data_GCU
#
_chem_comp.id GCU
_chem_comp.name "alpha-D-glucopyranuronic 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-glucuronic acid; D-glucuronic acid; glucuronic acid"
_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 194.139
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GCU
_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 1DBO
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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 GCU "alpha-D-glucuronic acid" PDB ?
2 GCU "D-glucuronic acid" PDB ?
3 GCU "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
GCU C1 C1 C 0 1 N N S N N N 39.729 20.518 29.321 1.509 -0.087 -1.086 C1 GCU 1
GCU C2 C2 C 0 1 N N R N N N 39.080 20.336 30.727 0.272 -0.527 -1.873 C2 GCU 2
GCU C3 C3 C 0 1 N N S N N N 40.146 20.692 31.763 -0.970 0.115 -1.253 C3 GCU 3
GCU C4 C4 C 0 1 N N S N N N 41.360 19.767 31.557 -0.999 -0.216 0.242 C4 GCU 4
GCU C5 C5 C 0 1 N N S N N N 41.946 19.940 30.133 0.332 0.199 0.871 C5 GCU 5
GCU C6 C6 C 0 1 N N N N N N 43.143 19.019 29.872 0.300 -0.093 2.349 C6 GCU 6
GCU O1 O1 O 0 1 N Y N N N N 40.076 21.907 29.105 1.609 1.337 -1.116 O1 GCU 7
GCU O2 O2 O 0 1 N N N N N N 37.968 21.229 30.860 0.399 -0.109 -3.234 O2 GCU 8
GCU O3 O3 O 0 1 N N N N N N 39.649 20.463 33.087 -2.146 -0.400 -1.881 O3 GCU 9
GCU O4 O4 O 0 1 N N N N N N 42.393 20.112 32.486 -2.067 0.493 0.871 O4 GCU 10
GCU O5 O5 O 0 1 N N N N N N 40.885 19.632 29.179 1.400 -0.526 0.266 O5 GCU 11
GCU O6A O6A O 0 1 N N N N N N 44.364 19.572 30.019 1.110 -0.848 2.832 O6A GCU 12
GCU O6B O6B O 0 1 N N N N N N 43.020 17.856 29.565 -0.627 0.483 3.128 O6B GCU 13
GCU H1 H1 H 0 1 N N N N N N 38.992 20.233 28.533 2.400 -0.523 -1.538 H1 GCU 14
GCU H2 H2 H 0 1 N N N N N N 38.717 19.290 30.867 0.181 -1.612 -1.832 H2 GCU 15
GCU H3 H3 H 0 1 N N N N N N 40.422 21.765 31.641 -0.929 1.196 -1.387 H3 GCU 16
GCU H4 H4 H 0 1 N N N N N N 41.016 18.716 31.707 -1.146 -1.288 0.375 H4 GCU 17
GCU H5 H5 H 0 1 N N N N N N 42.313 20.987 30.025 0.487 1.267 0.717 H5 GCU 18
GCU HO1 HO1 H 0 1 N Y N N N N 40.471 22.017 28.248 2.400 1.572 -0.612 HO1 GCU 19
GCU HO2 HO2 H 0 1 N Y N N N N 37.572 21.118 31.716 1.192 -0.536 -3.585 HO2 GCU 20
GCU HO3 HO3 H 0 1 N Y N N N N 40.311 20.684 33.730 -2.086 -0.169 -2.818 HO3 GCU 21
GCU HO4 HO4 H 0 1 N Y N N N N 43.141 19.541 32.358 -2.044 0.260 1.809 HO4 GCU 22
GCU HO6B HOB H 0 0 N N N N N N 43.761 17.285 29.403 -0.648 0.295 4.076 HO6B GCU 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
GCU C1 C2 SING N N 1
GCU C1 O1 SING N N 2
GCU C1 O5 SING N N 3
GCU C1 H1 SING N N 4
GCU C2 C3 SING N N 5
GCU C2 O2 SING N N 6
GCU C2 H2 SING N N 7
GCU C3 C4 SING N N 8
GCU C3 O3 SING N N 9
GCU C3 H3 SING N N 10
GCU C4 C5 SING N N 11
GCU C4 O4 SING N N 12
GCU C4 H4 SING N N 13
GCU C5 C6 SING N N 14
GCU C5 O5 SING N N 15
GCU C5 H5 SING N N 16
GCU C6 O6A DOUB N N 17
GCU C6 O6B SING N N 18
GCU O1 HO1 SING N N 19
GCU O2 HO2 SING N N 20
GCU O3 HO3 SING N N 21
GCU O4 HO4 SING N N 22
GCU 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
GCU SMILES ACDLabs 10.04 O=C(O)C1OC(O)C(O)C(O)C1O
GCU SMILES_CANONICAL CACTVS 3.341 O[C@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(O)=O
GCU SMILES CACTVS 3.341 O[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(O)=O
GCU 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"
GCU SMILES "OpenEye OEToolkits" 1.5.0 C1(C(C(OC(C1O)O)C(=O)O)O)O
GCU 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
GCU InChIKey InChI 1.03 AEMOLEFTQBMNLQ-WAXACMCWSA-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
GCU "SYSTEMATIC NAME" ACDLabs 10.04 "alpha-D-glucopyranuronic acid"
GCU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3S,4S,5R,6S)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid"
GCU "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DGlcpAa
GCU "COMMON NAME" GMML 1.0 "a-D-glucopyranuronic acid"
GCU "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 a-D-GlcpA
GCU "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
GCU "CARBOHYDRATE ISOMER" D PDB ?
