data_ADA
#
_chem_comp.id ADA
_chem_comp.name "alpha-D-galactopyranuronic acid"
_chem_comp.type "D-saccharide, alpha linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H10 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "alpha-D-galacturonic acid; D-galacturonic acid; galacturonic acid; ALPHA D-GALACTURONIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-04-08
_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 194.139
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ADA
_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 1GXO
_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 ADA "alpha-D-galacturonic acid" PDB ?
2 ADA "D-galacturonic acid" PDB ?
3 ADA "galacturonic acid" PDB ?
4 ADA "ALPHA D-GALACTURONIC ACID" 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
ADA C1 C1 C 0 1 N N S N N N 20.831 0.300 27.409 1.444 -0.340 -0.983 C1 ADA 1
ADA C2 C2 C 0 1 N N R N N N 22.110 1.081 27.771 0.164 -0.466 -1.813 C2 ADA 2
ADA C3 C3 C 0 1 N N S N N N 22.500 1.068 29.263 -0.882 0.509 -1.270 C3 ADA 3
ADA C4 C4 C 0 1 N N R N N N 21.314 1.144 30.251 -1.053 0.259 0.232 C4 ADA 4
ADA C5 C5 C 0 1 N N S N N N 20.268 0.099 29.789 0.317 0.330 0.908 C5 ADA 5
ADA C6 C6 C 0 1 N N N N N N 19.063 0.230 30.762 0.155 0.117 2.391 C6 ADA 6
ADA O1 O1 O 0 1 N Y N N N N 21.084 -1.043 27.040 1.924 1.003 -1.052 O1 ADA 7
ADA O2 O2 O 0 1 N N N N N N 23.189 0.600 26.989 0.447 -0.154 -3.179 O2 ADA 8
ADA O3 O3 O 0 1 N N N N N N 23.377 2.150 29.491 -2.129 0.300 -1.936 O3 ADA 9
ADA O4 O4 O 0 1 N N N N N N 20.615 2.407 30.202 -1.622 -1.034 0.441 O4 ADA 10
ADA O5 O5 O 0 1 N N N N N N 19.861 0.347 28.447 1.172 -0.678 0.374 O5 ADA 11
ADA O6B O6B O 0 1 N N N N N N 19.223 0.708 31.896 -0.611 0.952 3.109 O6B ADA 12
ADA O6A O6A O 0 1 N N N N N N 17.948 -0.130 30.412 0.715 -0.805 2.933 O6A ADA 13
ADA H1 H1 H 0 1 N N N N N N 20.382 0.803 26.521 2.201 -1.016 -1.381 H1 ADA 14
ADA H2 H2 H 0 1 N N N N N N 21.941 2.145 27.483 -0.216 -1.485 -1.744 H2 ADA 15
ADA H3 H3 H 0 1 N N N N N N 23.057 0.124 29.465 -0.548 1.534 -1.434 H3 ADA 16
ADA H4 H4 H 0 1 N N N N N N 21.655 0.925 31.290 -1.709 1.019 0.656 H4 ADA 17
ADA H5 H5 H 0 1 N N N N N N 20.702 -0.925 29.866 0.759 1.311 0.729 H5 ADA 18
ADA HO1 HA H 0 1 N Y N N N N 20.296 -1.524 26.817 2.730 1.039 -0.519 HO1 ADA 19
ADA HO2 HB H 0 1 N Y N N N N 23.977 1.081 27.212 1.108 -0.791 -3.480 HO2 ADA 20
ADA HO3 HC H 0 1 N Y N N N N 23.617 2.142 30.410 -1.976 0.468 -2.875 HO3 ADA 21
ADA HO4 HD H 0 1 N Y N N N N 19.886 2.454 30.809 -1.705 -1.152 1.397 HO4 ADA 22
ADA HO6B H6B H 0 0 N N N N N N 18.487 0.788 32.491 -0.716 0.815 4.060 HO6B ADA 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
ADA C1 C2 SING N N 1
ADA C1 O1 SING N N 2
ADA C1 O5 SING N N 3
ADA C1 H1 SING N N 4
ADA C2 C3 SING N N 5
ADA C2 O2 SING N N 6
ADA C2 H2 SING N N 7
ADA C3 C4 SING N N 8
ADA C3 O3 SING N N 9
ADA C3 H3 SING N N 10
ADA C4 C5 SING N N 11
ADA C4 O4 SING N N 12
ADA C4 H4 SING N N 13
ADA C5 C6 SING N N 14
