data_22L
#
_chem_comp.id 22L
_chem_comp.name 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H8 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 2013-08-28
_chem_comp.pdbx_modified_date 2013-09-23
_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 228.270
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 22L
_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 4MCD
_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
22L C1 C1 C 0 1 Y N N N N N 20.685 62.029 71.488 4.255 0.383 -0.003 C1 22L 1
22L C2 C2 C 0 1 Y N N N N N 21.510 63.074 71.872 3.816 -0.628 0.832 C2 22L 2
22L C3 C3 C 0 1 Y N N N N N 21.899 64.044 70.959 2.493 -1.018 0.812 C3 22L 3
22L C7 C7 C 0 1 Y N N N N N 21.863 65.088 68.718 0.174 -0.806 -0.080 C7 22L 4
22L C8 C8 C 0 1 Y N N N N N 23.126 65.634 68.831 -0.205 -2.079 -0.190 C8 22L 5
22L C10 C10 C 0 1 Y N N N N N 21.830 66.791 67.084 -2.166 -0.483 -0.024 C10 22L 6
22L C11 C11 C 0 1 Y N N N N N 21.119 65.777 67.692 -0.926 0.143 0.018 C11 22L 7
22L C12 C12 C 0 1 N N N N N N 19.758 65.582 67.224 -0.901 1.565 0.152 C12 22L 8
22L C15 C15 C 0 1 N N N N N N 20.232 67.440 65.696 -3.247 1.554 0.184 C15 22L 9
22L C4 C4 C 0 1 Y N N N N N 21.482 64.010 69.633 1.597 -0.391 -0.053 C4 22L 10
22L C5 C5 C 0 1 Y N N N N N 20.668 62.962 69.264 2.045 0.628 -0.893 C5 22L 11
22L C6 C6 C 0 1 Y N N N N N 20.281 61.983 70.164 3.370 1.013 -0.860 C6 22L 12
22L S9 S9 S 0 1 Y N N N N N 23.410 66.928 67.733 -1.952 -2.221 -0.190 S9 22L 13
22L O13 O13 O 0 1 N N N N N N 18.975 64.741 67.655 0.159 2.166 0.194 O13 22L 14
22L N14 N14 N 0 1 N N N N N N 19.407 66.463 66.214 -2.070 2.229 0.231 N14 22L 15
22L N16 N16 N 0 1 N N N N N N 21.450 67.639 66.098 -3.290 0.261 0.057 N16 22L 16
22L H1 H1 H 0 1 N N N N N N 20.368 61.277 72.196 5.292 0.686 0.017 H1 22L 17
22L H2 H2 H 0 1 N N N N N N 21.854 63.134 72.894 4.511 -1.113 1.502 H2 22L 18
22L H3 H3 H 0 1 N N N N N N 22.543 64.847 71.287 2.152 -1.809 1.464 H3 22L 19
22L H4 H4 H 0 1 N N N N N N 23.863 65.284 69.539 0.475 -2.914 -0.269 H4 22L 20
22L H5 H5 H 0 1 N N N N N N 19.843 68.074 64.913 -4.173 2.106 0.244 H5 22L 21
22L H6 H6 H 0 1 N N N N N N 20.321 62.902 68.243 1.356 1.117 -1.565 H6 22L 22
22L H7 H7 H 0 1 N N N N N N 19.654 61.170 69.828 3.718 1.802 -1.510 H7 22L 23
22L H8 H8 H 0 1 N N N N N N 18.486 66.385 65.832 -2.072 3.195 0.323 H8 22L 24
#
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
22L C15 N16 DOUB N N 1
22L C15 N14 SING N N 2
22L N16 C10 SING N N 3
22L N14 C12 SING N N 4
22L C10 C11 DOUB Y N 5
22L C10 S9 SING Y N 6
22L C12 O13 DOUB N N 7
22L C12 C11 SING N N 8
22L C11 C7 SING Y N 9
22L S9 C8 SING Y N 10
22L C7 C8 DOUB Y N 11
22L C7 C4 SING N N 12
22L C5 C4 DOUB Y N 13
22L C5 C6 SING Y N 14
22L C4 C3 SING Y N 15
22L C6 C1 DOUB Y N 16
