data_GLS
#
_chem_comp.id GLS
_chem_comp.name "BETA-D-GLUCOPYRANOSE SPIROHYDANTOIN"
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C8 H12 N2 O7"
_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 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 248.190
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GLS
_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 1A8I
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
GLS C1 C1 C 0 1 N N S N N N 33.945 22.824 27.575 0.009 -0.420 -0.711 C1 GLS 1
GLS C2 C2 C 0 1 N N R N N N 33.920 23.170 26.040 -1.407 -0.656 -0.195 C2 GLS 2
GLS O2 O2 O 0 1 N N N N N N 33.883 24.589 25.923 -2.351 -0.189 -1.161 O2 GLS 3
GLS C3 C3 C 0 1 N N S N N N 32.629 22.586 25.382 -1.597 0.108 1.119 C3 GLS 4
GLS O3 O3 O 0 1 N N N N N N 32.893 22.675 23.997 -2.859 -0.235 1.696 O3 GLS 5
GLS C4 C4 C 0 1 N N S N N N 32.568 21.114 25.758 -0.466 -0.281 2.078 C4 GLS 6
GLS O4 O4 O 0 1 N N N N N N 31.444 20.526 25.119 -0.543 0.518 3.259 O4 GLS 7
GLS C5 C5 C 0 1 N N R N N N 32.540 20.878 27.265 0.878 -0.043 1.386 C5 GLS 8
GLS C6 C6 C 0 1 N N N N N N 32.374 19.439 27.716 2.014 -0.384 2.352 C6 GLS 9
GLS O6 O6 O 0 1 N N N N N N 33.434 18.667 27.141 3.270 -0.160 1.708 O6 GLS 10
GLS O5 O5 O 0 1 N N N N N N 33.686 21.436 27.897 0.976 -0.870 0.227 O5 GLS 11
GLS N2 N2 N 0 1 N N N N N N 35.241 23.150 28.148 0.197 -1.089 -2.005 N2 GLS 12
GLS C8 C8 C 0 1 N N N N N N 35.063 23.988 29.175 0.468 -0.119 -2.900 C8 GLS 13
GLS O8 O8 O 0 1 N N N N N N 36.020 24.419 29.870 0.678 -0.327 -4.079 O8 GLS 14
GLS N1 N1 N 0 1 N N N N N N 33.811 24.356 29.431 0.479 1.098 -2.345 N1 GLS 15
GLS C7 C7 C 0 1 N N N N N N 33.060 23.672 28.497 0.214 1.044 -1.023 C7 GLS 16
GLS O7 O7 O 0 1 N N N N N N 31.844 23.772 28.471 0.154 1.975 -0.249 O7 GLS 17
GLS H2 H2 H 0 1 N N N N N N 34.815 22.739 25.534 -1.559 -1.721 -0.023 H2 GLS 18
GLS HO2 HO2 H 0 1 N N N N N N 33.867 24.797 24.996 -3.230 -0.357 -0.797 HO2 GLS 19
GLS H3 H3 H 0 1 N N N N N N 31.686 23.100 25.683 -1.562 1.180 0.928 H3 GLS 20
GLS HO3 HO3 H 0 1 N N N N N N 32.108 22.319 23.596 -2.936 0.267 2.519 HO3 GLS 21
GLS H4 H4 H 0 1 N N N N N N 33.506 20.627 25.403 -0.560 -1.334 2.343 H4 GLS 22
GLS HO4 HO4 H 0 1 N N N N N N 31.405 19.606 25.353 0.183 0.240 3.833 HO4 GLS 23
GLS H5 H5 H 0 1 N N N N N N 31.609 21.401 27.585 0.954 1.003 1.092 H5 GLS 24
GLS H61 H61 H 0 1 N N N N N N 32.321 19.338 28.825 1.939 -1.431 2.647 H61 GLS 25
GLS H62 H62 H 0 1 N N N N N N 31.364 19.027 27.480 1.941 0.247 3.237 H62 GLS 26
GLS HO6 HO6 H 0 1 N N N N N N 33.330 17.765 27.423 3.957 -0.386 2.350 HO6 GLS 27
GLS HN2 HN2 H 0 1 N N N N N N 35.891 23.518 27.454 0.138 -2.041 -2.181 HN2 GLS 28
GLS HN1 HN1 H 0 1 N N N N N N 33.504 25.000 30.159 0.655 1.917 -2.833 HN1 GLS 29
#
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
GLS C1 C2 SING N N 1
GLS C1 O5 SING N N 2
GLS C1 N2 SING N N 3
GLS C1 C7 SING N N 4
GLS C2 O2 SING N N 5
GLS C2 C3 SING N N 6
GLS C2 H2 SING N N 7
GLS O2 HO2 SING N N 8
GLS C3 O3 SING N N 9
GLS C3 C4 SING N N 10
GLS C3 H3 SING N N 11
GLS O3 HO3 SING N N 12
GLS C4 O4 SING N N 13
