data_GLT
#
_chem_comp.id GLT
_chem_comp.name 5-thio-alpha-D-glucopyranose
_chem_comp.type "D-saccharide, alpha linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H12 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "5-DEOXY-5-THIO-ALPHA-D-GLUCOSE; 5-thio-alpha-D-glucose; 5-thio-D-glucose; 5-thio-glucose"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2020-07-17
_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 196.221
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GLT
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1XLI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 GLT 5-DEOXY-5-THIO-ALPHA-D-GLUCOSE PDB ?
2 GLT 5-thio-alpha-D-glucose PDB ?
3 GLT 5-thio-D-glucose PDB ?
4 GLT 5-thio-glucose PDB ?
#
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
GLT C1 C1 C 0 1 N N S N N N 44.194 37.694 -0.479 1.582 -0.077 -0.897 C1 GLT 1
GLT C2 C2 C 0 1 N N R N N N 43.383 38.812 0.095 0.350 -0.514 -1.691 C2 GLT 2
GLT C3 C3 C 0 1 N N S N N N 42.639 38.664 1.412 -0.886 0.220 -1.183 C3 GLT 3
GLT C4 C4 C 0 1 N N S N N N 41.890 37.384 1.644 -1.248 -0.250 0.222 C4 GLT 4
GLT C5 C5 C 0 1 N N R N N N 42.670 36.101 1.356 -0.186 0.213 1.219 C5 GLT 5
GLT C6 C6 C 0 1 N N N N N N 41.686 34.954 1.388 -0.618 -0.163 2.638 C6 GLT 6
GLT S5 S5 S 0 1 N N N N N N 43.258 36.162 -0.343 1.392 -0.593 0.833 S5 GLT 7
GLT O1 O1 O 0 1 N Y N N N N 45.453 37.421 0.153 1.712 1.343 -0.959 O1 GLT 8
GLT O2 O2 O 0 1 N N N N N N 43.923 40.092 -0.092 0.545 -0.210 -3.074 O2 GLT 9
GLT O3 O3 O 0 1 N N N N N N 41.811 39.731 1.859 -1.982 -0.037 -2.063 O3 GLT 10
GLT O4 O4 O 0 1 N N N N N N 41.551 37.195 3.056 -2.516 0.295 0.592 O4 GLT 11
GLT O6 O6 O 0 1 N N N N N N 42.349 33.806 0.885 0.375 0.268 3.569 O6 GLT 12
GLT H1 H1 H 0 1 N N N N N N 44.407 38.033 -1.519 2.472 -0.543 -1.320 H1 GLT 13
GLT H2 H2 H 0 1 N N N N N N 42.517 38.677 -0.595 0.207 -1.588 -1.574 H2 GLT 14
GLT H3 H3 H 0 1 N N N N N N 43.564 38.672 2.034 -0.685 1.291 -1.163 H3 GLT 15
GLT H4 H4 H 0 1 N N N N N N 41.024 37.512 0.952 -1.305 -1.338 0.235 H4 GLT 16
GLT H5 H5 H 0 1 N N N N N N 43.502 35.987 2.089 -0.069 1.295 1.150 H5 GLT 17
GLT H61 H61 H 0 1 N N N N N N 41.242 34.791 2.397 -0.736 -1.244 2.707 H61 GLT 18
GLT H62 H62 H 0 1 N N N N N N 40.738 35.180 0.846 -1.568 0.320 2.869 H62 GLT 19
GLT HO1 HO1 H 0 1 N N N N N N 45.968 36.710 -0.211 2.497 1.575 -0.444 HO1 GLT 20
