data_GC1
#
_chem_comp.id GC1
_chem_comp.name "2,6-anhydro-L-gulonic acid"
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H10 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "1-deoxy-D-glucuronic acid"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-03-21
_chem_comp.pdbx_modified_date 2020-07-17
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 178.140
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GC1
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye OEToolkits"
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id GC1
_pdbx_chem_comp_synonyms.name "1-deoxy-D-glucuronic 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
GC1 O4 O4 O 0 1 N N N N N N -8.953 3.989 3.877 0.911 -1.974 -3.027 O4 GC1 1
GC1 C1 C1 C 0 1 N N N N N N -5.295 2.077 3.949 3.861 0.585 -1.707 C1 GC1 2
GC1 C2 C2 C 0 1 N N N N N N -5.899 2.165 2.546 4.358 -0.609 -2.508 C2 GC1 3
GC1 C3 C3 C 0 1 N N N N N N -7.059 3.182 2.524 3.197 -1.298 -3.222 C3 GC1 4
GC1 C4 C4 C 0 1 N N N N N N -8.044 2.897 3.676 2.045 -1.583 -2.255 C4 GC1 5
GC1 C5 C5 C 0 1 N N N N N N -7.285 2.757 5.008 1.706 -0.344 -1.429 C5 GC1 6
GC1 C6 C6 C 0 1 N N N N N N -8.263 2.401 6.135 0.808 -0.688 -0.286 C6 GC1 7
GC1 O2 O2 O 0 1 N N N N N N -4.864 2.596 1.658 5.312 -0.153 -3.461 O2 GC1 8
GC1 O3 O3 O 0 1 N N N N N N -7.749 2.999 1.280 3.670 -2.530 -3.767 O3 GC1 9
GC1 O5 O5 O 0 1 N N N N N N -6.305 1.725 4.886 2.859 0.185 -0.779 O5 GC1 10
GC1 O6B O6A O 0 1 N N N N N N -8.520 3.375 7.027 -0.384 -1.152 -0.736 O6B GC1 11
GC1 O6A O6B O 0 1 N N N N N N -8.781 1.310 6.246 1.099 -0.572 0.895 O6A GC1 12
GC1 H1A H1 H 0 1 N N N N N N -4.869 3.053 4.223 4.690 1.030 -1.146 H1A GC1 13
GC1 H2 H2 H 0 1 N N N N N N -6.296 1.186 2.240 4.864 -1.324 -1.850 H2 GC1 14
GC1 H3 H3 H 0 1 N N N N N N -6.671 4.205 2.636 2.853 -0.699 -4.074 H3 GC1 15
GC1 H4 H4 H 0 1 N N N N N N -8.580 1.977 3.398 2.304 -2.430 -1.608 H4 GC1 16
GC1 H5 H5 H 0 1 N N N N N N -6.794 3.712 5.247 1.207 0.432 -2.022 H5 GC1 17
GC1 H1 H11 H 0 1 N N N N N N -4.505 1.311 3.959 3.472 1.377 -2.360 H1 GC1 18
GC1 HO4 HO4 H 0 1 N Y N N N N -9.154 4.068 4.802 1.228 -2.108 -3.932 HO4 GC1 19
GC1 HO2 HO2 H 0 1 N Y N N N N -5.218 2.692 0.781 5.772 -0.941 -3.792 HO2 GC1 20
GC1 HO3 HO3 H 0 1 N Y N N N N -8.685 2.959 1.439 4.445 -2.781 -3.243 HO3 GC1 21
GC1 HO6B HO6A H 0 0 N N N N N N -9.126 3.052 7.683 -0.988 -1.385 0.001 HO6B GC1 22
#
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
GC1 O4 C4 SING N N 1
GC1 O4 HO4 SING N N 2
GC1 C1 C2 SING N N 3
GC1 C1 H1 SING N N 4
GC1 C1 H1A SING N N 5
GC1 C1 O5 SING N N 6
GC1 C2 O2 SING N N 7
GC1 C2 H2 SING N N 8
GC1 C2 C3 SING N N 9
GC1 C3 O3 SING N N 10
GC1 C3 H3 SING N N 11
GC1 C3 C4 SING N N 12
GC1 C4 H4 SING N N 13
GC1 C4 C5 SING N N 14
GC1 C5 O5 SING N N 15
GC1 C5 H5 SING N N 16
GC1 C5 C6 SING N N 17
GC1 C6 O6A DOUB N N 18
GC1 C6 O6B SING N N 19
GC1 O2 HO2 SING N N 20
GC1 O3 HO3 SING N N 21
GC1 O6B HO6B SING N N 22
#
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
GC1 SMILES ACDLabs 10.04 O=C(O)C1OCC(O)C(O)C1O
GC1 SMILES_CANONICAL CACTVS 3.341 O[C@H]1CO[C@@H]([C@@H](O)[C@@H]1O)C(O)=O
GC1 SMILES CACTVS 3.341 O[CH]1CO[CH]([CH](O)[CH]1O)C(O)=O
GC1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@@H]([C@H]([C@@H]([C@H](O1)C(=O)O)O)O)O
GC1 SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(C(C(O1)C(=O)O)O)O)O
GC1 InChI InChI 1.03 InChI=1S/C6H10O6/c7-2-1-12-5(6(10)11)4(9)3(2)8/h2-5,7-9H,1H2,(H,10,11)/t2-,3+,4-,5-/m0/s1
GC1 InChIKey InChI 1.03 KYIOVQZVBFQNEB-QTBDOELSSA-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
GC1 "SYSTEMATIC NAME" ACDLabs 10.04 "2,6-anhydro-L-gulonic acid"
GC1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3S,4R,5S)-3,4,5-trihydroxyoxane-2-carboxylic 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
GC1 "CARBOHYDRATE ISOMER" D PDB ?