GLS C4 C5 SING N N 14
GLS C4 H4 SING N N 15
GLS O4 HO4 SING N N 16
GLS C5 C6 SING N N 17
GLS C5 O5 SING N N 18
GLS C5 H5 SING N N 19
GLS C6 O6 SING N N 20
GLS C6 H61 SING N N 21
GLS C6 H62 SING N N 22
GLS O6 HO6 SING N N 23
GLS N2 C8 SING N N 24
GLS N2 HN2 SING N N 25
GLS C8 O8 DOUB N N 26
GLS C8 N1 SING N N 27
GLS N1 C7 SING N N 28
GLS N1 HN1 SING N N 29
GLS C7 O7 DOUB N N 30
#
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
GLS SMILES ACDLabs 10.04 O=C2NC(=O)NC21OC(C(O)C(O)C1O)CO
GLS SMILES_CANONICAL CACTVS 3.341 OC[C@H]1O[C@@]2(NC(=O)NC2=O)[C@H](O)[C@@H](O)[C@@H]1O
GLS SMILES CACTVS 3.341 OC[CH]1O[C]2(NC(=O)NC2=O)[CH](O)[CH](O)[CH]1O
GLS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H]1[C@H]([C@@H]([C@H]([C@]2(O1)C(=O)NC(=O)N2)O)O)O)O
GLS SMILES "OpenEye OEToolkits" 1.5.0 C(C1C(C(C(C2(O1)C(=O)NC(=O)N2)O)O)O)O
GLS InChI InChI 1.03 InChI=1S/C8H12N2O7/c11-1-2-3(12)4(13)5(14)8(17-2)6(15)9-7(16)10-8/h2-5,11-14H,1H2,(H2,9,10,15,16)/t2-,3-,4+,5-,8+/m1/s1
GLS InChIKey InChI 1.03 QRXBDPYWCAAAAI-WWHASAIZSA-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
GLS "SYSTEMATIC NAME" ACDLabs 10.04 (5S,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.5]decane-2,4-dione
GLS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (5S,6R,7S,8S,9R)-6,7,8-trihydroxy-9-(hydroxymethyl)-10-oxa-1,3-diazaspiro[4.5]decane-2,4-dione
#
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
GLS "CARBOHYDRATE ISOMER" D PDB ?
GLS "CARBOHYDRATE RING" pyranose PDB ?
GLS "CARBOHYDRATE ANOMER" beta PDB ?
GLS "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
GLS 'Create component' 1999-07-08 EBI
GLS 'Modify descriptor' 2011-06-04 RCSB
GLS 'Other modification' 2020-07-03 RCSB
GLS 'Modify linking type' 2020-07-17 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
GLS C1 C 7.965 0.015 1
GLS C2 C 7.215 1.314 2
GLS O2 O 7.475 2.791 3
GLS C3 C 5.715 1.314 4
GLS O3 O 4.965 2.613 5
GLS C4 C 4.965 0.015 6
GLS O4 O 3.465 0.015 7
GLS C5 C 5.715 -1.284 8
GLS C6 C 4.965 -2.583 9
GLS O6 O 3.465 -2.583 10
GLS O5 O 7.215 -1.284 11
GLS N2 N 8.847 1.228 12
GLS C8 C 10.273 0.765 13
GLS O8 O 11.487 1.646 14
GLS N1 N 10.273 -0.735 15
GLS C7 C 8.847 -1.199 16
GLS O7 O 8.383 -2.625 17
#
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
GLS C1 C2 SINGLE NONE 1
GLS C1 O5 SINGLE NONE 2
GLS C1 N2 SINGLE BEGINDASH 3
GLS C1 C7 SINGLE NONE 4
GLS C2 O2 SINGLE BEGINWEDGE 5
GLS C2 C3 SINGLE NONE 6
GLS C3 O3 SINGLE BEGINDASH 7
GLS C3 C4 SINGLE NONE 8
GLS C4 O4 SINGLE BEGINWEDGE 9
GLS C4 C5 SINGLE NONE 10
GLS C5 C6 SINGLE BEGINDASH 11
GLS C5 O5 SINGLE NONE 12
GLS C6 O6 SINGLE NONE 13
GLS N2 C8 SINGLE NONE 14
GLS C8 O8 DOUBLE NONE 15
GLS C8 N1 SINGLE NONE 16
GLS N1 C7 SINGLE NONE 17
GLS C7 O7 DOUBLE NONE 18
#
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
GLS MurckoScaffold S1 scaffold 'O=C1NC(=O)[C@@]2(CCCCO2)N1' InChI=1S/C7H10N2O3/c10-5-7(9-6(11)8-5)3-1-2-4-12-7/h1-4H2,(H2,8,9,10,11)/t7-/m0/s1 AVOVFCUESOCMML-ZETCQYMHSA-N
GLS acetylurea F1 fragment O=C1CNC(=O)N1 InChI=1S/C3H4N2O2/c6-2-1-4-3(7)5-2/h1H2,(H2,4,5,6,7) WJRBRSLFGCUECM-UHFFFAOYSA-N