GLT HO2 HO2 H 0 1 N N N N N N 43.407 40.802 0.272 1.330 -0.698 -3.359 HO2 GLT 21
GLT HO3 HO3 H 0 1 N N N N N N 41.346 39.638 2.682 -1.722 0.287 -2.936 HO3 GLT 22
GLT HO4 HO4 H 0 1 N N N N N N 41.077 36.384 3.202 -3.159 -0.026 -0.054 HO4 GLT 23
GLT HO6 HO6 H 0 1 N N N N N N 41.730 33.085 0.905 0.064 0.012 4.448 HO6 GLT 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
GLT C1 C2 SING N N 1
GLT C1 S5 SING N N 2
GLT C1 O1 SING N N 3
GLT C1 H1 SING N N 4
GLT C2 C3 SING N N 5
GLT C2 O2 SING N N 6
GLT C2 H2 SING N N 7
GLT C3 C4 SING N N 8
GLT C3 O3 SING N N 9
GLT C3 H3 SING N N 10
GLT C4 C5 SING N N 11
GLT C4 O4 SING N N 12
GLT C4 H4 SING N N 13
GLT C5 C6 SING N N 14
GLT C5 S5 SING N N 15
GLT C5 H5 SING N N 16
GLT C6 O6 SING N N 17
GLT C6 H61 SING N N 18
GLT C6 H62 SING N N 19
GLT O1 HO1 SING N N 20
GLT O2 HO2 SING N N 21
GLT O3 HO3 SING N N 22
GLT O4 HO4 SING N N 23
GLT O6 HO6 SING N N 24
#
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
GLT SMILES ACDLabs 10.04 OC1C(O)C(SC(O)C1O)CO
GLT SMILES_CANONICAL CACTVS 3.341 OC[C@H]1S[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
GLT SMILES CACTVS 3.341 OC[CH]1S[CH](O)[CH](O)[CH](O)[CH]1O
GLT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H]1[C@H]([C@@H]([C@H]([C@H](S1)O)O)O)O)O
GLT SMILES "OpenEye OEToolkits" 1.5.0 C(C1C(C(C(C(S1)O)O)O)O)O
GLT InChI InChI 1.03 InChI=1S/C6H12O5S/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
GLT InChIKey InChI 1.03 KNWYARBAEIMVMZ-DVKNGEFBSA-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
GLT "SYSTEMATIC NAME" ACDLabs 10.04 5-thio-alpha-D-glucopyranose
GLT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2S,3R,4S,5S,6R)-6-(hydroxymethyl)thiane-2,3,4,5-tetrol
#
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
GLT "CARBOHYDRATE ISOMER" D PDB ?
GLT "CARBOHYDRATE RING" thiopyranose PDB ?
GLT "CARBOHYDRATE ANOMER" alpha PDB ?
GLT "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GLT 'Create component' 1999-07-08 EBI
GLT 'Modify descriptor' 2011-06-04 RCSB
GLT 'Other modification' 2020-07-03 RCSB
GLT 'Modify name' 2020-07-17 RCSB
GLT 'Modify synonyms' 2020-07-17 RCSB
GLT 'Modify linking type' 2020-07-17 RCSB
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
GLT 5-DEOXY-5-THIO-ALPHA-D-GLUCOSE wwPDB ?
GLT 5-thio-alpha-D-glucose wwPDB ?
GLT 5-thio-D-glucose wwPDB ?
GLT 5-thio-glucose wwPDB ?