GCU "CARBOHYDRATE RING" pyranose PDB ?
GCU "CARBOHYDRATE ANOMER" alpha PDB ?
GCU "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
GCU 'Create component' 1999-07-08 RCSB
GCU 'Modify descriptor' 2011-06-04 RCSB
GCU 'Other modification' 2019-08-12 RCSB
GCU 'Other modification' 2019-12-19 RCSB
GCU 'Other modification' 2020-07-03 RCSB
GCU 'Modify name' 2020-07-17 RCSB
GCU 'Modify synonyms' 2020-07-17 RCSB
GCU 'Modify atom id' 2020-07-17 RCSB
GCU 'Modify component atom id' 2020-07-17 RCSB
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
GCU 'alpha-D-glucuronic acid' wwPDB ?
GCU 'D-glucuronic acid' wwPDB ?
GCU 'glucuronic acid' wwPDB ?
#
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
GCU C1 C 8.196 0.750 1
GCU C2 C 8.196 -0.750 2
GCU C3 C 6.897 -1.500 3
GCU C4 C 5.598 -0.750 4
GCU C5 C 5.598 0.750 5
GCU C6 C 4.299 1.500 6
GCU O1 O 9.495 1.500 7
GCU O2 O 9.495 -1.500 8
GCU O3 O 6.897 -3.000 9
GCU O4 O 4.299 -1.500 10
GCU O5 O 6.897 1.500 11
GCU O6A O 4.299 3.000 12
GCU 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
GCU C1 C2 SINGLE NONE 1
GCU C1 O1 SINGLE BEGINDASH 2
GCU C1 O5 SINGLE NONE 3
GCU C2 C3 SINGLE NONE 4
GCU C2 O2 SINGLE BEGINDASH 5
GCU C3 C4 SINGLE NONE 6
GCU C3 O3 SINGLE BEGINWEDGE 7
GCU C4 C5 SINGLE NONE 8
GCU C4 O4 SINGLE BEGINDASH 9
GCU C5 C6 SINGLE BEGINWEDGE 10
GCU C5 O5 SINGLE NONE 11
GCU C6 O6A DOUBLE NONE 12
GCU 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
GCU MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
GCU 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
GCU C1 S1 1
GCU C2 S1 1
GCU C3 S1 1
GCU C4 S1 1
GCU C5 S1 1
GCU O5 S1 1
GCU C4 F1 1
GCU C5 F1 1
GCU O5 F1 1
GCU C1 F1 1
GCU C2 F1 1
GCU C3 F1 1
GCU O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GCU
_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
GCU UniChem PDBe GCU
GCU UniChem ChEBI 42717
GCU UniChem ZINC ZINC000004213449
GCU UniChem fdasrs M7Y086VB5G
GCU UniChem SureChEMBL SCHEMBL6851
GCU UniChem HMDB HMDB0000127
GCU UniChem NMRShiftDB 60078575
GCU UniChem MetaboLights MTBLC42717
GCU UniChem BRENDA 121799
GCU UniChem BRENDA 131205
GCU UniChem BRENDA 20112
GCU UniChem BRENDA 45302
GCU UniChem BRENDA 96106
GCU UniChem Nikkaji J822.123E
GCU UniChem 'PubChem TPHARMA' 16878122
GCU UniChem PubChem 444791
#
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
GCU C1 -0.076 1.531 -0.031 ETKDGv3 1
GCU C2 -1.379 0.714 -0.098 ETKDGv3 2
GCU C3 -1.056 -0.769 -0.352 ETKDGv3 3
GCU C4 0.004 -1.271 0.653 ETKDGv3 4
GCU C5 1.205 -0.294 0.744 ETKDGv3 5
GCU C6 2.170 -0.378 -0.419 ETKDGv3 6
GCU O1 -0.377 2.871 0.254 ETKDGv3 7
GCU O2 -2.089 0.863 1.106 ETKDGv3 8
GCU O3 -0.593 -0.924 -1.669 ETKDGv3 9
GCU O4 -0.572 -1.394 1.930 ETKDGv3 10
GCU O5 0.781 1.041 0.990 ETKDGv3 11
GCU O6A 2.315 -1.454 -1.059 ETKDGv3 12
GCU O6B 2.974 0.716 -0.727 ETKDGv3 13
GCU H1 0.439 1.492 -1.020 ETKDGv3 14
GCU H2 -1.996 1.100 -0.943 ETKDGv3 15
GCU H3 -1.993 -1.360 -0.228 ETKDGv3 16
GCU H4 0.371 -2.275 0.334 ETKDGv3 17
GCU H5 1.799 -0.608 1.629 ETKDGv3 18
GCU HO1 -0.765 3.264 -0.572 ETKDGv3 19
GCU HO2 -3.020 0.566 0.929 ETKDGv3 20
GCU HO3 -0.651 -1.892 -1.882 ETKDGv3 21
GCU HO4 -1.139 -2.209 1.915 ETKDGv3 22
GCU HO6B 3.646 0.671 -1.483 ETKDGv3 23
#