GLS amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
GLS peptide F3 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-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
GLS C1 S1 1
GLS C2 S1 1
GLS C3 S1 1
GLS C4 S1 1
GLS C5 S1 1
GLS O5 S1 1
GLS N2 S1 1
GLS C8 S1 1
GLS O8 S1 1
GLS N1 S1 1
GLS C7 S1 1
GLS O7 S1 1
GLS C1 F1 1
GLS C7 F1 1
GLS O7 F1 1
GLS N1 F1 1
GLS C8 F1 1
GLS O8 F1 1
GLS N2 F1 1
GLS N1 F2 1
GLS C7 F2 1
GLS O7 F2 1
GLS C1 F2 1
GLS O7 F3 1
GLS C7 F3 1
GLS C1 F3 1
GLS N2 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GLS
_pdbe_chem_comp_rdkit_properties.exactmw 248.064
_pdbe_chem_comp_rdkit_properties.amw 248.191
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 1
_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 112.318
_pdbe_chem_comp_rdkit_properties.tpsa 148.350
_pdbe_chem_comp_rdkit_properties.CrippenClogP -4.004
_pdbe_chem_comp_rdkit_properties.CrippenMR 49.385
_pdbe_chem_comp_rdkit_properties.chi0v 7.752
_pdbe_chem_comp_rdkit_properties.chi1v 4.027
_pdbe_chem_comp_rdkit_properties.chi2v 2.009
_pdbe_chem_comp_rdkit_properties.chi3v 2.009
_pdbe_chem_comp_rdkit_properties.chi4v 1.252
_pdbe_chem_comp_rdkit_properties.chi0n 19.752
_pdbe_chem_comp_rdkit_properties.chi1n 9.555
_pdbe_chem_comp_rdkit_properties.chi2n 2.009
_pdbe_chem_comp_rdkit_properties.chi3n 2.009
_pdbe_chem_comp_rdkit_properties.chi4n 1.252
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.260
_pdbe_chem_comp_rdkit_properties.kappa1 4.140
_pdbe_chem_comp_rdkit_properties.kappa2 3.892
_pdbe_chem_comp_rdkit_properties.kappa3 1.594
_pdbe_chem_comp_rdkit_properties.Phi 0.948
#
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
GLS UniChem ChEMBL CHEMBL510975
GLS UniChem PDBe GLS
GLS UniChem ZINC ZINC000003833817
GLS UniChem 'PubChem TPHARMA' 15465378
GLS UniChem PubChem 444185
GLS UniChem BindingDb 50263768
GLS UniChem BRENDA 50751
GLS UniChem BRENDA 87905
GLS UniChem Nikkaji J860.262J
#
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
GLS C1 0.865 -0.335 0.324 ETKDGv3 1
GLS C2 0.630 0.768 -0.754 ETKDGv3 2
GLS O2 1.835 1.352 -1.195 ETKDGv3 3
GLS C3 -0.357 1.815 -0.218 ETKDGv3 4
GLS O3 -0.527 2.874 -1.129 ETKDGv3 5
GLS C4 -1.705 1.136 0.094 ETKDGv3 6
GLS O4 -2.480 1.964 0.927 ETKDGv3 7
GLS C5 -1.526 -0.285 0.722 ETKDGv3 8
GLS C6 -2.070 -1.441 -0.145 ETKDGv3 9
GLS O6 -1.628 -1.352 -1.470 ETKDGv3 10
GLS O5 -0.221 -0.552 1.223 ETKDGv3 11
GLS N2 1.255 -1.598 -0.311 ETKDGv3 12
GLS C8 2.560 -1.942 0.131 ETKDGv3 13
GLS O8 3.168 -2.978 -0.242 ETKDGv3 14
GLS N1 3.104 -1.005 1.036 ETKDGv3 15
GLS C7 2.080 -0.032 1.172 ETKDGv3 16
GLS O7 2.175 0.950 1.955 ETKDGv3 17
GLS H2 0.170 0.299 -1.649 ETKDGv3 18
GLS HO2 2.121 2.027 -0.526 ETKDGv3 19
GLS H3 0.062 2.241 0.721 ETKDGv3 20
GLS HO3 -0.827 2.487 -1.993 ETKDGv3 21
GLS H4 -2.268 1.033 -0.859 ETKDGv3 22
GLS HO4 -2.005 2.046 1.796 ETKDGv3 23
GLS H5 -2.179 -0.312 1.623 ETKDGv3 24
GLS H61 -3.183 -1.404 -0.135 ETKDGv3 25
GLS H62 -1.754 -2.413 0.296 ETKDGv3 26
GLS HO6 -2.007 -2.139 -1.941 ETKDGv3 27
GLS HN2 0.686 -2.165 -0.975 ETKDGv3 28
GLS HN1 4.027 -1.041 1.522 ETKDGv3 29
#