data_GCO
#
_chem_comp.id GCO
_chem_comp.name "D-gluconic acid"
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H12 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "GLUCONIC 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 196.155
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GCO
_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 1BGG
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id GCO
_pdbx_chem_comp_synonyms.name "GLUCONIC ACID"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
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
GCO C1 C1 C 0 1 N N N N N N 35.358 82.667 58.132 -0.362 0.157 -2.895 C1 GCO 1
GCO C2 C2 C 0 1 N N R N N N 36.519 82.145 57.697 0.321 0.635 -1.640 C2 GCO 2
GCO C3 C3 C 0 1 N N S N N N 37.053 80.904 58.152 -0.340 -0.008 -0.421 C3 GCO 3
GCO C4 C4 C 0 1 N N R N N N 37.489 81.016 59.588 0.354 0.477 0.852 C4 GCO 4
GCO C5 C5 C 0 1 N N R N N N 36.726 80.009 60.378 -0.308 -0.166 2.072 C5 GCO 5
GCO C6 C6 C 0 1 N N N N N N 37.321 79.615 61.685 0.386 0.319 3.345 C6 GCO 6
GCO O1A O11 O 0 1 N N N N N N 35.281 83.861 57.459 0.267 -0.436 -3.738 O1A GCO 7
GCO O1B O12 O 0 1 N N N N N N 35.683 83.153 59.283 -1.671 0.390 -3.076 O1B GCO 8
GCO O2 O2 O 0 1 N N N N N N 36.083 81.997 56.407 1.702 0.269 -1.681 O2 GCO 9
GCO O3 O3 O 0 1 N N N N N N 38.088 80.675 57.235 -0.227 -1.430 -0.512 O3 GCO 10
GCO O4 O4 O 0 1 N N N N N N 38.862 80.701 59.740 1.734 0.111 0.811 O4 GCO 11
GCO O5 O5 O 0 1 N N N N N N 35.480 80.691 60.720 -1.689 0.199 2.113 O5 GCO 12
GCO O6 O6 O 0 1 N N N N N N 38.043 80.656 62.306 -0.232 -0.282 4.485 O6 GCO 13
GCO H2 H2 H 0 1 N N N N N N 37.380 82.775 58.016 0.235 1.719 -1.570 H2 GCO 14
GCO H3 H3 H 0 1 N N N N N N 36.337 80.048 58.173 -1.393 0.271 -0.389 H3 GCO 15
GCO H4 H4 H 0 1 N N N N N N 37.309 82.062 59.928 0.267 1.561 0.922 H4 GCO 16
GCO H5 H5 H 0 1 N N N N N N 36.663 79.080 59.763 -0.222 -1.250 2.002 H5 GCO 17
GCO H61 H61 H 0 1 N N N N N N 36.539 79.211 62.370 0.300 1.403 3.415 H61 GCO 18
GCO H62 H62 H 0 1 N N N N N N 37.955 78.705 61.573 1.439 0.039 3.314 H62 GCO 19
GCO HO1B HO1 H 0 0 N N N N N N 34.863 83.521 59.590 -2.111 0.083 -3.881 HO1B GCO 20
GCO HO2 HO2 H 0 1 N N N N N N 36.902 81.628 56.099 1.733 -0.695 -1.743 HO2 GCO 21
GCO HO3 HO3 H 0 1 N N N N N N 38.443 79.848 57.538 0.717 -1.634 -0.537 HO3 GCO 22
GCO HO4 HO4 H 0 1 N N N N N N 39.137 80.771 60.646 1.766 -0.853 0.749 HO4 GCO 23
GCO HO5 HO5 H 0 1 N N N N N N 34.993 80.049 61.223 -1.720 1.164 2.174 HO5 GCO 24
GCO HO6 HO6 H 0 1 N N N N N N 38.422 80.404 63.139 0.234 0.049 5.264 HO6 GCO 25
#
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
GCO C1 C2 SING N N 1
GCO C1 O1A DOUB N N 2
GCO C1 O1B SING N N 3
GCO C2 C3 SING N N 4
GCO C2 O2 SING N N 5
GCO C2 H2 SING N N 6
GCO C3 C4 SING N N 7
GCO C3 O3 SING N N 8
GCO C3 H3 SING N N 9
GCO C4 C5 SING N N 10
GCO C4 O4 SING N N 11
GCO C4 H4 SING N N 12
GCO C5 C6 SING N N 13
GCO C5 O5 SING N N 14
GCO C5 H5 SING N N 15
GCO C6 O6 SING N N 16
GCO C6 H61 SING N N 17
GCO C6 H62 SING N N 18
GCO O1B HO1B SING N N 19
GCO O2 HO2 SING N N 20