22L C3 C2 DOUB Y N 17
22L C1 C2 SING Y N 18
22L C1 H1 SING N N 19
22L C2 H2 SING N N 20
22L C3 H3 SING N N 21
22L C8 H4 SING N N 22
22L C15 H5 SING N N 23
22L C5 H6 SING N N 24
22L C6 H7 SING N N 25
22L N14 H8 SING N N 26
#
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
22L SMILES ACDLabs 12.01 O=C2NC=Nc1scc(c12)c3ccccc3
22L InChI InChI 1.03 InChI=1S/C12H8N2OS/c15-11-10-9(8-4-2-1-3-5-8)6-16-12(10)14-7-13-11/h1-7H,(H,13,14,15)
22L InChIKey InChI 1.03 OLGMRBGIXZANNV-UHFFFAOYSA-N
22L SMILES_CANONICAL CACTVS 3.385 O=C1NC=Nc2scc(c3ccccc3)c12
22L SMILES CACTVS 3.385 O=C1NC=Nc2scc(c3ccccc3)c12
22L SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1ccc(cc1)c2csc3c2C(=O)NC=N3
22L SMILES "OpenEye OEToolkits" 1.7.6 c1ccc(cc1)c2csc3c2C(=O)NC=N3
#
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
22L "SYSTEMATIC NAME" ACDLabs 12.01 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one
22L "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 5-phenyl-3H-thieno[2,3-d]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
22L 'Create component' 2013-08-28 RCSB
22L 'Initial release' 2013-09-25 RCSB
22L 'Other modification' 2013-09-23 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
22L C1 C 9.221 3.492 1
22L C2 C 7.753 3.183 2
22L C3 C 7.287 1.757 3
22L C7 C 7.823 -0.785 4
22L C8 C 8.698 -1.992 5
22L C10 C 6.404 -2.742 6
22L C11 C 6.404 -1.242 7
22L C12 C 5.104 -0.492 8
22L C15 C 3.805 -2.742 9
22L C4 C 8.289 0.641 10
22L C5 C 9.757 0.950 11
22L C6 C 10.223 2.376 12
22L S9 S 7.823 -3.199 13
22L O13 O 5.104 1.008 14
22L N14 N 3.805 -1.242 15
22L N16 N 5.104 -3.492 16
#
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
22L C15 N16 DOUBLE NONE 1
22L C15 N14 SINGLE NONE 2
22L N16 C10 SINGLE NONE 3
22L N14 C12 SINGLE NONE 4
22L C10 C11 DOUBLE NONE 5
22L C10 S9 SINGLE NONE 6
22L C12 O13 DOUBLE NONE 7
22L C12 C11 SINGLE NONE 8
22L C11 C7 SINGLE NONE 9
22L S9 C8 SINGLE NONE 10
22L C7 C8 DOUBLE NONE 11
22L C7 C4 SINGLE NONE 12
22L C5 C4 DOUBLE NONE 13
22L C5 C6 SINGLE NONE 14
22L C4 C3 SINGLE NONE 15
22L C6 C1 DOUBLE NONE 16
22L C3 C2 DOUBLE NONE 17
22L C1 C2 SINGLE NONE 18
#
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
22L MurckoScaffold S1 scaffold 'O=c1[nH]cnc2scc(-c3ccccc3)c12' InChI=1S/C12H8N2OS/c15-11-10-9(8-4-2-1-3-5-8)6-16-12(10)14-7-13-11/h1-7H,(H,13,14,15) OLGMRBGIXZANNV-UHFFFAOYSA-N
22L phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
22L pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
22L thiophen F3 fragment c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-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
22L C1 S1 1
22L C2 S1 1
22L C3 S1 1
22L C7 S1 1
22L C8 S1 1
22L C10 S1 1
22L C11 S1 1
22L C12 S1 1
22L C15 S1 1
22L C4 S1 1
22L C5 S1 1
22L C6 S1 1
22L S9 S1 1
22L O13 S1 1
