data_GLA
#
_chem_comp.id GLA
_chem_comp.name alpha-D-galactopyranose
_chem_comp.type 'D-saccharide, alpha linking'
_chem_comp.pdbx_type ATOMS
_chem_comp.formula 'C6 H12 O6'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 'alpha-D-galactose; D-galactose; galactose; ALPHA D-GALACTOSE'
_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 180.156
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GLA
_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 8ABP
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_chem_comp.pdbx_pcm Y
#
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 GLA alpha-D-galactose PDB ?
2 GLA D-galactose PDB ?
3 GLA galactose PDB ?
4 GLA 'ALPHA D-GALACTOSE' 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
GLA C1 C1 C 0 1 N N S N N N 14.312 56.846 55.116 1.424 -0.489 -0.382 C1 GLA 1
GLA C2 C2 C 0 1 N N R N N N 12.873 57.140 54.749 0.392 -0.498 -1.512 C2 GLA 2
GLA C3 C3 C 0 1 N N S N N N 12.373 56.256 53.626 -0.650 0.592 -1.244 C3 GLA 3
GLA C4 C4 C 0 1 N N R N N N 13.334 56.364 52.401 -1.222 0.387 0.163 C4 GLA 4
GLA C5 C5 C 0 1 N N R N N N 14.735 56.054 52.846 -0.068 0.330 1.166 C5 GLA 5
GLA C6 C6 C 0 1 N N N N N N 15.685 56.357 51.684 -0.630 0.161 2.579 C6 GLA 6
GLA O1 O1 O 0 1 N Y N N N N 14.401 55.565 55.685 2.043 0.797 -0.316 O1 GLA 7
GLA O2 O2 O 0 1 N N N N N N 12.023 56.989 55.927 1.044 -0.242 -2.757 O2 GLA 8
GLA O3 O3 O 0 1 N N N N N N 11.068 56.630 53.244 -1.700 0.498 -2.209 O3 GLA 9
GLA O4 O4 O 0 1 N N N N N N 13.184 57.694 51.793 -1.958 -0.836 0.206 O4 GLA 10
GLA O5 O5 O 0 1 N N N N N N 15.135 56.882 53.922 0.783 -0.771 0.859 O5 GLA 11
GLA O6 O6 O 0 1 N N N N N N 16.890 55.781 52.074 0.446 0.112 3.517 O6 GLA 12
GLA H1 H1 H 0 1 N N N N N N 14.665 57.611 55.845 2.183 -1.246 -0.578 H1 GLA 13
GLA H2 H2 H 0 1 N N N N N N 12.827 58.192 54.382 -0.097 -1.470 -1.550 H2 GLA 14
GLA H3 H3 H 0 1 N N N N N N 12.349 55.201 53.986 -0.180 1.573 -1.309 H3 GLA 15
GLA H4 H4 H 0 1 N N N N N N 13.079 55.619 51.611 -1.881 1.218 0.414 H4 GLA 16
GLA H5 H5 H 0 1 N N N N N N 14.766 54.985 53.164 0.504 1.256 1.112 H5 GLA 17
GLA H61 H61 H 0 1 N N N N N N 15.315 56.016 50.688 -1.202 -0.764 2.634 H61 GLA 18
GLA H62 H62 H 0 1 N N N N N N 15.757 57.438 51.421 -1.279 1.004 2.815 H62 GLA 19
GLA HO1 HO1 H 0 1 N Y N N N N 15.304 55.380 55.915 2.688 0.760 0.403 HO1 GLA 20
GLA HO2 HO2 H 0 1 N Y N N N N 11.120 57.173 55.696 1.695 -0.947 -2.882 HO2 GLA 21
GLA HO3 HO3 H 0 1 N Y N N N N 10.754 56.075 52.539 -1.293 0.620 -3.078 HO3 GLA 22
GLA HO4 HO4 H 0 1 N Y N N N N 13.769 57.759 51.047 -2.669 -0.758 -0.443 HO4 GLA 23
GLA HO6 HO6 H 0 1 N Y N N N N 17.479 55.969 51.353 0.050 0.005 4.393 HO6 GLA 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
GLA C1 C2 SING N N 1
GLA C1 O1 SING N N 2
GLA C1 O5 SING N N 3
GLA C1 H1 SING N N 4
GLA C2 C3 SING N N 5
GLA C2 O2 SING N N 6
GLA C2 H2 SING N N 7
GLA C3 C4 SING N N 8
GLA C3 O3 SING N N 9
GLA C3 H3 SING N N 10
GLA C4 C5 SING N N 11
GLA C4 O4 SING N N 12
GLA C4 H4 SING N N 13
GLA C5 C6 SING N N 14
GLA C5 O5 SING N N 15
