data_YC5
#
_chem_comp.id YC5
_chem_comp.name 4-azanyl-3-fluoranyl-benzenethiol
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C6 H6 F N S'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-06-13
_chem_comp.pdbx_modified_date 2024-09-27
_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 143.182
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YC5
_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 8PDJ
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_chem_comp.pdbx_pcm Y
#
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
YC5 C1 C1 C 0 1 Y N N N N N -31.250 9.192 6.977 0.705 1.401 0.014 C1 YC5 1
YC5 C2 C2 C 0 1 Y N N N N N -30.836 7.983 7.510 -0.655 1.640 0.001 C2 YC5 2
YC5 C3 C3 C 0 1 Y N N N N N -30.917 6.820 6.761 -1.547 0.577 -0.004 C3 YC5 3
YC5 C4 C4 C 0 1 Y N N N N N -31.425 6.898 5.482 -1.071 -0.730 0.003 C4 YC5 4
YC5 C5 C5 C 0 1 Y N N N N N -31.816 8.098 4.934 0.291 -0.969 0.016 C5 YC5 5
YC5 C6 C6 C 0 1 Y N N N N N -31.739 9.270 5.693 1.182 0.097 0.015 C6 YC5 6
YC5 S1 S1 S 0 1 N N N N N N -32.251 10.832 5.039 2.918 -0.206 0.031 S1 YC5 7
YC5 F1 F1 F 0 1 N N N N N N -31.459 5.776 4.737 -1.938 -1.766 -0.001 F1 YC5 8
YC5 N1 N1 N 0 1 N N N N N N -30.548 5.617 7.262 -2.927 0.819 -0.016 N1 YC5 9
YC5 H1 H1 H 0 1 N N N N N N -31.188 10.087 7.578 1.399 2.229 0.019 H1 YC5 10
YC5 H2 H2 H 0 1 N N N N N N -30.447 7.946 8.517 -1.026 2.655 -0.004 H2 YC5 11
YC5 H3 H3 H 0 1 N N N N N N -32.182 8.135 3.919 0.661 -1.983 0.022 H3 YC5 12
YC5 H4 H4 H 0 1 N N N N N N -32.021 11.632 6.038 3.226 -0.267 -1.277 H4 YC5 13
YC5 H5 H5 H 0 1 N N N N N N -30.203 5.735 8.193 -3.259 1.731 -0.021 H5 YC5 14
YC5 H6 H6 H 0 1 N N N N N N -31.338 5.004 7.274 -3.550 0.076 -0.019 H6 YC5 15
#
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
YC5 F1 C4 SING N N 1
YC5 C5 C4 DOUB Y N 2
YC5 C5 C6 SING Y N 3
YC5 S1 C6 SING N N 4
YC5 C4 C3 SING Y N 5
YC5 C6 C1 DOUB Y N 6
YC5 C3 N1 SING N N 7
YC5 C3 C2 DOUB Y N 8
YC5 C1 C2 SING Y N 9
YC5 C1 H1 SING N N 10
YC5 C2 H2 SING N N 11
YC5 C5 H3 SING N N 12
YC5 S1 H4 SING N N 13
YC5 N1 H5 SING N N 14
YC5 N1 H6 SING N N 15
#
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
YC5 InChI InChI 1.06 'InChI=1S/C6H6FNS/c7-5-3-4(9)1-2-6(5)8/h1-3,9H,8H2'
YC5 InChIKey InChI 1.06 MAOWDGRYXPTHRM-UHFFFAOYSA-N
YC5 SMILES_CANONICAL CACTVS 3.385 'Nc1ccc(S)cc1F'
YC5 SMILES CACTVS 3.385 'Nc1ccc(S)cc1F'
YC5 SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'c1cc(c(cc1S)F)N'
YC5 SMILES 'OpenEye OEToolkits' 2.0.7 'c1cc(c(cc1S)F)N'
#
_pdbx_chem_comp_identifier.comp_id YC5
_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 4-azanyl-3-fluoranyl-benzenethiol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YC5 'Create component' 2023-06-13 PDBE
YC5 'Initial release' 2023-06-28 RCSB
YC5 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id YC5
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom S1
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
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