ADA C5 O5 SING N N 15
ADA C5 H5 SING N N 16
ADA C6 O6B SING N N 17
ADA C6 O6A DOUB N N 18
ADA O1 HO1 SING N N 19
ADA O2 HO2 SING N N 20
ADA O3 HO3 SING N N 21
ADA O4 HO4 SING N N 22
ADA O6B HO6B 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
ADA SMILES ACDLabs 10.04 O=C(O)C1OC(O)C(O)C(O)C1O
ADA SMILES_CANONICAL CACTVS 3.341 O[C@H]1O[C@@H]([C@H](O)[C@H](O)[C@H]1O)C(O)=O
ADA SMILES CACTVS 3.341 O[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(O)=O
ADA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[C@@H]1([C@H]([C@H](O[C@@H]([C@@H]1O)O)C(=O)O)O)O"
ADA SMILES "OpenEye OEToolkits" 1.5.0 C1(C(C(OC(C1O)O)C(=O)O)O)O
ADA InChI InChI 1.03 InChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)/t1-,2+,3+,4-,6-/m0/s1
ADA InChIKey InChI 1.03 AEMOLEFTQBMNLQ-BKBMJHBISA-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
ADA "SYSTEMATIC NAME" ACDLabs 10.04 "alpha-D-galactopyranuronic acid"
ADA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3R,4S,5R,6S)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid"
ADA "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DGalpAa
ADA "COMMON NAME" GMML 1.0 "a-D-galactopyranuronic acid"
ADA "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 a-D-GalpA
ADA "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 GalA
#
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
ADA "CARBOHYDRATE ISOMER" D PDB ?
ADA "CARBOHYDRATE RING" pyranose PDB ?
ADA "CARBOHYDRATE ANOMER" alpha PDB ?
ADA "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
ADA 'Create component' 2002-04-08 EBI
ADA 'Modify descriptor' 2011-06-04 RCSB
ADA 'Other modification' 2019-08-12 RCSB
ADA 'Other modification' 2019-12-19 RCSB
ADA 'Other modification' 2020-07-03 RCSB
ADA 'Modify name' 2020-07-17 RCSB
ADA 'Modify synonyms' 2020-07-17 RCSB
ADA 'Modify atom id' 2020-07-17 RCSB
ADA 'Modify component atom id' 2020-07-17 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id ADA
_pdbe_chem_comp_drugbank_details.drugbank_id DB03511
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'alpha-D-galacturonic acid'
_pdbe_chem_comp_drugbank_details.description 'The α-anomer of D-galacturonic acid.'
_pdbe_chem_comp_drugbank_details.cas_number 6294-16-2
_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
ADA 'alpha-D-galacturonic acid' wwPDB ?
ADA 'D-galacturonic acid' wwPDB ?
ADA 'galacturonic acid' wwPDB ?
ADA 'ALPHA D-GALACTURONIC ACID' wwPDB ?
ADA 'alpha-D-galactopyranuronic acid' DrugBank ?
ADA 'α-D-galactopyranuronic acid' DrugBank ?
ADA 'α-D-galacturonic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id ADA
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03511
_pdbe_chem_comp_drugbank_classification.parent 'Glucuronic acid derivatives'
_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 glucuronic acid derivatives. These are compounds containing a glucuronic acid moiety (or a derivative), which consists of a glucose moiety with the C6 carbon oxidized to a carboxylic acid.'