GLA C5 H5 SING N N 16
GLA C6 O6 SING N N 17
GLA C6 H61 SING N N 18
GLA C6 H62 SING N N 19
GLA O1 HO1 SING N N 20
GLA O2 HO2 SING N N 21
GLA O3 HO3 SING N N 22
GLA O4 HO4 SING N N 23
GLA 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
GLA SMILES ACDLabs 10.04 'OC1C(O)C(OC(O)C1O)CO'
GLA SMILES_CANONICAL CACTVS 3.341 'OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@H]1O'
GLA SMILES CACTVS 3.341 'OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O'
GLA SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@@H]1[C@@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O'
GLA SMILES 'OpenEye OEToolkits' 1.5.0 'C(C1C(C(C(C(O1)O)O)O)O)O'
GLA InChI InChI 1.03 'InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6+/m1/s1'
GLA InChIKey InChI 1.03 WQZGKKKJIJFFOK-PHYPRBDBSA-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
GLA 'SYSTEMATIC NAME' ACDLabs 10.04 alpha-D-galactopyranose
GLA 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S,3R,4S,5R,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol'
GLA 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGalpa
GLA 'COMMON NAME' GMML 1.0 a-D-galactopyranose
GLA 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-Galp
GLA 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Gal
#
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
GLA 'CARBOHYDRATE ISOMER' D PDB ?
GLA 'CARBOHYDRATE RING' pyranose PDB ?
GLA 'CARBOHYDRATE ANOMER' alpha PDB ?
GLA '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
GLA 'Create component' 1999-07-08 EBI
GLA 'Modify descriptor' 2011-06-04 RCSB
GLA 'Other modification' 2019-08-12 RCSB
GLA 'Other modification' 2019-12-19 RCSB
GLA 'Other modification' 2020-07-03 RCSB
GLA 'Modify name' 2020-07-17 RCSB
GLA 'Modify synonyms' 2020-07-17 RCSB
GLA 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id GLA
_pdbx_chem_comp_pcm.modified_residue_id SER
_pdbx_chem_comp_pcm.type O-Glycosylation
_pdbx_chem_comp_pcm.category Carbohydrate
_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 C1
_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 ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
GLA alpha-D-galactose wwPDB ?
GLA D-galactose wwPDB ?
GLA galactose wwPDB ?
GLA 'ALPHA D-GALACTOSE' wwPDB ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
GLA C1 C 7.702 0.750 1
GLA C2 C 7.702 -0.750 2
GLA C3 C 6.404 -1.500 3
GLA C4 C 5.104 -0.750 4
GLA C5 C 5.104 0.750 5
GLA C6 C 3.805 1.500 6
GLA O1 O 9.002 1.500 7
GLA O2 O 9.002 -1.500 8
GLA O3 O 6.404 -3.000 9
GLA O4 O 3.805 -1.500 10
GLA O5 O 6.404 1.500 11
GLA 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
GLA C1 C2 SINGLE NONE 1
GLA C1 O1 SINGLE BEGINDASH 2
GLA C1 O5 SINGLE NONE 3
GLA C2 C3 SINGLE NONE 4
GLA C2 O2 SINGLE BEGINDASH 5
GLA C3 C4 SINGLE NONE 6
GLA C3 O3 SINGLE BEGINWEDGE 7
GLA C4 C5 SINGLE NONE 8
GLA C4 O4 SINGLE BEGINWEDGE 9
GLA C5 C6 SINGLE BEGINWEDGE 10
GLA C5 O5 SINGLE NONE 11
GLA C6 O6 SINGLE NONE 12
#
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
GLA MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