#
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
GLT C1 C 7.702 0.750 1
GLT C2 C 7.702 -0.750 2
GLT C3 C 6.404 -1.500 3
GLT C4 C 5.104 -0.750 4
GLT C5 C 5.104 0.750 5
GLT C6 C 3.805 1.500 6
GLT S5 S 6.404 1.500 7
GLT O1 O 9.002 1.500 8
GLT O2 O 9.002 -1.500 9
GLT O3 O 6.404 -3.000 10
GLT O4 O 3.805 -1.500 11
GLT O6 O 3.805 3.000 12
#
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
GLT C1 C2 SINGLE NONE 1
GLT C1 S5 SINGLE NONE 2
GLT C1 O1 SINGLE BEGINDASH 3
GLT C2 C3 SINGLE NONE 4
GLT C2 O2 SINGLE BEGINDASH 5
GLT C3 C4 SINGLE NONE 6
GLT C3 O3 SINGLE BEGINWEDGE 7
GLT C4 C5 SINGLE NONE 8
GLT C4 O4 SINGLE BEGINDASH 9
GLT C5 C6 SINGLE BEGINWEDGE 10
GLT C5 S5 SINGLE NONE 11
GLT C6 O6 SINGLE NONE 12
#
_pdbe_chem_comp_substructure.comp_id GLT
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles C1CCSCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H10S/c1-2-4-6-5-3-1/h1-5H2
_pdbe_chem_comp_substructure.substructure_inchikeys YPWFISCTZQNZAU-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
GLT C1 S1 1
GLT C2 S1 1
GLT C3 S1 1
GLT C4 S1 1
GLT C5 S1 1
GLT S5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GLT
_pdbe_chem_comp_rdkit_properties.exactmw 196.041
_pdbe_chem_comp_rdkit_properties.amw 196.224
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 90.945
_pdbe_chem_comp_rdkit_properties.tpsa 101.150
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.505
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.492
_pdbe_chem_comp_rdkit_properties.chi0v 6.266
_pdbe_chem_comp_rdkit_properties.chi1v 3.495
_pdbe_chem_comp_rdkit_properties.chi2v 1.935
_pdbe_chem_comp_rdkit_properties.chi3v 1.935
_pdbe_chem_comp_rdkit_properties.chi4v 1.149
_pdbe_chem_comp_rdkit_properties.chi0n 17.449
_pdbe_chem_comp_rdkit_properties.chi1n 8.220
_pdbe_chem_comp_rdkit_properties.chi2n 1.092
_pdbe_chem_comp_rdkit_properties.chi3n 1.092
_pdbe_chem_comp_rdkit_properties.chi4n 0.552
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.150
_pdbe_chem_comp_rdkit_properties.kappa1 2.590
_pdbe_chem_comp_rdkit_properties.kappa2 3.906
_pdbe_chem_comp_rdkit_properties.kappa3 1.732
_pdbe_chem_comp_rdkit_properties.Phi 0.843
#
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
GLT UniChem ZINC ZINC000004134459
GLT UniChem eMolecules 30154853
GLT UniChem fdasrs 08DDM61Q8P
GLT UniChem SureChEMBL SCHEMBL5390805
GLT UniChem 'PubChem TPHARMA' 15219937
GLT UniChem BRENDA 91971
GLT UniChem BindingDb 50422213
GLT UniChem PubChem 5288443
GLT UniChem ACTor 20408-97-3
GLT UniChem Nikkaji J12.251C
#
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
GLT C1 -1.363 0.471 1.406 ETKDGv3 1
GLT C2 -1.704 0.837 -0.049 ETKDGv3 2
GLT C3 -0.985 -0.071 -1.065 ETKDGv3 3
GLT C4 0.554 0.022 -0.934 ETKDGv3 4
GLT C5 1.041 -0.406 0.472 ETKDGv3 5
GLT C6 2.574 -0.458 0.562 ETKDGv3 6
GLT S5 0.412 0.746 1.749 ETKDGv3 7
GLT O1 -1.719 -0.859 1.679 ETKDGv3 8
GLT O2 -3.091 0.729 -0.245 ETKDGv3 9
GLT O3 -1.367 0.321 -2.360 ETKDGv3 10
GLT O4 1.168 -0.759 -1.931 ETKDGv3 11
GLT O6 3.129 0.793 0.260 ETKDGv3 12
GLT H1 -1.938 1.149 2.077 ETKDGv3 13
GLT H2 -1.387 1.891 -0.236 ETKDGv3 14
GLT H3 -1.307 -1.125 -0.884 ETKDGv3 15
GLT H4 0.854 1.079 -1.107 ETKDGv3 16
GLT H5 0.660 -1.427 0.698 ETKDGv3 17
GLT H61 2.968 -1.225 -0.141 ETKDGv3 18
GLT H62 2.869 -0.759 1.592 ETKDGv3 19
GLT HO1 -1.622 -0.980 2.660 ETKDGv3 20
GLT HO2 -3.506 1.526 0.178 ETKDGv3 21
GLT HO3 -1.259 -0.472 -2.949 ETKDGv3 22
GLT HO4 0.908 -1.705 -1.773 ETKDGv3 23
GLT HO6 4.112 0.685 0.339 ETKDGv3 24
#