.875 3
W40 C7 C 6.897 -2.625 4
W40 C8 C 8.196 -0.375 5
W40 C9 C 8.196 1.125 6
W40 C10 C 9.495 1.875 7
W40 C11 C 10.794 -0.375 8
W40 C12 C 6.897 1.875 9
W40 C13 C 6.897 3.375 10
W40 C14 C 5.598 4.125 11
W40 C15 C 4.299 3.375 12
W40 C16 C 4.299 1.875 13
W40 N N 9.495 -1.125 14
W40 C C 10.794 -3.375 15
W40 O O 9.495 3.375 16
W40 N1 N 10.794 1.125 17
W40 O1 O 12.093 -1.125 18
W40 C4 C 6.897 -5.625 19
W40 C5 C 5.598 -4.875 20
W40 C6 C 5.598 -3.375 21
W40 C17 C 5.598 1.125 22
W40 F F 3.000 1.125 23
W40 F1 F 5.598 5.625 24
#
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
W40 F C16 SINGLE NONE 1
W40 C16 C15 DOUBLE NONE 2
W40 C16 C17 SINGLE NONE 3
W40 C15 C14 SINGLE NONE 4
W40 C17 C12 DOUBLE NONE 5
W40 O C10 DOUBLE NONE 6
W40 C14 F1 SINGLE NONE 7
W40 C14 C13 DOUBLE NONE 8
W40 C12 C13 SINGLE NONE 9
W40 C12 C9 SINGLE NONE 10
W40 C10 C9 SINGLE NONE 11
W40 C10 N1 SINGLE NONE 12
W40 C9 C8 DOUBLE NONE 13
W40 N1 C11 SINGLE NONE 14
W40 C8 N SINGLE NONE 15
W40 C11 N SINGLE NONE 16
W40 C11 O1 DOUBLE NONE 17
W40 N C1 SINGLE NONE 18
W40 C1 C SINGLE BEGINWEDGE 19
W40 C1 C2 SINGLE NONE 20
W40 C2 C3 DOUBLE NONE 21
W40 C2 C7 SINGLE NONE 22
W40 C3 C4 SINGLE NONE 23
W40 C7 C6 DOUBLE NONE 24
W40 C4 C5 DOUBLE NONE 25
W40 C6 C5 SINGLE NONE 26
#
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
W40 MurckoScaffold S1 scaffold 'O=c1[nH]c(=O)n(Cc2ccccc2)cc1-c1ccccc1' InChI=1S/C17H14N2O2/c20-16-15(14-9-5-2-6-10-14)12-19(17(21)18-16)11-13-7-3-1-4-8-13/h1-10,12H,11H2,(H,18,20,21) BZEGKXDIFIZLCJ-UHFFFAOYSA-N
W40 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
W40 pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
W40 C1 S1 1
W40 C2 S1 1
W40 C3 S1 1
W40 C7 S1 1
W40 C8 S1 1
W40 C9 S1 1
W40 C10 S1 1
W40 C11 S1 1
W40 C12 S1 1
W40 C13 S1 1
W40 C14 S1 1
W40 C15 S1 1
W40 C16 S1 1
W40 N S1 1
W40 O S1 1
W40 N1 S1 1
W40 O1 S1 1
W40 C4 S1 1
W40 C5 S1 1
W40 C6 S1 1
W40 C17 S1 1
W40 C2 F1 1
W40 C3 F1 1
W40 C4 F1 1
W40 C5 F1 1
W40 C6 F1 1
W40 C7 F1 1
W40 C12 F1 2
W40 C17 F1 2
W40 C16 F1 2
W40 C15 F1 2
W40 C14 F1 2
W40 C13 F1 2
W40 C9 F2 1
W40 C10 F2 1
W40 N1 F2 1
W40 C11 F2 1
W40 N F2 1
W40 C8 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W40
_pdbe_chem_comp_rdkit_properties.exactmw 328.102
_pdbe_chem_comp_rdkit_properties.amw 328.318
_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 24
_pdbe_chem_comp_rdkit_properties.NumAtoms 38
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.111
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 155.307