GLA 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
GLA C1 S1 1
GLA C2 S1 1
GLA C3 S1 1
GLA C4 S1 1
GLA C5 S1 1
GLA O5 S1 1
GLA C4 F1 1
GLA C5 F1 1
GLA O5 F1 1
GLA C1 F1 1
GLA C2 F1 1
GLA C3 F1 1
GLA O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GLA
_pdbe_chem_comp_rdkit_properties.exactmw 180.063
_pdbe_chem_comp_rdkit_properties.amw 180.156
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_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 85.936
_pdbe_chem_comp_rdkit_properties.tpsa 110.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.221
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.986
_pdbe_chem_comp_rdkit_properties.chi0v 5.449
_pdbe_chem_comp_rdkit_properties.chi1v 2.679
_pdbe_chem_comp_rdkit_properties.chi2v 1.092
_pdbe_chem_comp_rdkit_properties.chi3v 1.092
_pdbe_chem_comp_rdkit_properties.chi4v 0.552
_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 -0.240
_pdbe_chem_comp_rdkit_properties.kappa1 2.412
_pdbe_chem_comp_rdkit_properties.kappa2 3.649
_pdbe_chem_comp_rdkit_properties.kappa3 1.582
_pdbe_chem_comp_rdkit_properties.Phi 0.733
#
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
GLA UniChem ChEMBL CHEMBL1233058
GLA UniChem 'Guide to Pharmacology' 4646
GLA UniChem 'KEGG LIGAND' C00984
GLA UniChem 'KEGG LIGAND' C01582
GLA UniChem ChEBI 28061
GLA UniChem ZINC ZINC000000901155
GLA UniChem eMolecules 30555480
GLA UniChem fdasrs 7IOF6H4H77
GLA UniChem HMDB HMDB0000143
GLA UniChem 'PubChem TPHARMA' 14968276
GLA UniChem NMRShiftDB 20077721
GLA UniChem ACTor 3646-73-9
GLA UniChem Recon gal
GLA UniChem Nikkaji J292.885J
GLA UniChem BindingDb 50423644
GLA UniChem 'EPA CompTox Dashboard' DTXSID90189974
GLA UniChem DrugCentral 1271
GLA UniChem MetaboLights MTBLC28061
GLA UniChem BRENDA 1087
GLA UniChem BRENDA 6705
GLA UniChem Rhea 28061
GLA UniChem ClinicalTrials D-GALACTOSE
GLA UniChem ClinicalTrials GALACTOSE
GLA UniChem rxnorm GALACTOSE
GLA UniChem 'Probes And Drugs' PD052080
GLA UniChem CCDC ADGALA
GLA UniChem PubChem 439357
GLA UniChem SureChEMBL SCHEMBL18314
#
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
GLA C1 -1.150 1.244 -0.924 ETKDGv3 1
GLA C2 -1.951 0.040 -0.367 ETKDGv3 2
GLA C3 -1.032 -1.011 0.305 ETKDGv3 3
GLA C4 0.201 -0.321 0.921 ETKDGv3 4
GLA C5 0.966 0.523 -0.156 ETKDGv3 5
GLA C6 2.237 -0.171 -0.675 ETKDGv3 6
GLA O1 -1.116 2.314 -0.010 ETKDGv3 7
GLA O2 -2.972 0.466 0.503 ETKDGv3 8
GLA O3 -0.625 -1.955 -0.656 ETKDGv3 9
GLA O4 1.038 -1.269 1.537 ETKDGv3 10
GLA O5 0.161 0.843 -1.289 ETKDGv3 11
GLA O6 3.223 -0.191 0.321 ETKDGv3 12
GLA H1 -1.670 1.592 -1.846 ETKDGv3 13
GLA H2 -2.454 -0.457 -1.227 ETKDGv3 14
GLA H3 -1.607 -1.529 1.109 ETKDGv3 15
GLA H4 -0.160 0.388 1.703 ETKDGv3 16
GLA H5 1.299 1.476 0.316 ETKDGv3 17
GLA H61 2.625 0.392 -1.554 ETKDGv3 18
GLA H62 1.999 -1.207 -1.004 ETKDGv3 19
GLA HO1 -0.700 3.078 -0.488 ETKDGv3 20
GLA HO2 -2.549 0.759 1.352 ETKDGv3 21
GLA HO3 -0.336 -2.766 -0.162 ETKDGv3 22
GLA HO4 0.574 -1.571 2.362 ETKDGv3 23
GLA HO6 4.000 -0.669 -0.070 ETKDGv3 24
#