data_GKR
#
_chem_comp.id GKR
_chem_comp.name D-GLUCARATE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H8 O8"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge -2
_chem_comp.pdbx_initial_date 2001-06-26
_chem_comp.pdbx_modified_date 2011-06-04
_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 208.123
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GKR
_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 1JCT
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
GKR O1B O1B O 0 1 N N N N N N 24.248 14.487 20.122 3.443 -1.484 -0.474 O1B GKR 1
GKR O1A O1A O -1 1 N N N N N N 25.533 16.267 20.432 3.906 0.470 0.446 O1A GKR 2
GKR C1 C1 C 0 1 N N N N N N 24.417 15.681 20.513 3.115 -0.279 -0.218 C1 GKR 3
GKR C2 C2 C 0 1 N N R N N N 23.266 16.427 21.105 1.793 0.261 -0.700 C2 GKR 4
GKR O2 O2 O 0 1 N N N N N N 23.601 17.874 21.426 1.707 1.655 -0.393 O2 GKR 5
GKR C3 C3 C 0 1 N N S N N N 22.740 15.683 22.331 0.653 -0.485 -0.004 C3 GKR 6
GKR O3 O3 O 0 1 N N N N N N 23.754 15.500 23.308 0.822 -0.399 1.413 O3 GKR 7
GKR C4 C4 C 0 1 N N S N N N 21.517 16.359 22.954 -0.684 0.145 -0.397 C4 GKR 8
GKR O4 O4 O 0 1 N N N N N N 21.295 15.896 24.280 -0.657 1.544 -0.105 O4 GKR 9
GKR O5 O5 O 0 1 N N N N N N 20.390 15.652 20.832 -1.841 -1.917 0.100 O5 GKR 10
GKR C5 C5 C 0 1 N N S N N N 20.222 16.178 22.149 -1.813 -0.519 0.393 C5 GKR 11
GKR C6 C6 C 0 1 N N N N N N 19.425 17.446 22.106 -3.131 0.102 0.005 C6 GKR 12
GKR O6A O6A O 0 1 N N N N N N 19.999 18.569 22.214 -3.978 -0.569 -0.560 O6A GKR 13
GKR O6B O6B O -1 1 N N N N N N 18.182 17.359 21.952 -3.350 1.275 0.257 O6B GKR 14
GKR H21 1H2 H 0 1 N N N N N N 22.460 16.469 20.335 1.714 0.121 -1.778 H21 GKR 15
GKR HO21 1HO2 H 0 0 N N N N N N 22.869 18.348 21.802 1.781 1.734 0.568 HO21 GKR 16
GKR H31 1H3 H 0 1 N N N N N N 22.415 14.681 21.964 0.665 -1.532 -0.308 H31 GKR 17
GKR HO31 1HO3 H 0 0 N N N N N N 23.426 15.037 24.070 0.805 0.541 1.639 HO31 GKR 18
GKR H42 2H4 H 0 1 N N N N N N 21.762 17.446 22.952 -0.854 0.001 -1.464 H42 GKR 19
GKR H41 1H4 H 0 1 N N N N N N 20.535 16.315 24.666 -0.505 1.627 0.847 H41 GKR 20
GKR HO51 1HO5 H 0 0 N N N N N N 19.588 15.540 20.334 -1.993 -2.001 -0.851 HO51 GKR 21
GKR H51 1H5 H 0 1 N N N N N N 19.658 15.395 22.709 -1.644 -0.375 1.460 H51 GKR 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
GKR O1B C1 DOUB N N 1
GKR O1A C1 SING N N 2
GKR C1 C2 SING N N 3
GKR C2 O2 SING N N 4
GKR C2 C3 SING N N 5
GKR C2 H21 SING N N 6
GKR O2 HO21 SING N N 7
GKR C3 O3 SING N N 8
GKR C3 C4 SING N N 9
GKR C3 H31 SING N N 10
GKR O3 HO31 SING N N 11
GKR C4 O4 SING N N 12
GKR C4 C5 SING N N 13
GKR C4 H42 SING N N 14
GKR O4 H41 SING N N 15
GKR O5 C5 SING N N 16
GKR O5 HO51 SING N N 17
GKR C5 C6 SING N N 18
GKR C5 H51 SING N N 19
GKR C6 O6A DOUB N N 20
GKR C6 O6B SING N N 21
#
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
GKR SMILES ACDLabs 10.04 "[O-]C(=O)C(O)C(O)C(O)C(O)C([O-])=O"
GKR SMILES_CANONICAL CACTVS 3.341 O[C@@H]([C@H](O)[C@H](O)C([O-])=O)[C@@H](O)C([O-])=O
GKR SMILES CACTVS 3.341 O[CH]([CH](O)[CH](O)C([O-])=O)[CH](O)C([O-])=O
GKR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[C@H]([C@@H]([C@@H](C(=O)[O-])O)O)([C@H](C(=O)[O-])O)O"
GKR SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(C(=O)[O-])O)O)(C(C(=O)[O-])O)O
GKR InChI InChI 1.03 InChI=1S/C6H10O8/c7-1(3(9)5(11)12)2(8)4(10)6(13)14/h1-4,7-10H,(H,11,12)(H,13,14)/p-2/t1-,2-,3-,4+/m0/s1