GCO O3 HO3 SING N N 21
GCO O4 HO4 SING N N 22
GCO O5 HO5 SING N N 23
GCO 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
GCO SMILES ACDLabs 10.04 O=C(O)C(O)C(O)C(O)C(O)CO
GCO SMILES_CANONICAL CACTVS 3.341 OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O
GCO SMILES CACTVS 3.341 OC[CH](O)[CH](O)[CH](O)[CH](O)C(O)=O
GCO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)O
GCO SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(C(C(C(=O)O)O)O)O)O)O
GCO InChI InChI 1.03 InChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)/t2-,3-,4+,5-/m1/s1
GCO InChIKey InChI 1.03 RGHNJXZEOKUKBD-SQOUGZDYSA-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
GCO "SYSTEMATIC NAME" ACDLabs 10.04 "D-gluconic acid"
GCO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3S,4R,5R)-2,3,4,5,6-pentahydroxyhexanoic acid"
#
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
GCO "CARBOHYDRATE ISOMER" D PDB ?
GCO "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
GCO 'Create component' 1999-07-08 RCSB
GCO 'Modify descriptor' 2011-06-04 RCSB
GCO 'Other modification' 2020-07-03 RCSB
GCO 'Modify name' 2020-07-17 RCSB
GCO 'Modify synonyms' 2020-07-17 RCSB
GCO 'Modify linking type' 2020-07-17 RCSB
GCO 'Modify atom id' 2020-07-17 RCSB
GCO 'Modify component atom id' 2020-07-17 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id GCO
_pdbe_chem_comp_drugbank_details.drugbank_id DB13180
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Gluconic Acid'
_pdbe_chem_comp_drugbank_details.description
'Commonly found in salts with sodium and calcium. Gluconic acid or gluconate is used to maintain the cation-anion balance on electrolyte solutions.'
_pdbe_chem_comp_drugbank_details.cas_number 526-95-4
_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
GCO 'GLUCONIC ACID' wwPDB ?
GCO 'D-Gluconic Acid' DrugBank ?
GCO 'Dextronic acid' DrugBank ?
GCO 'Maltonic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GCO
_pdbe_chem_comp_drugbank_classification.drugbank_id DB13180
_pdbe_chem_comp_drugbank_classification.parent 'Sugar acids and 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 sugar acids and derivatives. These are compounds containing a saccharide unit which bears a carboxylic acid group.'
#
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
GCO C1 C 5.104 -0.375 1
GCO C2 C 6.404 0.375 2
GCO C3 C 7.702 -0.375 3
GCO C4 C 9.002 0.375 4
GCO C5 C 10.301 -0.375 5
GCO C6 C 11.600 0.375 6
GCO O1A O 3.805 0.375 7
GCO O1B O 5.104 -1.875 8
GCO O2 O 6.404 1.875 9
GCO O3 O 7.702 -1.875 10
GCO O4 O 9.002 1.875 11
GCO O5 O 10.301 -1.875 12
GCO O6 O 12.899 -0.375 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
GCO C1 C2 SINGLE NONE 1
GCO C1 O1A DOUBLE NONE 2
GCO C1 O1B SINGLE NONE 3
GCO C2 C3 SINGLE NONE 4
GCO C2 O2 SINGLE BEGINDASH 5
GCO C3 C4 SINGLE NONE 6
GCO C3 O3 SINGLE BEGINDASH 7
GCO C4 C5 SINGLE NONE 8
GCO C4 O4 SINGLE BEGINDASH 9
GCO C5 C6 SINGLE NONE 10
GCO C5 O5 SINGLE BEGINWEDGE 11
GCO C6 O6 SINGLE NONE 12
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id GCO