22L N14 S1 1
22L N16 S1 1
22L C1 F1 1
22L C6 F1 1
22L C5 F1 1
22L C4 F1 1
22L C3 F1 1
22L C2 F1 1
22L C11 F2 1
22L C10 F2 1
22L N16 F2 1
22L C15 F2 1
22L N14 F2 1
22L C12 F2 1
22L C8 F3 1
22L C7 F3 1
22L C11 F3 1
22L C10 F3 1
22L S9 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 22L
_pdbe_chem_comp_rdkit_properties.exactmw 228.036
_pdbe_chem_comp_rdkit_properties.amw 228.276
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 106.709
_pdbe_chem_comp_rdkit_properties.tpsa 45.750
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.743
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.257
_pdbe_chem_comp_rdkit_properties.chi0v 8.527
_pdbe_chem_comp_rdkit_properties.chi1v 5.073
_pdbe_chem_comp_rdkit_properties.chi2v 2.776
_pdbe_chem_comp_rdkit_properties.chi3v 2.776
_pdbe_chem_comp_rdkit_properties.chi4v 2.089
_pdbe_chem_comp_rdkit_properties.chi0n 15.711
_pdbe_chem_comp_rdkit_properties.chi1n 8.204
_pdbe_chem_comp_rdkit_properties.chi2n 1.981
_pdbe_chem_comp_rdkit_properties.chi3n 1.981
_pdbe_chem_comp_rdkit_properties.chi4n 1.308
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.940
_pdbe_chem_comp_rdkit_properties.kappa1 4.143
_pdbe_chem_comp_rdkit_properties.kappa2 3.572
_pdbe_chem_comp_rdkit_properties.kappa3 1.350
_pdbe_chem_comp_rdkit_properties.Phi 0.925
#
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
22L UniChem ChEMBL CHEMBL1369722
22L UniChem PDBe 22L
22L UniChem ZINC ZINC000008578704
22L UniChem eMolecules 3795758
22L UniChem eMolecules 815735
22L UniChem 'PubChem TPHARMA' 15788641
22L UniChem 'PubChem TPHARMA' 15813737
22L UniChem ACTor 35978-39-3
22L UniChem 'EPA CompTox Dashboard' DTXSID50189531
22L UniChem ChemicalBook CB31458184
22L UniChem SureChEMBL SCHEMBL2368706
22L UniChem PubChem 215639
22L UniChem Mcule MCULE-8508752142
#
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
22L C1 3.538 0.987 -0.749 ETKDGv3 1
22L C2 2.395 1.864 -0.424 ETKDGv3 2
22L C3 1.268 1.339 0.074 ETKDGv3 3
22L C7 -0.081 -0.693 0.866 ETKDGv3 4
22L C8 -0.071 -1.460 1.965 ETKDGv3 5
22L C10 -2.415 -0.968 1.090 ETKDGv3 6
22L C11 -1.453 -0.425 0.350 ETKDGv3 7
22L C12 -1.841 0.265 -0.892 ETKDGv3 8
22L C15 -4.201 -0.228 -0.303 ETKDGv3 9
22L C4 1.157 -0.125 0.294 ETKDGv3 10
22L C5 2.210 -0.914 0.013 ETKDGv3 11
22L C6 3.451 -0.332 -0.539 ETKDGv3 12
22L S9 -1.738 -1.872 2.455 ETKDGv3 13
22L O13 -0.985 0.714 -1.698 ETKDGv3 14
22L N14 -3.240 0.377 -1.186 ETKDGv3 15
22L N16 -3.808 -0.867 0.763 ETKDGv3 16
22L H1 4.447 1.415 -1.154 ETKDGv3 17
22L H2 2.473 2.931 -0.583 ETKDGv3 18
22L H3 0.440 1.991 0.325 ETKDGv3 19
22L H4 0.821 -1.748 2.507 ETKDGv3 20
22L H5 -5.256 -0.162 -0.529 ETKDGv3 21
22L H6 2.159 -1.984 0.176 ETKDGv3 22
22L H7 4.289 -0.975 -0.774 ETKDGv3 23
22L H8 -3.562 0.871 -2.047 ETKDGv3 24
#