data_4H2
#
_chem_comp.id 4H2
_chem_comp.name 4-methylpyridine-2(1H)-thione
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H7 N S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-04-29
_chem_comp.pdbx_modified_date 2015-03-06
_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 125.191
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 4H2
_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 4Q90
_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
4H2 C6 C6 C 0 1 N N N N N N 14.965 5.116 15.387 2.690 1.420 0.001 C6 4H2 1
4H2 C3 C3 C 0 1 N N N N N N 15.405 3.685 15.098 1.536 0.451 0.001 C3 4H2 2
4H2 C2 C2 C 0 1 N N N N N N 15.042 2.632 15.992 0.251 0.909 0.001 C2 4H2 3
4H2 C1 C1 C 0 1 N N N N N N 15.448 1.369 15.746 -0.808 -0.013 0.001 C1 4H2 4
4H2 S1 S1 S 0 1 N N N N N N 15.011 0.061 16.865 -2.427 0.543 -0.001 S1 4H2 5
4H2 N1 N1 N 0 1 N N N N N N 16.223 1.092 14.615 -0.551 -1.335 0.001 N1 4H2 6
4H2 C5 C5 C 0 1 N N N N N N 16.530 2.098 13.730 0.728 -1.794 0.002 C5 4H2 7
4H2 C4 C4 C 0 1 N N N N N N 16.118 3.410 13.991 1.771 -0.932 -0.004 C4 4H2 8
4H2 H1 H1 H 0 1 N N N N N N 14.397 5.142 16.329 2.968 1.655 1.028 H1 4H2 9
4H2 H2 H2 H 0 1 N N N N N N 15.851 5.761 15.475 3.540 0.972 -0.513 H2 4H2 10
4H2 H3 H3 H 0 1 N N N N N N 14.329 5.477 14.565 2.396 2.335 -0.514 H3 4H2 11
4H2 H4 H4 H 0 1 N N N N N N 14.443 2.847 16.865 0.050 1.970 0.001 H4 4H2 12
4H2 H6 H6 H 0 1 N N N N N N 17.089 1.876 12.833 0.914 -2.858 -0.002 H6 4H2 13
4H2 H7 H7 H 0 1 N N N N N N 16.373 4.202 13.303 2.783 -1.308 -0.004 H7 4H2 14
4H2 H5 H5 H 0 1 N N N N N N 16.554 0.163 14.450 -1.287 -1.967 0.001 H5 4H2 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
4H2 C5 C4 DOUB N N 1
4H2 C5 N1 SING N N 2
4H2 C4 C3 SING N N 3
4H2 N1 C1 SING N N 4
4H2 C3 C6 SING N N 5
4H2 C3 C2 DOUB N N 6
4H2 C1 C2 SING N N 7
4H2 C1 S1 DOUB N N 8
4H2 C6 H1 SING N N 9
4H2 C6 H2 SING N N 10
4H2 C6 H3 SING N N 11
4H2 C2 H4 SING N N 12
4H2 C5 H6 SING N N 13
4H2 C4 H7 SING N N 14
4H2 N1 H5 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
4H2 SMILES ACDLabs 12.01 S=C1C=C(C=CN1)C
4H2 InChI InChI 1.03 InChI=1S/C6H7NS/c1-5-2-3-7-6(8)4-5/h2-4H,1H3,(H,7,8)
4H2 InChIKey InChI 1.03 KGYJCSZMSPBJFS-UHFFFAOYSA-N
4H2 SMILES_CANONICAL CACTVS 3.385 CC1=CC(=S)NC=C1
4H2 SMILES CACTVS 3.385 CC1=CC(=S)NC=C1
4H2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CC1=CC(=S)NC=C1
4H2 SMILES "OpenEye OEToolkits" 1.7.6 CC1=CC(=S)NC=C1
#
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
4H2 "SYSTEMATIC NAME" ACDLabs 12.01 4-methylpyridine-2(1H)-thione
4H2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 4-methyl-1H-pyridine-2-thione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
4H2 'Create component' 2014-04-29 RCSB
4H2 'Initial release' 2015-03-11 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
4H2 C6 C 3.000 -1.785 1