_pdbe_chem_comp_rdkit_properties.exactmw 196.058
_pdbe_chem_comp_rdkit_properties.amw 196.155
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_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 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 90.871
_pdbe_chem_comp_rdkit_properties.tpsa 138.450
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.493
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.749
_pdbe_chem_comp_rdkit_properties.chi0v 5.858
_pdbe_chem_comp_rdkit_properties.chi1v 2.679
_pdbe_chem_comp_rdkit_properties.chi2v 0.897
_pdbe_chem_comp_rdkit_properties.chi3v 0.897
_pdbe_chem_comp_rdkit_properties.chi4v 0.345
_pdbe_chem_comp_rdkit_properties.chi0n 17.858
_pdbe_chem_comp_rdkit_properties.chi1n 8.128
_pdbe_chem_comp_rdkit_properties.chi2n 0.897
_pdbe_chem_comp_rdkit_properties.chi3n 0.897
_pdbe_chem_comp_rdkit_properties.chi4n 0.345
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.730
_pdbe_chem_comp_rdkit_properties.kappa1 2.878
_pdbe_chem_comp_rdkit_properties.kappa2 5.098
_pdbe_chem_comp_rdkit_properties.kappa3 3.247
_pdbe_chem_comp_rdkit_properties.Phi 1.129
#
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
GCO UniChem DrugBank DB13180
GCO UniChem 'KEGG LIGAND' C00257
GCO UniChem ChEBI 33198
GCO UniChem ZINC ZINC000001531008
GCO UniChem eMolecules 514559
GCO UniChem fdasrs R4R8J0Q44B
GCO UniChem SureChEMBL SCHEMBL971
GCO UniChem PharmGKB PA449770
GCO UniChem HMDB HMDB0000625
GCO UniChem 'PubChem TPHARMA' 16703474
GCO UniChem NMRShiftDB 60019532
GCO UniChem Nikkaji J3.286G
GCO UniChem 'EPA CompTox Dashboard' DTXSID8027169
GCO UniChem 'EPA CompTox Dashboard' DTXSID8042000
GCO UniChem DrugCentral 3264
GCO UniChem MetaboLights MTBLC33198
GCO UniChem BRENDA 108654
GCO UniChem BRENDA 4525
GCO UniChem BRENDA 6505
GCO UniChem BRENDA 698
GCO UniChem BRENDA 96548
GCO UniChem ChemicalBook CB2252915
GCO UniChem MedChemExpress HY-Y0569
GCO UniChem 'Probes And Drugs' PD014403
GCO UniChem CCDC CAKZAP
GCO UniChem 'PubChem TPHARMA' 16118822
GCO UniChem PubChem 10690
GCO UniChem ChemicalBook CB9965678
#
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
GCO C1 -1.776 0.911 -0.890 ETKDGv3 1
GCO C2 -1.842 -0.504 -0.392 ETKDGv3 2
GCO C3 -0.792 -0.782 0.727 ETKDGv3 3
GCO C4 0.629 -1.148 0.188 ETKDGv3 4
GCO C5 1.358 -0.037 -0.620 ETKDGv3 5
GCO C6 1.670 1.236 0.191 ETKDGv3 6
GCO O1A -1.650 1.142 -2.122 ETKDGv3 7
GCO O1B -1.912 1.972 0.001 ETKDGv3 8
GCO O2 -3.141 -0.714 0.101 ETKDGv3 9
GCO O3 -1.247 -1.823 1.559 ETKDGv3 10
GCO O4 1.448 -1.614 1.234 ETKDGv3 11
GCO O5 2.537 -0.552 -1.188 ETKDGv3 12
GCO O6 2.287 2.179 -0.640 ETKDGv3 13
GCO H2 -1.652 -1.192 -1.251 ETKDGv3 14
GCO H3 -0.712 0.113 1.378 ETKDGv3 15
GCO H4 0.496 -2.004 -0.511 ETKDGv3 16
GCO H5 0.710 0.255 -1.469 ETKDGv3 17
GCO H61 2.348 0.994 1.039 ETKDGv3 18
GCO H62 0.734 1.673 0.597 ETKDGv3 19
GCO HO1B -1.883 2.931 -0.324 ETKDGv3 20
GCO HO2 -3.366 -1.668 -0.055 ETKDGv3 21
GCO HO3 -1.308 -2.645 1.004 ETKDGv3 22
GCO HO4 1.426 -0.938 1.961 ETKDGv3 23
GCO HO5 3.167 -0.757 -0.448 ETKDGv3 24
GCO HO6 2.470 2.972 -0.072 ETKDGv3 25
#