data_I1J
#
_chem_comp.id I1J
_chem_comp.name '1,3-bis(sulfanyl)propan-2-one'
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C3 H6 O S2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-01-06
_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 122.209
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code I1J
_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 7TB1
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_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
I1J C1 C1 C 0 1 N N N N N N -5.476 17.963 -13.379 1.305 -0.935 -0.000 C1 I1J 1
I1J C2 C2 C 0 1 N N N N N N -4.248 18.503 -12.666 0.000 -0.182 0.000 C2 I1J 2
I1J C3 C3 C 0 1 N N N N N N -2.994 17.647 -12.601 -1.305 -0.935 0.000 C3 I1J 3
I1J O4 O1 O 0 1 N N N N N N -4.260 19.582 -12.174 -0.000 1.026 -0.000 O4 I1J 4
I1J S5 S1 S 0 1 N N N N N N -5.163 18.119 -15.155 2.684 0.244 -0.000 S5 I1J 5
I1J S6 S2 S 0 1 N N N N N N -1.538 18.707 -12.806 -2.684 0.244 0.000 S6 I1J 6
I1J H1 H1 H 0 1 N N N N N N -6.364 18.548 -13.099 1.363 -1.562 0.890 H1 I1J 7
I1J H2 H2 H 0 1 N N N N N N -5.634 16.907 -13.114 1.363 -1.562 -0.890 H2 I1J 8
I1J H3 H3 H 0 1 N N N N N N -3.019 16.896 -13.405 -1.363 -1.562 -0.890 H3 I1J 9
I1J H4 H4 H 0 1 N N N N N N -2.945 17.139 -11.626 -1.363 -1.562 0.890 H4 I1J 10
I1J H5 H5 H 0 1 N N N N N N -6.257 17.637 -15.666 3.766 -0.556 -0.000 H5 I1J 11
I1J H6 H6 H 0 1 N N N N N N -2.035 19.891 -12.602 -3.766 -0.556 0.000 H6 I1J 12
#
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
I1J S5 C1 SING N N 1
I1J C1 C2 SING N N 2
I1J S6 C3 SING N N 3
I1J C2 C3 SING N N 4
I1J C2 O4 DOUB N N 5
I1J C1 H1 SING N N 6
I1J C1 H2 SING N N 7
I1J C3 H3 SING N N 8
I1J C3 H4 SING N N 9
I1J S5 H5 SING N N 10
I1J S6 H6 SING N N 11
#
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
I1J SMILES ACDLabs 12.01 'SCC(=O)CS'
I1J InChI InChI 1.03 'InChI=1S/C3H6OS2/c4-3(1-5)2-6/h5-6H,1-2H2'
I1J InChIKey InChI 1.03 QCBZCEKWIGTIMT-UHFFFAOYSA-N
I1J SMILES_CANONICAL CACTVS 3.385 'SCC(=O)CS'
I1J SMILES CACTVS 3.385 'SCC(=O)CS'
I1J SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'C(C(=O)CS)S'
I1J SMILES 'OpenEye OEToolkits' 2.0.7 'C(C(=O)CS)S'
#
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
I1J 'SYSTEMATIC NAME' ACDLabs 12.01 '1,3-bis(sulfanyl)propan-2-one'
I1J 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.7 '1,3-bis(sulfanyl)propan-2-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
I1J 'Create component' 2022-01-06 RCSB
I1J 'Initial release' 2022-07-27 RCSB
I1J 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 I1J CYS None Crosslinker 'Amino-acid side chain' 'Any position' S5 CB ? ?
2 I1J CYS None Crosslinker 'Amino-acid side chain' 'Any position' S6 CB ? ?
#
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
I1J C1 C 7.702 1.125 1
I1J C2 C 6.404 0.375 2
I1J C3 C 5.104 1.125 3
I1J O4 O 6.404 -1.125 4
I1J S5 S 9.002 0.375 5
I1J S6 S 3.805 0.375 6
#
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
I1J S5 C1 SINGLE NONE 1
I1J C1 C2 SINGLE NONE 2
I1J S6 C3 SINGLE NONE 3
I1J C2 C3 SINGLE NONE 4
I1J C2 O4 DOUBLE NONE 5
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id I1J
_pdbe_chem_comp_rdkit_properties.exactmw 121.986
_pdbe_chem_comp_rdkit_properties.amw 122.214
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 6
_pdbe_chem_comp_rdkit_properties.NumAtoms 12
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 55.732
_pdbe_chem_comp_rdkit_properties.tpsa 17.070
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.415
_pdbe_chem_comp_rdkit_properties.CrippenMR 32.713
_pdbe_chem_comp_rdkit_properties.chi0v 4.358
_pdbe_chem_comp_rdkit_properties.chi1v 1.929
_pdbe_chem_comp_rdkit_properties.chi2v 0.556
_pdbe_chem_comp_rdkit_properties.chi3v 0.556
_pdbe_chem_comp_rdkit_properties.chi4v 0.187
_pdbe_chem_comp_rdkit_properties.chi0n 8.725
_pdbe_chem_comp_rdkit_properties.chi1n 3.929
_pdbe_chem_comp_rdkit_properties.chi2n 0.185
_pdbe_chem_comp_rdkit_properties.chi3n 0.185
_pdbe_chem_comp_rdkit_properties.chi4n 0.021
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.370
_pdbe_chem_comp_rdkit_properties.kappa1 1.421
_pdbe_chem_comp_rdkit_properties.kappa2 3.556
_pdbe_chem_comp_rdkit_properties.kappa3 2.599
_pdbe_chem_comp_rdkit_properties.Phi 0.842
#
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
I1J UniChem ZINC ZINC000005496914
I1J UniChem ACTor 60973-55-9
I1J UniChem Nikkaji J556.616I
I1J UniChem 'EPA CompTox Dashboard' DTXSID60308690
I1J UniChem SureChEMBL SCHEMBL562731
I1J UniChem 'PubChem TPHARMA' 16901656
I1J UniChem PubChem 308054
#
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
I1J C1 1.302 -0.256 0.449 ETKDGv3 1
I1J C2 -0.177 -0.444 0.638 ETKDGv3 2
I1J C3 -1.087 -0.707 -0.528 ETKDGv3 3
I1J O4 -0.646 -0.405 1.766 ETKDGv3 4
I1J S5 1.789 1.424 0.946 ETKDGv3 5
I1J S6 -2.276 0.656 -0.716 ETKDGv3 6
I1J H1 1.849 -0.992 1.075 ETKDGv3 7
I1J H2 1.597 -0.415 -0.610 ETKDGv3 8
I1J H3 -0.513 -0.813 -1.472 ETKDGv3 9
I1J H4 -1.644 -1.652 -0.354 ETKDGv3 10
I1J H5 1.085 2.025 -0.114 ETKDGv3 11
I1J H6 -1.277 1.579 -1.080 ETKDGv3 12
#