4H2 C3 C 4.299 -1.035 2
4H2 C2 C 4.299 0.465 3
4H2 C1 C 5.598 1.215 4
4H2 S1 S 5.598 2.715 5
4H2 N1 N 6.897 0.465 6
4H2 C5 C 6.897 -1.035 7
4H2 C4 C 5.598 -1.785 8
#
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
4H2 C5 C4 DOUBLE NONE 1
4H2 C5 N1 SINGLE NONE 2
4H2 C4 C3 SINGLE NONE 3
4H2 N1 C1 SINGLE NONE 4
4H2 C3 C6 SINGLE NONE 5
4H2 C3 C2 DOUBLE NONE 6
4H2 C1 C2 SINGLE NONE 7
4H2 C1 S1 DOUBLE NONE 8
#
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
4H2 MurckoScaffold S1 scaffold 'S=c1cccc[nH]1' InChI=1S/C5H5NS/c7-5-3-1-2-4-6-5/h1-4H,(H,6,7) WHMDPDGBKYUEMW-UHFFFAOYSA-N
4H2 pyridine F1 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
4H2 C3 S1 1
4H2 C2 S1 1
4H2 C1 S1 1
4H2 S1 S1 1
4H2 N1 S1 1
4H2 C5 S1 1
4H2 C4 S1 1
4H2 C1 F1 1
4H2 C2 F1 1
4H2 C3 F1 1
4H2 C4 F1 1
4H2 C5 F1 1
4H2 N1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 4H2
_pdbe_chem_comp_rdkit_properties.exactmw 125.030
_pdbe_chem_comp_rdkit_properties.amw 125.196
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.167
_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 63.268
_pdbe_chem_comp_rdkit_properties.tpsa 15.790
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.998
_pdbe_chem_comp_rdkit_properties.CrippenMR 36.098
_pdbe_chem_comp_rdkit_properties.chi0v 4.672
_pdbe_chem_comp_rdkit_properties.chi1v 2.310
_pdbe_chem_comp_rdkit_properties.chi2v 0.764
_pdbe_chem_comp_rdkit_properties.chi3v 0.764
_pdbe_chem_comp_rdkit_properties.chi4v 0.448
_pdbe_chem_comp_rdkit_properties.chi0n 10.855
_pdbe_chem_comp_rdkit_properties.chi1n 5.349
_pdbe_chem_comp_rdkit_properties.chi2n 0.570
_pdbe_chem_comp_rdkit_properties.chi3n 0.570
_pdbe_chem_comp_rdkit_properties.chi4n 0.301
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.630
_pdbe_chem_comp_rdkit_properties.kappa1 1.448
_pdbe_chem_comp_rdkit_properties.kappa2 2.092
_pdbe_chem_comp_rdkit_properties.kappa3 1.168
_pdbe_chem_comp_rdkit_properties.Phi 0.379
#
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
4H2 UniChem ZINC ZINC000014983130
4H2 UniChem eMolecules 3725887
4H2 UniChem NMRShiftDB 75355
4H2 UniChem Nikkaji J100.540E
4H2 UniChem 'EPA CompTox Dashboard' DTXSID80394959
4H2 UniChem SureChEMBL SCHEMBL2642944
4H2 UniChem PubChem 3681029
#
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
4H2 C6 -2.235 -0.018 0.099 ETKDGv3 1
4H2 C3 -0.736 0.009 0.063 ETKDGv3 2
4H2 C2 -0.083 1.182 0.115 ETKDGv3 3
4H2 C1 1.386 1.201 0.044 ETKDGv3 4
4H2 S1 2.205 2.616 0.118 ETKDGv3 5
4H2 N1 2.088 -0.039 -0.096 ETKDGv3 6
4H2 C5 1.353 -1.267 -0.171 ETKDGv3 7
4H2 C4 0.016 -1.262 -0.101 ETKDGv3 8
4H2 H1 -2.603 -1.020 0.403 ETKDGv3 9
4H2 H2 -2.634 0.221 -0.909 ETKDGv3 10
4H2 H3 -2.621 0.726 0.829 ETKDGv3 11
4H2 H4 -0.630 2.113 0.209 ETKDGv3 12
4H2 H6 1.883 -2.204 -0.288 ETKDGv3 13
4H2 H7 -0.520 -2.200 -0.164 ETKDGv3 14
4H2 H5 3.131 -0.058 -0.151 ETKDGv3 15
#