data_BDP
#
_chem_comp.id BDP
_chem_comp.name "beta-D-glucopyranuronic acid"
_chem_comp.type "D-saccharide, beta linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H10 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "beta-D-glucuronic acid; D-glucuronic acid; glucuronic acid"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-11-26
_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 BDP
_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 1GQK
_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 BDP "beta-D-glucuronic acid" PDB ?
2 BDP "D-glucuronic acid" PDB ?
3 BDP "glucuronic 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
BDP C1 C1 C 0 1 N N R N N N 8.748 -11.725 3.342 -1.248 1.252 0.387 C1 BDP 1
BDP C2 C2 C 0 1 N N R N N N 9.125 -11.206 4.727 -1.851 -0.001 -0.255 C2 BDP 2
BDP C3 C3 C 0 1 N N S N N N 8.484 -11.996 5.851 -1.037 -1.226 0.173 C3 BDP 3
BDP C4 C4 C 0 1 N N S N N N 6.984 -12.052 5.582 0.427 -1.017 -0.224 C4 BDP 4
BDP C5 C5 C 0 1 N N S N N N 6.755 -12.709 4.238 0.942 0.275 0.417 C5 BDP 5
BDP C6 C6 C 0 1 N N N N N N 5.298 -12.692 3.781 2.364 0.519 -0.016 C6 BDP 6
BDP O2 O2 O 0 1 N N N N N N 10.540 -11.232 4.784 -3.205 -0.153 0.174 O2 BDP 7
BDP O3 O3 O 0 1 N N N N N N 8.730 -11.292 7.057 -1.548 -2.390 -0.480 O3 BDP 8
BDP O4 O4 O 0 1 N N N N N N 6.322 -12.815 6.554 1.209 -2.121 0.235 O4 BDP 9
BDP O5 O5 O 0 1 N N N N N N 7.382 -11.957 3.235 0.123 1.370 0.002 O5 BDP 10
BDP O6A O6A O 0 1 N N N N N N 4.562 -13.559 4.253 2.632 1.482 -0.695 O6A BDP 11
BDP O1 O1 O 0 1 N Y N N N N 8.947 -10.588 2.508 -1.968 2.406 -0.053 O1 BDP 12
BDP O6B O6B O 0 1 N N N N N N 4.954 -11.847 2.932 3.334 -0.333 0.352 O6B BDP 13
BDP H1 H1 H 0 1 N N N N N N 9.311 -12.642 3.111 -1.316 1.173 1.472 H1 BDP 14
BDP H2 H2 H 0 1 N N N N N N 8.743 -10.185 4.873 -1.820 0.096 -1.341 H2 BDP 15
BDP H3 H3 H 0 1 N N N N N N 8.887 -13.017 5.921 -1.108 -1.351 1.253 H3 BDP 16
BDP H4 H4 H 0 1 N N N N N N 6.591 -11.025 5.602 0.504 -0.941 -1.308 H4 BDP 17
BDP H5 H5 H 0 1 N N N N N N 7.127 -13.736 4.371 0.903 0.183 1.503 H5 BDP 18
BDP HO2 HB H 0 1 N Y N N N N 10.829 -10.916 5.632 -3.778 0.591 -0.060 HO2 BDP 19
BDP HO3 HC H 0 1 N Y N N N N 8.340 -11.763 7.784 -2.474 -2.579 -0.279 HO3 BDP 20
BDP HO4 HD H 0 1 N Y N N N N 5.590 -13.271 6.155 2.149 -2.055 0.018 HO4 BDP 21
BDP HO1 HA H 0 1 N Y N N N N 8.735 -10.813 1.610 -1.640 3.237 0.315 HO1 BDP 22
BDP HO6B H6B H 0 0 N N N N N N 4.040 -11.977 2.708 4.231 -0.135 0.050 HO6B BDP 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
BDP C1 C2 SING N N 1
BDP C1 O5 SING N N 2
BDP C1 O1 SING N N 3