_pdbe_chem_comp_rdkit_properties.tpsa 54.860
_pdbe_chem_comp_rdkit_properties.CrippenClogP 4.456
_pdbe_chem_comp_rdkit_properties.CrippenMR 85.558
_pdbe_chem_comp_rdkit_properties.chi0v 11.467
_pdbe_chem_comp_rdkit_properties.chi1v 6.154
_pdbe_chem_comp_rdkit_properties.chi2v 2.725
_pdbe_chem_comp_rdkit_properties.chi3v 2.725
_pdbe_chem_comp_rdkit_properties.chi4v 1.729
_pdbe_chem_comp_rdkit_properties.chi0n 25.467
_pdbe_chem_comp_rdkit_properties.chi1n 13.101
_pdbe_chem_comp_rdkit_properties.chi2n 2.725
_pdbe_chem_comp_rdkit_properties.chi3n 2.725
_pdbe_chem_comp_rdkit_properties.chi4n 1.729
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.020
_pdbe_chem_comp_rdkit_properties.kappa1 6.124
_pdbe_chem_comp_rdkit_properties.kappa2 6.234
_pdbe_chem_comp_rdkit_properties.kappa3 3.033
_pdbe_chem_comp_rdkit_properties.Phi 1.591
#
_pdbe_chem_comp_external_mappings.comp_id W40
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id W40
#
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
W40 C1 -1.763 -0.854 -0.558 ETKDGv3 1
W40 C2 -2.846 0.085 -0.049 ETKDGv3 2
W40 C3 -3.972 -0.340 0.564 ETKDGv3 3
W40 C7 -2.621 1.548 -0.195 ETKDGv3 4
W40 C8 0.695 -0.390 -0.295 ETKDGv3 5
W40 C9 1.832 -0.312 0.420 ETKDGv3 6
W40 C10 1.813 -0.659 1.860 ETKDGv3 7
W40 C11 -0.609 -1.098 1.706 ETKDGv3 8
W40 C12 3.091 0.110 -0.244 ETKDGv3 9
W40 C13 3.491 -0.498 -1.541 ETKDGv3 10
W40 C14 4.619 -0.112 -2.150 ETKDGv3 11
W40 C15 5.475 0.924 -1.536 ETKDGv3 12
W40 C16 5.123 1.478 -0.370 ETKDGv3 13
W40 N -0.563 -0.781 0.298 ETKDGv3 14
W40 C -2.196 -2.315 -0.760 ETKDGv3 15
W40 O 2.877 -0.658 2.536 ETKDGv3 16
W40 N1 0.584 -1.028 2.484 ETKDGv3 17
W40 O1 -1.689 -1.436 2.260 ETKDGv3 18
W40 C4 -4.968 0.634 1.059 ETKDGv3 19
W40 C5 -4.756 1.946 0.914 ETKDGv3 20
W40 C6 -3.524 2.425 0.258 ETKDGv3 21
W40 C17 3.877 1.056 0.305 ETKDGv3 22
W40 F 5.905 2.431 0.193 ETKDGv3 23
W40 F1 4.982 -0.674 -3.330 ETKDGv3 24
W40 H1 -1.512 -0.488 -1.579 ETKDGv3 25
W40 H2 -4.175 -1.390 0.716 ETKDGv3 26
W40 H3 -1.718 1.910 -0.671 ETKDGv3 27
W40 H4 0.720 -0.129 -1.347 ETKDGv3 28
W40 H5 2.876 -1.265 -1.994 ETKDGv3 29
W40 H6 6.386 1.232 -2.032 ETKDGv3 30
W40 H7 -3.096 -2.362 -1.410 ETKDGv3 31
W40 H8 -2.415 -2.816 0.204 ETKDGv3 32
W40 H9 -1.378 -2.877 -1.260 ETKDGv3 33
W40 H10 0.562 -1.263 3.501 ETKDGv3 34
W40 H11 -5.870 0.281 1.543 ETKDGv3 35
W40 H12 -5.485 2.659 1.278 ETKDGv3 36
W40 H13 -3.353 3.488 0.147 ETKDGv3 37
W40 H14 3.600 1.537 1.235 ETKDGv3 38
#