data_PWS
#
_chem_comp.id PWS
_chem_comp.name 3-methyl-2-(methylsulfanyl)-6-(trifluoromethyl)pyrimidin-4(3H)-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H7 F3 N2 O S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-08-27
_chem_comp.pdbx_modified_date 2019-12-20
_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 224.203
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PWS
_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 5QTS
_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
PWS N1 N1 N 0 1 N N N N N N -4.694 2.391 2.583 0.031 -0.673 -0.000 N1 PWS 1
PWS C4 C1 C 0 1 N N N N N N -6.065 0.389 2.032 -2.397 -0.294 -0.000 C4 PWS 2
PWS C5 C2 C 0 1 N N N N N N -4.158 0.287 3.610 -0.716 1.540 0.000 C5 PWS 3
PWS C6 C3 C 0 1 N N N N N N -3.038 0.879 4.290 0.620 1.976 0.000 C6 PWS 4
PWS N N2 N 0 1 N N N N N N -2.800 2.268 4.072 1.605 1.052 -0.000 N PWS 5
PWS C C4 C 0 1 N N N N N N -4.668 5.322 1.831 1.597 -2.992 0.001 C PWS 6
PWS O O1 O 0 1 N N N N N N -2.322 0.276 5.009 0.886 3.167 0.000 O PWS 7
PWS C1 C5 C 0 1 N N N N N N -3.667 2.954 3.218 1.288 -0.273 -0.000 C1 PWS 8
PWS C2 C6 C 0 1 N N N N N N -1.654 2.903 4.790 3.008 1.473 -0.000 C2 PWS 9
PWS C3 C7 C 0 1 N N N N N N -4.905 1.043 2.805 -0.973 0.199 -0.000 C3 PWS 10
PWS F F1 F 0 1 N N N N N N -5.981 0.691 0.732 -2.622 -1.069 1.142 F PWS 11
PWS F1 F2 F 0 1 N N N N N N -6.127 -0.958 2.101 -3.269 0.800 0.000 F1 PWS 12
PWS F2 F3 F 0 1 N N N N N N -7.298 0.832 2.425 -2.622 -1.069 -1.142 F2 PWS 13
PWS S S1 S 0 1 N N N N N N -3.400 4.675 2.928 2.579 -1.472 0.000 S PWS 14
PWS H1 H1 H 0 1 N N N N N N -4.392 -0.758 3.750 -1.527 2.254 0.001 H1 PWS 15
PWS H2 H2 H 0 1 N N N N N N -4.492 6.394 1.658 2.263 -3.855 0.001 H2 PWS 16
PWS H3 H3 H 0 1 N N N N N N -4.632 4.785 0.872 0.968 -3.018 0.891 H3 PWS 17
PWS H4 H4 H 0 1 N N N N N N -5.657 5.183 2.292 0.968 -3.018 -0.890 H4 PWS 18
PWS H5 H5 H 0 1 N N N N N N -1.134 2.145 5.394 3.061 2.561 0.001 H5 PWS 19
PWS H6 H6 H 0 1 N N N N N N -0.954 3.331 4.057 3.503 1.084 0.890 H6 PWS 20
PWS H7 H7 H 0 1 N N N N N N -2.030 3.701 5.447 3.503 1.085 -0.890 H7 PWS 21
#
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
PWS F C4 SING N N 1
PWS C S SING N N 2
PWS C4 F1 SING N N 3
PWS C4 F2 SING N N 4
PWS C4 C3 SING N N 5
PWS N1 C3 SING N N 6
PWS N1 C1 DOUB N N 7
PWS C3 C5 DOUB N N 8
PWS S C1 SING N N 9
PWS C1 N SING N N 10
PWS C5 C6 SING N N 11
PWS N C6 SING N N 12
PWS N C2 SING N N 13
PWS C6 O DOUB N N 14
PWS C5 H1 SING N N 15
PWS C H2 SING N N 16
PWS C H3 SING N N 17
PWS C H4 SING N N 18
PWS C2 H5 SING N N 19
PWS C2 H6 SING N N 20
PWS C2 H7 SING N N 21
#
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
PWS SMILES ACDLabs 12.01 N=1C(C(F)(F)F)=CC(=O)N(C)C=1SC
PWS InChI InChI 1.03 InChI=1S/C7H7F3N2OS/c1-12-5(13)3-4(7(8,9)10)11-6(12)14-2/h3H,1-2H3
PWS InChIKey InChI 1.03 PBQNVDKEOYJSNU-UHFFFAOYSA-N
PWS SMILES_CANONICAL CACTVS 3.385 CSC1=NC(=CC(=O)N1C)C(F)(F)F
PWS SMILES CACTVS 3.385 CSC1=NC(=CC(=O)N1C)C(F)(F)F
PWS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CN1C(=O)C=C(N=C1SC)C(F)(F)F
PWS SMILES "OpenEye OEToolkits" 2.0.6 CN1C(=O)C=C(N=C1SC)C(F)(F)F
#
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
PWS "SYSTEMATIC NAME" ACDLabs 12.01 3-methyl-2-(methylsulfanyl)-6-(trifluoromethyl)pyrimidin-4(3H)-one
PWS "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 3-methyl-2-methylsulfanyl-6-(trifluoromethyl)pyrimidin-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
