data_G6D
#
_chem_comp.id G6D
_chem_comp.name alpha-D-quinovopyranose
_chem_comp.type "D-saccharide, alpha linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H12 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
"alpha-D-quinovose; 6-deoxy-alpha-D-glucopyranose; D-quinovose; quinovose; 6-DEOXY-ALPHA-D-GLUCOSE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-08-04
_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 GLW
_chem_comp.formula_weight 164.156
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code G6D
_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 1B2Y
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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 G6D alpha-D-quinovose PDB ?
2 G6D 6-deoxy-alpha-D-glucopyranose PDB ?
3 G6D D-quinovose PDB ?
4 G6D quinovose PDB ?
5 G6D 6-DEOXY-ALPHA-D-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
G6D C1 C1 C 0 1 N N S N N N 24.522 3.027 45.032 -0.845 1.417 -0.243 C1 G6D 1
G6D O2 O2 O 0 1 N N N N N N 23.895 3.507 42.722 -2.707 -0.123 -0.142 O2 G6D 2
G6D C2 C2 C 0 1 N N R N N N 24.413 2.502 43.591 -1.345 0.004 -0.554 C2 G6D 3
G6D C3 C3 C 0 1 N N S N N N 23.518 1.276 43.558 -0.484 -1.012 0.203 C3 G6D 4
G6D O3 O3 O 0 1 N N N N N N 23.460 0.747 42.243 -0.896 -2.337 -0.138 O3 G6D 5
G6D C4 C4 C 0 1 N N S N N N 24.093 0.235 44.500 0.984 -0.814 -0.189 C4 G6D 6
G6D O4 O4 O 0 1 N N N N N N 23.244 -0.903 44.507 1.804 -1.708 0.567 O4 G6D 7
G6D C5 C5 C 0 1 N N R N N N 24.183 0.829 45.903 1.393 0.631 0.109 C5 G6D 8
G6D O5 O5 O 0 1 N N N N N N 25.015 1.999 45.872 0.534 1.524 -0.603 O5 G6D 9
G6D C6 C6 C 0 1 N N N N N N 24.728 -0.184 46.913 2.840 0.853 -0.336 C6 G6D 10
G6D O1 O1 O 0 1 N Y N N N N 23.285 3.525 45.467 -0.995 1.678 1.154 O1 G6D 11
G6D H1 H1 H 0 1 N N N N N N 25.251 3.851 45.021 -1.427 2.142 -0.813 H1 G6D 12
G6D HO2 HO2 H 0 1 N Y N N N N 23.836 3.163 41.839 -3.309 0.495 -0.579 HO2 G6D 13
G6D H2 HC2 H 0 1 N N N N N N 25.419 2.207 43.257 -1.270 -0.181 -1.626 H2 G6D 14
G6D H3 HC3 H 0 1 N N N N N N 22.512 1.557 43.904 -0.600 -0.860 1.276 H3 G6D 15
G6D HO3 HO3 H 0 1 N Y N N N N 22.898 -0.019 42.234 -1.819 -2.530 0.076 HO3 G6D 16
G6D H4 HC4 H 0 1 N N N N N N 25.103 -0.040 44.161 1.107 -1.018 -1.252 H4 G6D 17
G6D HO4 HO4 H 0 1 N Y N N N N 23.598 -1.559 45.095 2.748 -1.637 0.369 HO4 G6D 18
G6D H5 HC5 H 0 1 N N N N N N 23.169 1.113 46.219 1.308 0.820 1.179 H5 G6D 19
G6D H61 HC61 H 0 1 N N N N N N 24.778 0.281 47.909 2.924 0.664 -1.406 H61 G6D 20
G6D H62 HC62 H 0 1 N N N N N N 24.063 -1.059 46.950 3.131 1.881 -0.124 H62 G6D 21
G6D H63 HC63 H 0 1 N N N N N N 25.735 -0.502 46.606 3.495 0.170 0.206 H63 G6D 22
G6D HO1 HO1 H 0 1 N Y N N N N 23.368 3.845 46.358 -0.698 2.558 1.424 HO1 G6D 23
#
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
G6D C1 C2 SING N N 1
G6D C1 O5 SING N N 2
G6D C1 O1 SING N N 3
G6D C1 H1 SING N N 4
G6D O2 C2 SING N N 5
