data_SGL
#
_chem_comp.id SGL
_chem_comp.name 1-HYDROXY-1-THIO-GLYCEROL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C3 H8 O3 S'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 124.159
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SGL
_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 1QFM
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
SGL C1 C1 C 0 1 N N N N N N 44.352 37.513 87.041 -0.330 -0.938 -0.435 C1 SGL 1
SGL S1 S1 S 0 1 N N N N N N 45.659 36.417 86.373 -1.926 -0.486 0.300 S1 SGL 2
SGL C2 C2 C 0 1 N N R N N N 43.552 38.181 85.911 0.785 -0.132 0.233 C2 SGL 3
SGL O2 O2 O 0 1 N N N N N N 42.259 38.562 86.404 0.548 1.264 0.036 O2 SGL 4
SGL C3 C3 C 0 1 N N N N N N 43.378 37.268 84.695 2.131 -0.513 -0.387 C3 SGL 5
SGL O3 O3 O 0 1 N N N N N N 42.306 37.715 83.871 3.184 0.152 0.314 O3 SGL 6
SGL O4 O4 O 0 1 N N N N N N 45.338 35.067 86.850 -2.209 0.880 -0.309 O4 SGL 7
SGL H11 H11 H 0 1 N N N N N N 43.665 36.913 87.657 -0.149 -2.002 -0.285 H11 SGL 8
SGL H12 H12 H 0 1 N N N N N N 44.823 38.296 87.654 -0.347 -0.720 -1.503 H12 SGL 9
SGL H2 H2 H 0 1 N N N N N N 44.121 39.063 85.584 0.802 -0.350 1.301 H2 SGL 10
SGL HO2 HO2 H 0 1 N N N N N N 41.763 38.975 85.707 0.520 1.530 -0.893 HO2 SGL 11
SGL H31 H31 H 0 1 N N N N N N 44.308 37.274 84.107 2.272 -1.591 -0.315 H31 SGL 12
SGL H32 H32 H 0 1 N N N N N N 43.160 36.247 85.042 2.146 -0.213 -1.435 H32 SGL 13
SGL HO3 HO3 H 0 1 N N N N N N 42.217 37.135 83.124 4.068 -0.043 -0.026 HO3 SGL 14
SGL HO4 HO4 H 0 1 N N N N N N 45.990 34.454 86.530 -3.042 1.275 -0.017 HO4 SGL 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
SGL C1 S1 SING N N 1
SGL C1 C2 SING N N 2
SGL C1 H11 SING N N 3
SGL C1 H12 SING N N 4
SGL S1 O4 SING N N 5
SGL C2 O2 SING N N 6
SGL C2 C3 SING N N 7
SGL C2 H2 SING N N 8
SGL O2 HO2 SING N N 9
SGL C3 O3 SING N N 10
SGL C3 H31 SING N N 11
SGL C3 H32 SING N N 12
SGL O3 HO3 SING N N 13
SGL O4 HO4 SING N N 14
#
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
SGL SMILES ACDLabs 11.02 'OCC(O)CSO'
SGL SMILES_CANONICAL CACTVS 3.352 'OC[C@@H](O)CSO'
SGL SMILES CACTVS 3.352 'OC[CH](O)CSO'
SGL SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 'C([C@H](CSO)O)O'
SGL SMILES 'OpenEye OEToolkits' 1.7.0 'C(C(CSO)O)O'
SGL InChI InChI 1.03 'InChI=1S/C3H8O3S/c4-1-3(5)2-7-6/h3-6H,1-2H2/t3-/m1/s1'
SGL InChIKey InChI 1.03 DLQCXFUWHQZWJQ-GSVOUGTGSA-N
#
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
SGL 'SYSTEMATIC NAME' ACDLabs 11.02 '(2R)-2,3-dihydroxypropane-1-sulfenic acid'
SGL 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.6.1 '(2R)-3-hydroxysulfanylpropane-1,2-diol'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SGL 'Create component' 1999-07-08 EBI
SGL 'Modify descriptor' 2011-06-04 RCSB
SGL 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id SGL
_pdbx_chem_comp_pcm.modified_residue_id SER
_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 C2
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id SGL
_pdbe_chem_comp_drugbank_details.drugbank_id DB01684
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 1-Hydroxy-1-Thio-Glycerol
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id SGL
_pdbe_chem_comp_synonyms.name 1-Hydroxy-1-Thio-Glycerol
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id SGL
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01684
_pdbe_chem_comp_drugbank_classification.parent 1,2-diols
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions.'