GC1 "CARBOHYDRATE RING" pyranose PDB ?
GC1 "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
GC1 'Create component' 2007-03-21 RCSB
GC1 'Modify descriptor' 2011-06-04 RCSB
GC1 'Other modification' 2020-07-03 RCSB
GC1 'Modify name' 2020-07-17 RCSB
GC1 'Modify synonyms' 2020-07-17 RCSB
GC1 'Modify linking type' 2020-07-17 RCSB
GC1 'Modify atom id' 2020-07-17 RCSB
GC1 'Modify component atom id' 2020-07-17 RCSB
GC1 'Modify leaving atom flag' 2020-07-17 RCSB
#
_pdbe_chem_comp_synonyms.comp_id GC1
_pdbe_chem_comp_synonyms.name '1-deoxy-D-glucuronic acid'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
GC1 O4 O 6.404 2.482 1
GC1 C1 C 6.404 -2.018 2
GC1 C2 C 5.104 -1.268 3
GC1 C3 C 5.104 0.233 4
GC1 C4 C 6.404 0.983 5
GC1 C5 C 7.702 0.233 6
GC1 C6 C 9.002 0.983 7
GC1 O2 O 3.805 -2.018 8
GC1 O3 O 3.805 0.983 9
GC1 O5 O 7.702 -1.268 10
GC1 O6B O 9.002 2.482 11
GC1 O6A O 10.301 0.233 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
GC1 C4 O4 SINGLE BEGINDASH 1
GC1 C1 C2 SINGLE NONE 2
GC1 C1 O5 SINGLE NONE 3
GC1 C2 O2 SINGLE BEGINDASH 4
GC1 C2 C3 SINGLE NONE 5
GC1 C3 O3 SINGLE BEGINWEDGE 6
GC1 C3 C4 SINGLE NONE 7
GC1 C4 C5 SINGLE NONE 8
GC1 C5 O5 SINGLE NONE 9
GC1 C5 C6 SINGLE BEGINWEDGE 10
GC1 C6 O6A DOUBLE NONE 11
GC1 C6 O6B SINGLE NONE 12
#
_pdbe_chem_comp_substructure.comp_id GC1
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles C1CCOCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2
_pdbe_chem_comp_substructure.substructure_inchikeys DHXVGJBLRPWPCS-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
GC1 C1 S1 1
GC1 C2 S1 1
GC1 C3 S1 1
GC1 C4 S1 1
GC1 C5 S1 1
GC1 O5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GC1
_pdbe_chem_comp_rdkit_properties.exactmw 178.048
_pdbe_chem_comp_rdkit_properties.amw 178.140
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 82.407
_pdbe_chem_comp_rdkit_properties.tpsa 107.220
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.447
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.396
_pdbe_chem_comp_rdkit_properties.chi0v 5.449
_pdbe_chem_comp_rdkit_properties.chi1v 2.679
_pdbe_chem_comp_rdkit_properties.chi2v 1.050
_pdbe_chem_comp_rdkit_properties.chi3v 1.050
_pdbe_chem_comp_rdkit_properties.chi4v 0.531
_pdbe_chem_comp_rdkit_properties.chi0n 15.449
_pdbe_chem_comp_rdkit_properties.chi1n 7.312
_pdbe_chem_comp_rdkit_properties.chi2n 1.050
_pdbe_chem_comp_rdkit_properties.chi3n 1.050
_pdbe_chem_comp_rdkit_properties.chi4n 0.531
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.690
_pdbe_chem_comp_rdkit_properties.kappa1 2.647
_pdbe_chem_comp_rdkit_properties.kappa2 3.359
_pdbe_chem_comp_rdkit_properties.kappa3 1.559
_pdbe_chem_comp_rdkit_properties.Phi 0.741
#
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
GC1 UniChem ZINC ZINC000016052237
GC1 UniChem SureChEMBL SCHEMBL4267050
GC1 UniChem PubChem 44176350
#
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
GC1 O4 1.355 -1.439 1.157 ETKDGv3 1
GC1 C1 -1.104 0.730 -1.303 ETKDGv3 2
GC1 C2 -1.838 0.113 -0.102 ETKDGv3 3
GC1 C3 -0.958 -0.975 0.569 ETKDGv3 4
GC1 C4 0.536 -0.820 0.194 ETKDGv3 5
GC1 C5 0.895 0.681 0.020 ETKDGv3 6
GC1 C6 2.341 0.824 -0.351 ETKDGv3 7
GC1 O2 -2.142 1.133 0.815 ETKDGv3 8
GC1 O3 -1.412 -2.265 0.240 ETKDGv3 9
GC1 O5 0.108 1.380 -0.944 ETKDGv3 10
GC1 O6B 3.272 1.193 0.615 ETKDGv3 11
GC1 O6A 2.719 0.581 -1.529 ETKDGv3 12
GC1 H1A -1.771 1.479 -1.779 ETKDGv3 13
GC1 H2 -2.787 -0.339 -0.475 ETKDGv3 14
GC1 H3 -1.059 -0.869 1.672 ETKDGv3 15
GC1 H4 0.722 -1.329 -0.778 ETKDGv3 16
GC1 H5 0.746 1.190 0.999 ETKDGv3 17
GC1 H1 -0.898 -0.047 -2.071 ETKDGv3 18
GC1 HO4 1.260 -0.933 2.006 ETKDGv3 19
GC1 HO2 -2.852 0.779 1.412 ETKDGv3 20
GC1 HO3 -1.388 -2.348 -0.750 ETKDGv3 21
GC1 HO6B 4.254 1.281 0.382 ETKDGv3 22
#