G6D O2 HO2 SING N N 6
G6D C2 C3 SING N N 7
G6D C2 H2 SING N N 8
G6D C3 O3 SING N N 9
G6D C3 C4 SING N N 10
G6D C3 H3 SING N N 11
G6D O3 HO3 SING N N 12
G6D C4 O4 SING N N 13
G6D C4 C5 SING N N 14
G6D C4 H4 SING N N 15
G6D O4 HO4 SING N N 16
G6D C5 O5 SING N N 17
G6D C5 C6 SING N N 18
G6D C5 H5 SING N N 19
G6D C6 H61 SING N N 20
G6D C6 H62 SING N N 21
G6D C6 H63 SING N N 22
G6D O1 HO1 SING N N 23
#
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
G6D SMILES ACDLabs 12.01 C1(C(O)C(O)C(O)C(O1)C)O
G6D InChI InChI 1.03 InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5-,6+/m1/s1
G6D InChIKey InChI 1.03 SHZGCJCMOBCMKK-DVKNGEFBSA-N
G6D SMILES_CANONICAL CACTVS 3.385 C[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
G6D SMILES CACTVS 3.385 C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
G6D SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O
G6D SMILES "OpenEye OEToolkits" 1.7.6 CC1C(C(C(C(O1)O)O)O)O
#
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
G6D "SYSTEMATIC NAME" ACDLabs 12.01 6-deoxy-alpha-D-glucopyranose
G6D "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 (2S,3R,4S,5S,6R)-6-methyloxane-2,3,4,5-tetrol
G6D "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DQuipa
G6D "COMMON NAME" GMML 1.0 a-D-quinovopyranose
G6D "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 a-D-6-deoxy-Glcp
G6D "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Qui
#
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
G6D "CARBOHYDRATE ISOMER" D PDB ?
G6D "CARBOHYDRATE RING" pyranose PDB ?
G6D "CARBOHYDRATE ANOMER" alpha PDB ?
G6D "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
G6D 'Create component' 1999-08-04 PDBJ
G6D 'Modify descriptor' 2011-06-04 RCSB
G6D 'Modify atom id' 2017-10-13 RCSB
G6D 'Other modification' 2019-08-12 RCSB
G6D 'Other modification' 2019-12-19 RCSB
G6D 'Other modification' 2020-07-03 RCSB
G6D 'Modify name' 2020-07-17 RCSB
G6D 'Modify synonyms' 2020-07-17 RCSB
G6D 'Modify atom id' 2020-07-17 RCSB
G6D 'Modify component atom id' 2020-07-17 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id G6D
_pdbe_chem_comp_drugbank_details.drugbank_id DB03773
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name alpha-D-quinovopyranose
_pdbe_chem_comp_drugbank_details.description
'The pyranose form of D-quinovose with an α-configuration at the anomeric position .'
_pdbe_chem_comp_drugbank_details.cas_number 7658-08-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
G6D alpha-D-quinovose wwPDB ?
G6D 6-deoxy-alpha-D-glucopyranose wwPDB ?
G6D D-quinovose wwPDB ?
G6D quinovose wwPDB ?
G6D 6-DEOXY-ALPHA-D-GLUCOSE wwPDB ?
G6D alpha-D-quinovopyranose DrugBank ?
G6D D-Chinovose DrugBank ?
G6D D-Epifucose DrugBank ?
G6D D-Glucomethylose DrugBank ?
G6D D-Quinovose DrugBank ?
G6D Isorhamnose DrugBank ?
G6D Isorhodeose DrugBank ?
G6D Quinovose DrugBank ?