GKR InChIKey InChI 1.03 DSLZVSRJTYRBFB-LLEIAEIESA-L
#
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
GKR "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanedioate (non-preferred name)"
GKR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanedioate
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GKR 'Create component' 2001-06-26 RCSB
GKR 'Modify descriptor' 2011-06-04 RCSB
#
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
GKR O1B O 3.000 0.375 1
GKR O1A O 4.299 -1.875 2
GKR C1 C 4.299 -0.375 3
GKR C2 C 5.598 0.375 4
GKR O2 O 5.598 1.875 5
GKR C3 C 6.897 -0.375 6
GKR O3 O 6.897 -1.875 7
GKR C4 C 8.196 0.375 8
GKR O4 O 8.196 1.875 9
GKR O5 O 9.495 -1.875 10
GKR C5 C 9.495 -0.375 11
GKR C6 C 10.794 0.375 12
GKR O6A O 12.093 -0.375 13
GKR O6B O 10.794 1.875 14
#
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
GKR O1B C1 DOUBLE NONE 1
GKR O1A C1 SINGLE NONE 2
GKR C1 C2 SINGLE NONE 3
GKR C2 O2 SINGLE BEGINDASH 4
GKR C2 C3 SINGLE NONE 5
GKR C3 O3 SINGLE BEGINDASH 6
GKR C3 C4 SINGLE NONE 7
GKR C4 O4 SINGLE BEGINDASH 8
GKR C4 C5 SINGLE NONE 9
GKR C5 O5 SINGLE BEGINWEDGE 10
GKR C5 C6 SINGLE NONE 11
GKR C6 O6A DOUBLE NONE 12
GKR C6 O6B SINGLE NONE 13
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id GKR
_pdbe_chem_comp_rdkit_properties.exactmw 208.023
_pdbe_chem_comp_rdkit_properties.amw 208.122
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 89.239
_pdbe_chem_comp_rdkit_properties.tpsa 161.180
_pdbe_chem_comp_rdkit_properties.CrippenClogP -6.070
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.041
_pdbe_chem_comp_rdkit_properties.chi0v 6.266
_pdbe_chem_comp_rdkit_properties.chi1v 2.883
_pdbe_chem_comp_rdkit_properties.chi2v 0.989
_pdbe_chem_comp_rdkit_properties.chi3v 0.989
_pdbe_chem_comp_rdkit_properties.chi4v 0.392
_pdbe_chem_comp_rdkit_properties.chi0n 14.266
_pdbe_chem_comp_rdkit_properties.chi1n 6.516
_pdbe_chem_comp_rdkit_properties.chi2n 0.989
_pdbe_chem_comp_rdkit_properties.chi3n 0.989
_pdbe_chem_comp_rdkit_properties.chi4n 0.392
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.220
_pdbe_chem_comp_rdkit_properties.kappa1 4.533
_pdbe_chem_comp_rdkit_properties.kappa2 4.862
_pdbe_chem_comp_rdkit_properties.kappa3 2.924
_pdbe_chem_comp_rdkit_properties.Phi 1.574
#
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
GKR UniChem ChEBI 30612
GKR UniChem Recon glcr
GKR UniChem MetaboLights MTBLC30612
GKR UniChem Rhea 30612
GKR UniChem CCDC CAGLAR
GKR UniChem PubChem 5288393
#
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
GKR O1B -3.036 1.520 -0.035 ETKDGv3 1
GKR O1A -2.273 1.413 2.121 ETKDGv3 2
GKR C1 -2.438 0.861 0.857 ETKDGv3 3
GKR C2 -1.886 -0.501 0.549 ETKDGv3 4
GKR O2 -2.345 -1.392 1.533 ETKDGv3 5
GKR C3 -0.334 -0.487 0.532 ETKDGv3 6
GKR O3 0.172 -1.795 0.409 ETKDGv3 7
GKR C4 0.249 0.449 -0.570 ETKDGv3 8
GKR O4 -0.230 0.098 -1.846 ETKDGv3 9
GKR O5 2.373 -0.721 -0.789 ETKDGv3 10
GKR C5 1.797 0.543 -0.571 ETKDGv3 11
GKR C6 2.310 1.142 0.711 ETKDGv3 12
GKR O6A 2.690 0.402 1.657 ETKDGv3 13
GKR O6B 2.322 2.521 0.872 ETKDGv3 14
GKR H21 -2.267 -0.820 -0.450 ETKDGv3 15
GKR HO21 -2.338 -2.300 1.132 ETKDGv3 16
GKR H31 -0.001 -0.103 1.521 ETKDGv3 17
GKR HO31 -0.244 -2.210 -0.391 ETKDGv3 18
GKR H42 -0.123 1.477 -0.366 ETKDGv3 19
GKR H41 0.197 -0.757 -2.112 ETKDGv3 20
GKR HO51 3.316 -0.565 -1.057 ETKDGv3 21
GKR H51 2.088 1.224 -1.405 ETKDGv3 22
#