#
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
ADA C1 C 8.196 0.750 1
ADA C2 C 8.196 -0.750 2
ADA C3 C 6.897 -1.500 3
ADA C4 C 5.598 -0.750 4
ADA C5 C 5.598 0.750 5
ADA C6 C 4.299 1.500 6
ADA O1 O 9.495 1.500 7
ADA O2 O 9.495 -1.500 8
ADA O3 O 6.897 -3.000 9
ADA O4 O 4.299 -1.500 10
ADA O5 O 6.897 1.500 11
ADA O6B O 4.299 3.000 12
ADA O6A O 3.000 0.750 13
#
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
ADA C1 C2 SINGLE NONE 1
ADA C1 O1 SINGLE BEGINDASH 2
ADA C1 O5 SINGLE NONE 3
ADA C2 C3 SINGLE NONE 4
ADA C2 O2 SINGLE BEGINDASH 5
ADA C3 C4 SINGLE NONE 6
ADA C3 O3 SINGLE BEGINWEDGE 7
ADA C4 C5 SINGLE NONE 8
ADA C4 O4 SINGLE BEGINWEDGE 9
ADA C5 C6 SINGLE BEGINWEDGE 10
ADA C5 O5 SINGLE NONE 11
ADA C6 O6B SINGLE NONE 12
ADA C6 O6A DOUBLE NONE 13
#
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
ADA MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
ADA 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
ADA C1 S1 1
ADA C2 S1 1
ADA C3 S1 1
ADA C4 S1 1
ADA C5 S1 1
ADA O5 S1 1
ADA C4 F1 1
ADA C5 F1 1
ADA O5 F1 1
ADA C1 F1 1
ADA C2 F1 1
ADA C3 F1 1
ADA O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ADA
_pdbe_chem_comp_rdkit_properties.exactmw 194.043
_pdbe_chem_comp_rdkit_properties.amw 194.139
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_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 87.287
_pdbe_chem_comp_rdkit_properties.tpsa 127.450
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.129
_pdbe_chem_comp_rdkit_properties.CrippenMR 36.536
_pdbe_chem_comp_rdkit_properties.chi0v 5.858
_pdbe_chem_comp_rdkit_properties.chi1v 2.883
_pdbe_chem_comp_rdkit_properties.chi2v 1.184
_pdbe_chem_comp_rdkit_properties.chi3v 1.184
_pdbe_chem_comp_rdkit_properties.chi4v 0.619
_pdbe_chem_comp_rdkit_properties.chi0n 15.858
_pdbe_chem_comp_rdkit_properties.chi1n 7.424
_pdbe_chem_comp_rdkit_properties.chi2n 1.184
_pdbe_chem_comp_rdkit_properties.chi3n 1.184
_pdbe_chem_comp_rdkit_properties.chi4n 0.619
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.730
_pdbe_chem_comp_rdkit_properties.kappa1 3.142
_pdbe_chem_comp_rdkit_properties.kappa2 3.561
_pdbe_chem_comp_rdkit_properties.kappa3 1.789
_pdbe_chem_comp_rdkit_properties.Phi 0.861
#
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
ADA UniChem DrugBank DB03511
ADA UniChem ChEBI 33885
ADA UniChem ZINC ZINC000004228259
ADA UniChem eMolecules 1972285
ADA UniChem fdasrs CEP8I6411H
ADA UniChem HMDB HMDB0003363
ADA UniChem PubChem 445929
ADA UniChem NMRShiftDB 60078576
ADA UniChem ACTor 25990-10-7
ADA UniChem ACTor 9046-38-2
ADA UniChem 'EPA CompTox Dashboard' DTXSID60873878
ADA UniChem MetaboLights MTBLC33885
ADA UniChem BRENDA 157464
ADA UniChem 'Probes And Drugs' PD006851
ADA UniChem CCDC ODEKIR
ADA UniChem Nikkaji J506.522D
ADA UniChem SureChEMBL SCHEMBL12468784
ADA UniChem 'PubChem TPHARMA' 14772975
#
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
ADA C1 1.471 -0.496 -0.088 ETKDGv3 1
ADA C2 1.462 1.054 -0.129 ETKDGv3 2
ADA C3 0.046 1.617 0.165 ETKDGv3 3
ADA C4 -1.044 0.593 -0.196 ETKDGv3 4
ADA C5 -0.781 -0.723 0.601 ETKDGv3 5
ADA C6 -1.413 -1.928 -0.041 ETKDGv3 6
ADA O1 2.768 -0.958 0.176 ETKDGv3 7
ADA O2 2.399 1.601 0.768 ETKDGv3 8
ADA O3 -0.165 2.847 -0.484 ETKDGv3 9
ADA O4 -1.035 0.360 -1.585 ETKDGv3 10
ADA O5 0.590 -0.971 0.916 ETKDGv3 11
ADA O6B -2.783 -2.134 0.085 ETKDGv3 12
ADA O6A -0.719 -2.730 -0.722 ETKDGv3 13
ADA H1 1.165 -0.887 -1.088 ETKDGv3 14
ADA H2 1.771 1.353 -1.155 ETKDGv3 15
ADA H3 -0.043 1.806 1.259 ETKDGv3 16
ADA H4 -2.032 1.015 0.110 ETKDGv3 17
ADA H5 -1.293 -0.596 1.580 ETKDGv3 18
ADA HO1 2.735 -1.947 0.100 ETKDGv3 19
ADA HO2 2.187 1.251 1.673 ETKDGv3 20
ADA HO3 -0.096 2.693 -1.462 ETKDGv3 21
ADA HO4 -1.959 0.110 -1.845 ETKDGv3 22
ADA HO6B -3.231 -2.929 -0.353 ETKDGv3 23
#