G6D 'α-D-quinovopyranose' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id G6D
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03773
_pdbe_chem_comp_drugbank_classification.parent Hexoses
_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 hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
G6D DB03773 'Pancreatic alpha-amylase' Humans P04746 unknown 1
G6D DB03773 'Cyclomaltodextrin glucanotransferase' 'Bacillus circulans' P30920 unknown 2
G6D DB03773 Alpha-amylase 'Bacillus amyloliquefaciens' P00692 unknown 3
G6D DB03773 'Aldose 1-epimerase' 'Lactococcus lactis' Q9ZB17 unknown 4
G6D DB03773 'Cyclomaltodextrin glucanotransferase' 'Thermoanaerobacterium thermosulfurigenes' P26827 unknown 5
#
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
G6D C1 C 5.104 1.268 1
G6D O2 O 3.805 -0.983 2
G6D C2 C 5.104 -0.233 3
G6D C3 C 6.404 -0.983 4
G6D O3 O 6.404 -2.482 5
G6D C4 C 7.702 -0.233 6
G6D O4 O 9.002 -0.983 7
G6D C5 C 7.702 1.268 8
G6D O5 O 6.404 2.018 9
G6D C6 C 9.002 2.018 10
G6D O1 O 3.805 2.018 11
#
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
G6D C1 C2 SINGLE NONE 1
G6D C1 O5 SINGLE NONE 2
G6D C1 O1 SINGLE BEGINWEDGE 3
G6D C2 O2 SINGLE BEGINWEDGE 4
G6D C2 C3 SINGLE NONE 5
G6D C3 O3 SINGLE BEGINDASH 6
G6D C3 C4 SINGLE NONE 7
G6D C4 O4 SINGLE BEGINWEDGE 8
G6D C4 C5 SINGLE NONE 9
G6D C5 O5 SINGLE NONE 10
G6D C5 C6 SINGLE BEGINDASH 11
#
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
G6D MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
G6D pyranose F1 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-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
G6D C1 S1 1
G6D C2 S1 1
G6D C3 S1 1
G6D C4 S1 1
G6D C5 S1 1
G6D O5 S1 1
G6D C4 F1 1
G6D C5 F1 1
G6D O5 F1 1
G6D C1 F1 1
G6D C2 F1 1
G6D C3 F1 1
G6D O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id G6D
_pdbe_chem_comp_rdkit_properties.exactmw 164.068
_pdbe_chem_comp_rdkit_properties.amw 164.157
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 81.055
_pdbe_chem_comp_rdkit_properties.tpsa 90.150
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.194
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.574
_pdbe_chem_comp_rdkit_properties.chi0v 5.041
_pdbe_chem_comp_rdkit_properties.chi1v 2.475
_pdbe_chem_comp_rdkit_properties.chi2v 0.999
_pdbe_chem_comp_rdkit_properties.chi3v 0.999
_pdbe_chem_comp_rdkit_properties.chi4v 0.484
_pdbe_chem_comp_rdkit_properties.chi0n 17.041
_pdbe_chem_comp_rdkit_properties.chi1n 8.108
_pdbe_chem_comp_rdkit_properties.chi2n 0.999
_pdbe_chem_comp_rdkit_properties.chi3n 0.999
_pdbe_chem_comp_rdkit_properties.chi4n 0.484
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.200
_pdbe_chem_comp_rdkit_properties.kappa1 1.995
_pdbe_chem_comp_rdkit_properties.kappa2 3.040
_pdbe_chem_comp_rdkit_properties.kappa3 1.521
_pdbe_chem_comp_rdkit_properties.Phi 0.551
#
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
G6D UniChem DrugBank DB03773
G6D UniChem 'KEGG LIGAND' C08352
G6D UniChem ChEBI 42606
G6D UniChem ZINC ZINC000002042980
G6D UniChem fdasrs 68BDH91OBS
G6D UniChem NMRShiftDB 60078700
G6D UniChem Nikkaji J22.169D
G6D UniChem MetaboLights MTBLC42606
G6D UniChem BRENDA 35272
G6D UniChem 'Probes And Drugs' PD059480
G6D UniChem PubChem 441480
G6D UniChem SureChEMBL SCHEMBL79180
#
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
G6D C1 -1.226 -1.110 -0.202 ETKDGv3 1
G6D O2 -2.759 0.714 -0.616 ETKDGv3 2
G6D C2 -1.621 0.345 0.121 ETKDGv3 3
G6D C3 -0.463 1.300 -0.209 ETKDGv3 4
G6D O3 -0.752 2.590 0.266 ETKDGv3 5
G6D C4 0.829 0.795 0.454 ETKDGv3 6
G6D O4 1.922 1.598 0.077 ETKDGv3 7
G6D C5 1.068 -0.691 0.091 ETKDGv3 8
G6D O5 -0.039 -1.488 0.482 ETKDGv3 9
G6D C6 2.315 -1.226 0.798 ETKDGv3 10
G6D O1 -1.097 -1.298 -1.590 ETKDGv3 11
G6D H1 -2.049 -1.764 0.166 ETKDGv3 12
G6D HO2 -3.534 0.262 -0.190 ETKDGv3 13
G6D H2 -1.840 0.422 1.213 ETKDGv3 14
G6D H3 -0.313 1.328 -1.315 ETKDGv3 15
G6D HO3 -1.372 3.006 -0.388 ETKDGv3 16
G6D H4 0.711 0.874 1.559 ETKDGv3 17
G6D HO4 2.043 1.500 -0.903 ETKDGv3 18
G6D H5 1.250 -0.789 -1.004 ETKDGv3 19
G6D H61 2.204 -1.139 1.901 ETKDGv3 20
G6D H62 3.218 -0.664 0.478 ETKDGv3 21
G6D H63 2.462 -2.296 0.540 ETKDGv3 22
G6D HO1 -0.955 -2.271 -1.728 ETKDGv3 23
#