YC5 C1 C 6.897 -0.750 1
YC5 C2 C 6.897 0.750 2
YC5 C3 C 5.598 1.500 3
YC5 C4 C 4.299 0.750 4
YC5 C5 C 4.299 -0.750 5
YC5 C6 C 5.598 -1.500 6
YC5 S1 S 5.598 -3.000 7
YC5 F1 F 3.000 1.500 8
YC5 N1 N 5.598 3.000 9
#
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
YC5 F1 C4 SINGLE NONE 1
YC5 C5 C4 DOUBLE NONE 2
YC5 C5 C6 SINGLE NONE 3
YC5 S1 C6 SINGLE NONE 4
YC5 C4 C3 SINGLE NONE 5
YC5 C6 C1 DOUBLE NONE 6
YC5 C3 N1 SINGLE NONE 7
YC5 C3 C2 DOUBLE NONE 8
YC5 C1 C2 SINGLE NONE 9
#
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
YC5 MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
YC5 phenyl F1 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
YC5 C1 S1 1
YC5 C2 S1 1
YC5 C3 S1 1
YC5 C4 S1 1
YC5 C5 S1 1
YC5 C6 S1 1
YC5 C1 F1 1
YC5 C6 F1 1
YC5 C5 F1 1
YC5 C4 F1 1
YC5 C3 F1 1
YC5 C2 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YC5
_pdbe_chem_comp_rdkit_properties.exactmw 143.020
_pdbe_chem_comp_rdkit_properties.amw 143.186
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_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 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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 66.319
_pdbe_chem_comp_rdkit_properties.tpsa 26.020
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.208
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.810
_pdbe_chem_comp_rdkit_properties.chi0v 5.050
_pdbe_chem_comp_rdkit_properties.chi1v 2.525
_pdbe_chem_comp_rdkit_properties.chi2v 0.930
_pdbe_chem_comp_rdkit_properties.chi3v 0.930
_pdbe_chem_comp_rdkit_properties.chi4v 0.502
_pdbe_chem_comp_rdkit_properties.chi0n 10.233
_pdbe_chem_comp_rdkit_properties.chi1n 4.919
_pdbe_chem_comp_rdkit_properties.chi2n 0.726
_pdbe_chem_comp_rdkit_properties.chi3n 0.726
_pdbe_chem_comp_rdkit_properties.chi4n 0.361
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.700
_pdbe_chem_comp_rdkit_properties.kappa1 2.163
_pdbe_chem_comp_rdkit_properties.kappa2 2.269
_pdbe_chem_comp_rdkit_properties.kappa3 1.355
_pdbe_chem_comp_rdkit_properties.Phi 0.545
#
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
YC5 UniChem ZINC ZINC000020247140
YC5 UniChem ChemicalBook CB2949358
YC5 UniChem eMolecules 17257017
YC5 UniChem SureChEMBL SCHEMBL1094017
YC5 UniChem PubChem 14517551
YC5 UniChem Mcule MCULE-2901462702
YC5 UniChem 'EPA CompTox Dashboard' DTXSID30561215
#
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
YC5 C1 0.942 -1.215 -0.158 ETKDGv3 1
YC5 C2 -0.516 -1.212 0.088 ETKDGv3 2
YC5 C3 -1.196 -0.053 0.111 ETKDGv3 3
YC5 C4 -0.473 1.224 -0.113 ETKDGv3 4
YC5 C5 0.848 1.217 -0.336 ETKDGv3 5
YC5 C6 1.591 -0.061 -0.360 ETKDGv3 6
YC5 S1 3.356 -0.059 -0.658 ETKDGv3 7
YC5 F1 -1.144 2.403 -0.093 ETKDGv3 8
YC5 N1 -2.607 -0.049 0.350 ETKDGv3 9
YC5 H1 1.476 -2.156 -0.174 ETKDGv3 10
YC5 H2 -1.025 -2.153 0.249 ETKDGv3 11
YC5 H3 1.374 2.150 -0.499 ETKDGv3 12
YC5 H4 3.643 0.057 0.715 ETKDGv3 13
YC5 H5 -3.142 0.847 0.369 ETKDGv3 14
YC5 H6 -3.129 -0.940 0.509 ETKDGv3 15
#