#
_pdbe_chem_comp_drugbank_targets.comp_id SGL
_pdbe_chem_comp_drugbank_targets.drugbank_id DB01684
_pdbe_chem_comp_drugbank_targets.name 'Prolyl endopeptidase'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P48147
_pdbe_chem_comp_drugbank_targets.pharmacologically_active yes
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
SGL C1 C 7.702 1.357 1
SGL S1 S 9.002 0.608 2
SGL C2 C 6.404 0.608 3
SGL O2 O 6.404 -0.892 4
SGL C3 C 5.104 1.357 5
SGL O3 O 3.805 0.608 6
SGL O4 O 10.301 1.357 7
#
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
SGL C1 S1 SINGLE NONE 1
SGL C1 C2 SINGLE NONE 2
SGL S1 O4 SINGLE NONE 3
SGL C2 O2 SINGLE BEGINDASH 4
SGL C2 C3 SINGLE NONE 5
SGL C3 O3 SINGLE NONE 6
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id SGL
_pdbe_chem_comp_rdkit_properties.exactmw 124.019
_pdbe_chem_comp_rdkit_properties.amw 124.161
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 57.684
_pdbe_chem_comp_rdkit_properties.tpsa 60.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.454
_pdbe_chem_comp_rdkit_properties.CrippenMR 28.179
_pdbe_chem_comp_rdkit_properties.chi0v 3.949
_pdbe_chem_comp_rdkit_properties.chi1v 2.021
_pdbe_chem_comp_rdkit_properties.chi2v 0.496
_pdbe_chem_comp_rdkit_properties.chi3v 0.496
_pdbe_chem_comp_rdkit_properties.chi4v 0.176
_pdbe_chem_comp_rdkit_properties.chi0n 11.133
_pdbe_chem_comp_rdkit_properties.chi1n 5.004
_pdbe_chem_comp_rdkit_properties.chi2n 0.227
_pdbe_chem_comp_rdkit_properties.chi3n 0.227
_pdbe_chem_comp_rdkit_properties.chi4n 0.059
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.230
_pdbe_chem_comp_rdkit_properties.kappa1 1.386
_pdbe_chem_comp_rdkit_properties.kappa2 4.391
_pdbe_chem_comp_rdkit_properties.kappa3 4.075
_pdbe_chem_comp_rdkit_properties.Phi 0.869
#
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
SGL UniChem DrugBank DB01684
SGL UniChem SureChEMBL SCHEMBL5003699
SGL UniChem PubChem 5289354
SGL UniChem 'Probes And Drugs' PD008501
#
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
SGL C1 0.625 -0.287 -0.531 ETKDGv3 1
SGL S1 1.733 -1.659 -0.069 ETKDGv3 2
SGL C2 -0.577 -0.213 0.423 ETKDGv3 3
SGL O2 -1.372 -1.363 0.278 ETKDGv3 4
SGL C3 -1.443 1.019 0.121 ETKDGv3 5
SGL O3 -0.728 2.204 0.348 ETKDGv3 6
SGL O4 2.815 -1.334 -1.364 ETKDGv3 7
SGL H11 0.272 -0.438 -1.574 ETKDGv3 8
SGL H12 1.206 0.659 -0.485 ETKDGv3 9
SGL H2 -0.209 -0.126 1.473 ETKDGv3 10
SGL HO2 -1.012 -2.048 0.900 ETKDGv3 11
SGL H31 -1.772 0.997 -0.940 ETKDGv3 12
SGL H32 -2.358 1.000 0.756 ETKDGv3 13
SGL HO3 -0.680 2.323 1.333 ETKDGv3 14
SGL HO4 3.500 -0.735 -0.973 ETKDGv3 15
#