BDP C1 H1 SING N N 4
BDP C2 C3 SING N N 5
BDP C2 O2 SING N N 6
BDP C2 H2 SING N N 7
BDP C3 C4 SING N N 8
BDP C3 O3 SING N N 9
BDP C3 H3 SING N N 10
BDP C4 C5 SING N N 11
BDP C4 O4 SING N N 12
BDP C4 H4 SING N N 13
BDP C5 C6 SING N N 14
BDP C5 O5 SING N N 15
BDP C5 H5 SING N N 16
BDP C6 O6A DOUB N N 17
BDP C6 O6B SING N N 18
BDP O2 HO2 SING N N 19
BDP O3 HO3 SING N N 20
BDP O4 HO4 SING N N 21
BDP O1 HO1 SING N N 22
BDP 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
BDP SMILES ACDLabs 12.01 O=C(O)C1OC(O)C(O)C(O)C1O
BDP SMILES_CANONICAL CACTVS 3.370 O[C@@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(O)=O
BDP SMILES CACTVS 3.370 O[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(O)=O
BDP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "[C@@H]1([C@@H]([C@H](O[C@H]([C@@H]1O)O)C(=O)O)O)O"
BDP SMILES "OpenEye OEToolkits" 1.7.0 C1(C(C(OC(C1O)O)C(=O)O)O)O
BDP 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
BDP InChIKey InChI 1.03 AEMOLEFTQBMNLQ-QIUUJYRFSA-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
BDP "SYSTEMATIC NAME" ACDLabs 12.01 "beta-D-glucopyranuronic acid"
BDP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2S,3S,4S,5R,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid"
BDP "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DGlcpAb
BDP "COMMON NAME" GMML 1.0 "b-D-glucopyranuronic acid"
BDP "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-GlcpA
BDP "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 GlcA
#
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
BDP "CARBOHYDRATE ISOMER" D PDB ?
BDP "CARBOHYDRATE RING" pyranose PDB ?
BDP "CARBOHYDRATE ANOMER" beta PDB ?
BDP "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
BDP 'Create component' 2001-11-26 EBI
BDP 'Modify descriptor' 2011-06-04 RCSB
BDP 'Other modification' 2019-08-12 RCSB
BDP 'Other modification' 2019-12-19 RCSB
BDP 'Other modification' 2020-07-03 RCSB
BDP 'Modify name' 2020-07-17 RCSB
BDP 'Modify synonyms' 2020-07-17 RCSB
BDP 'Modify atom id' 2020-07-17 RCSB
BDP 'Modify component atom id' 2020-07-17 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id BDP
_pdbe_chem_comp_drugbank_details.drugbank_id DB03156
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'beta-D-glucuronic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 23018-83-9
_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
BDP 'beta-D-glucuronic acid' wwPDB ?
BDP 'D-glucuronic acid' wwPDB ?
BDP 'glucuronic acid' wwPDB ?
BDP 'beta-D-Glucopyranuronic acid' DrugBank ?
BDP GlcAb DrugBank ?
BDP 'GlcAβ' DrugBank ?