PWS 'Create component' 2019-08-27 RCSB
PWS 'Initial release' 2019-12-25 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
PWS N1 N 6.897 0.000 1
PWS C4 C 5.598 2.250 2
PWS C5 C 4.299 0.000 3
PWS C6 C 4.299 -1.500 4
PWS N N 5.598 -2.250 5
PWS C C 9.495 -1.500 6
PWS O O 3.000 -2.250 7
PWS C1 C 6.897 -1.500 8
PWS C2 C 5.598 -3.750 9
PWS C3 C 5.598 0.750 10
PWS F F 5.598 3.750 11
PWS F1 F 7.098 2.250 12
PWS F2 F 4.098 2.250 13
PWS S S 8.196 -2.250 14
#
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
PWS F C4 SINGLE NONE 1
PWS C S SINGLE NONE 2
PWS C4 F1 SINGLE NONE 3
PWS C4 F2 SINGLE NONE 4
PWS C4 C3 SINGLE NONE 5
PWS N1 C3 SINGLE NONE 6
PWS N1 C1 DOUBLE NONE 7
PWS C3 C5 DOUBLE NONE 8
PWS S C1 SINGLE NONE 9
PWS C1 N SINGLE NONE 10
PWS C5 C6 SINGLE NONE 11
PWS N C6 SINGLE NONE 12
PWS N C2 SINGLE NONE 13
PWS C6 O DOUBLE NONE 14
#
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
PWS MurckoScaffold S1 scaffold 'O=c1ccnc[nH]1' InChI=1S/C4H4N2O/c7-4-1-2-5-3-6-4/h1-3H,(H,5,6,7) DNCYBUMDUBHIJZ-UHFFFAOYSA-N
PWS pyrimidine F1 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
PWS N1 S1 1
PWS C5 S1 1
PWS C6 S1 1
PWS N S1 1
PWS O S1 1
PWS C1 S1 1
PWS C3 S1 1
PWS C5 F1 1
PWS C3 F1 1
PWS N1 F1 1
PWS C1 F1 1
PWS N F1 1
PWS C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PWS
_pdbe_chem_comp_rdkit_properties.exactmw 224.023
_pdbe_chem_comp_rdkit_properties.amw 224.207
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.429
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 91.792
_pdbe_chem_comp_rdkit_properties.tpsa 34.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.258
_pdbe_chem_comp_rdkit_properties.CrippenMR 46.673
_pdbe_chem_comp_rdkit_properties.chi0v 7.161
_pdbe_chem_comp_rdkit_properties.chi1v 3.864
_pdbe_chem_comp_rdkit_properties.chi2v 1.643
_pdbe_chem_comp_rdkit_properties.chi3v 1.643
_pdbe_chem_comp_rdkit_properties.chi4v 0.932
_pdbe_chem_comp_rdkit_properties.chi0n 13.345
_pdbe_chem_comp_rdkit_properties.chi1n 6.547
_pdbe_chem_comp_rdkit_properties.chi2n 1.187
_pdbe_chem_comp_rdkit_properties.chi3n 1.187
_pdbe_chem_comp_rdkit_properties.chi4n 0.620
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.980
_pdbe_chem_comp_rdkit_properties.kappa1 4.693
_pdbe_chem_comp_rdkit_properties.kappa2 3.642
_pdbe_chem_comp_rdkit_properties.kappa3 2.088
_pdbe_chem_comp_rdkit_properties.Phi 1.221
#
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
PWS UniChem ZINC ZINC000001400831
PWS UniChem SureChEMBL SCHEMBL6565139
PWS UniChem PubChem 1486660
PWS UniChem Mcule MCULE-7400310501
#
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
PWS N1 0.548 -0.846 -0.766 ETKDGv3 1
PWS C4 2.628 -1.973 0.158 ETKDGv3 2
PWS C5 1.779 0.167 1.040 ETKDGv3 3
PWS C6 0.802 1.260 1.027 ETKDGv3 4
PWS N -0.251 1.247 0.045 ETKDGv3 5
PWS C -2.743 -0.997 -0.884 ETKDGv3 6
PWS O 0.895 2.192 1.870 ETKDGv3 7
PWS C1 -0.343 0.101 -0.829 ETKDGv3 8
PWS C2 -1.249 2.320 -0.004 ETKDGv3 9
PWS C3 1.648 -0.836 0.162 ETKDGv3 10
PWS F 2.571 -2.642 1.368 ETKDGv3 11
PWS F1 3.909 -1.488 -0.034 ETKDGv3 12
PWS F2 2.331 -2.862 -0.859 ETKDGv3 13
PWS S -1.677 -0.062 -2.024 ETKDGv3 14
PWS H1 2.592 0.178 1.757 ETKDGv3 15
PWS H2 -3.698 -1.235 -1.395 ETKDGv3 16
PWS H3 -2.246 -1.945 -0.590 ETKDGv3 17
PWS H4 -2.960 -0.393 0.021 ETKDGv3 18
PWS H5 -2.181 1.986 0.498 ETKDGv3 19
PWS H6 -1.472 2.591 -1.057 ETKDGv3 20
PWS H7 -0.881 3.239 0.497 ETKDGv3 21
#