BDP 'β-D-glucopyranuronic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id BDP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03156
_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_
_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
BDP DB03156 'Hyaluronate lyase' 'Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)' Q54873 unknown 1
BDP DB03156 Chondroitinase-AC 'Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / NCIB 9290)' Q59288 unknown 2
BDP DB03156 'Xylan alpha-1,2-glucuronidase' 'Geobacillus stearothermophilus' Q8VVD2 unknown 3
#
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
BDP C1 C 8.196 0.750 1
BDP C2 C 8.196 -0.750 2
BDP C3 C 6.897 -1.500 3
BDP C4 C 5.598 -0.750 4
BDP C5 C 5.598 0.750 5
BDP C6 C 4.299 1.500 6
BDP O2 O 9.495 -1.500 7
BDP O3 O 6.897 -3.000 8
BDP O4 O 4.299 -1.500 9
BDP O5 O 6.897 1.500 10
BDP O6A O 4.299 3.000 11
BDP O1 O 9.495 1.500 12
BDP O6B 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
BDP C1 C2 SINGLE NONE 1
BDP C1 O5 SINGLE NONE 2
BDP C1 O1 SINGLE BEGINWEDGE 3
BDP C2 C3 SINGLE NONE 4
BDP C2 O2 SINGLE BEGINDASH 5
BDP C3 C4 SINGLE NONE 6
BDP C3 O3 SINGLE BEGINWEDGE 7
BDP C4 C5 SINGLE NONE 8
BDP C4 O4 SINGLE BEGINDASH 9
BDP C5 C6 SINGLE BEGINWEDGE 10
BDP C5 O5 SINGLE NONE 11
BDP C6 O6A DOUBLE NONE 12
BDP C6 O6B SINGLE 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
BDP MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
BDP 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
BDP C1 S1 1
BDP C2 S1 1
BDP C3 S1 1
BDP C4 S1 1
BDP C5 S1 1
BDP O5 S1 1
BDP C4 F1 1
BDP C5 F1 1
BDP O5 F1 1
BDP C1 F1 1
BDP C2 F1 1
BDP C3 F1 1
BDP O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id BDP
_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
BDP UniChem ChEMBL CHEMBL1159524
BDP UniChem DrugBank DB03156
BDP UniChem PDBe BDP
BDP UniChem 'KEGG LIGAND' C08350
BDP UniChem ChEBI 28860
BDP UniChem ZINC ZINC000004097543
BDP UniChem eMolecules 30069645
BDP UniChem fdasrs 00A9JB14O6
BDP UniChem SureChEMBL SCHEMBL5975
BDP UniChem 'PubChem TPHARMA' 15265971
BDP UniChem MetaboLights MTBLC28860
BDP UniChem BRENDA 131501
BDP UniChem BRENDA 8590
BDP UniChem BRENDA 96212
BDP UniChem 'Probes And Drugs' PD007337
BDP UniChem Nikkaji J283.110D
BDP UniChem PubChem 441478
#
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
BDP C1 -0.881 1.386 0.181 ETKDGv3 1
BDP C2 -1.603 0.109 -0.306 ETKDGv3 2
BDP C3 -0.881 -1.133 0.248 ETKDGv3 3
BDP C4 0.630 -1.053 -0.050 ETKDGv3 4
BDP C5 1.182 0.317 0.407 ETKDGv3 5
BDP C6 2.633 0.431 0.045 ETKDGv3 6
BDP O2 -2.934 0.103 0.141 ETKDGv3 7
BDP O3 -1.436 -2.314 -0.277 ETKDGv3 8
BDP O4 1.315 -2.114 0.571 ETKDGv3 9
BDP O5 0.476 1.370 -0.229 ETKDGv3 10
BDP O6A 3.519 0.281 0.929 ETKDGv3 11
BDP O1 -1.493 2.514 -0.387 ETKDGv3 12
BDP O6B 3.004 0.668 -1.276 ETKDGv3 13
BDP H1 -0.944 1.458 1.296 ETKDGv3 14
BDP H2 -1.568 0.079 -1.422 ETKDGv3 15
BDP H3 -1.024 -1.153 1.352 ETKDGv3 16
BDP H4 0.780 -1.144 -1.149 ETKDGv3 17
BDP H5 1.097 0.411 1.516 ETKDGv3 18
BDP HO2 -3.464 0.621 -0.519 ETKDGv3 19
BDP HO3 -1.312 -2.295 -1.262 ETKDGv3 20
BDP HO4 1.203 -2.012 1.552 ETKDGv3 21
BDP HO1 -2.280 2.736 0.177 ETKDGv3 22
BDP HO6B 3.981 0.734 -1.537 ETKDGv3 23
#