data_TK8
#
_chem_comp.id TK8
_chem_comp.name "D-xylonic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H10 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
"(2~{R},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentanoic acid; (2R,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid; xylonic acid"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-12-23
_chem_comp.pdbx_modified_date 2021-04-09
_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 166.129
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code TK8
_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 7BCN
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
TK8 C02 C1 C 0 1 N N N N N N -19.894 6.044 -2.760 -2.590 0.823 -0.183 C02 TK8 1
TK8 C03 C2 C 0 1 N N R N N N -20.887 5.272 -3.237 -1.485 -0.010 0.469 C03 TK8 2
TK8 C04 C3 C 0 1 N N S N N N -20.590 3.942 -4.010 -0.120 0.576 0.100 C04 TK8 3
TK8 C05 C4 C 0 1 N N R N N N -21.958 3.227 -4.134 0.987 -0.327 0.647 C05 TK8 4
TK8 C06 C5 C 0 1 N N N N N N -22.485 2.714 -2.796 2.327 0.181 0.180 C06 TK8 5
TK8 O01 O1 O 0 1 N N N N N N -19.220 6.871 -2.251 -3.865 0.349 0.255 O01 TK8 6
TK8 O07 O2 O 0 1 N N N N N N -22.881 3.487 -1.899 2.770 1.380 0.591 O07 TK8 7
TK8 O08 O3 O 0 1 N N N N N N -22.556 1.463 -2.610 3.002 -0.490 -0.564 O08 TK8 8
TK8 O09 O4 O 0 1 N N N N N N -21.916 2.309 -4.963 0.792 -1.661 0.173 O09 TK8 9
TK8 O10 O5 O 0 1 N N N N N N -20.108 4.158 -5.105 -0.007 0.660 -1.322 O10 TK8 10
TK8 O11 O6 O 0 1 N N N N N N -21.342 6.075 -4.081 -1.566 -1.358 0.003 O11 TK8 11
TK8 H1 H1 H 0 1 N N N N N N -19.420 5.218 -2.210 -2.474 1.869 0.103 H1 TK8 12
TK8 H2 H2 H 0 1 N N N N N N -19.412 6.155 -3.743 -2.522 0.733 -1.267 H2 TK8 13
TK8 H031 H3 H 0 0 N N N N N N -21.615 5.042 -2.445 -1.607 0.008 1.552 H031 TK8 14
TK8 H041 H4 H 0 0 N N N N N N -19.943 3.323 -3.371 -0.023 1.572 0.532 H041 TK8 15
TK8 H051 H5 H 0 0 N N N N N N -22.670 3.998 -4.465 0.956 -0.321 1.737 H051 TK8 16
TK8 H3 H6 H 0 1 N N N N N N -18.304 6.656 -2.378 -4.614 0.832 -0.119 H3 TK8 17
TK8 H4 H7 H 0 1 N N N N N N -23.198 2.980 -1.161 3.635 1.663 0.264 H4 TK8 18
TK8 H5 H8 H 0 1 N N N N N N -22.133 1.488 -4.538 0.808 -1.742 -0.791 H5 TK8 19
TK8 H6 H9 H 0 1 N N N N N N -19.271 4.596 -5.002 -0.084 -0.192 -1.774 H6 TK8 20
TK8 H7 H10 H 0 1 N N N N N N -21.539 6.902 -3.658 -1.466 -1.450 -0.955 H7 TK8 21
#
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
TK8 O10 C04 SING N N 1
TK8 O09 C05 SING N N 2
TK8 C05 C04 SING N N 3
TK8 C05 C06 SING N N 4
TK8 O11 C03 SING N N 5
TK8 C04 C03 SING N N 6
TK8 C03 C02 SING N N 7
TK8 C06 O08 DOUB N N 8
TK8 C06 O07 SING N N 9
TK8 C02 O01 SING N N 10
TK8 C02 H1 SING N N 11
TK8 C02 H2 SING N N 12
TK8 C03 H031 SING N N 13
TK8 C04 H041 SING N N 14
TK8 C05 H051 SING N N 15
TK8 O01 H3 SING N N 16
TK8 O07 H4 SING N N 17
TK8 O09 H5 SING N N 18
TK8 O10 H6 SING N N 19
TK8 O11 H7 SING N N 20
#
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
TK8 InChI InChI 1.03 InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4-/m1/s1
TK8 InChIKey InChI 1.03 QXKAIJAYHKCRRA-FLRLBIABSA-N
TK8 SMILES_CANONICAL CACTVS 3.385 OC[C@@H](O)[C@H](O)[C@@H](O)C(O)=O
TK8 SMILES CACTVS 3.385 OC[CH](O)[CH](O)[CH](O)C(O)=O
TK8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O
TK8 SMILES "OpenEye OEToolkits" 2.0.7 C(C(C(C(C(=O)O)O)O)O)O
#
_pdbx_chem_comp_identifier.comp_id TK8
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "(2~{R},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentanoic acid"
#
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 TK8 "(2~{R},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentanoic acid" PDB ?
2 TK8 6602431 PUBCHEM ?
3 TK8 "(2R,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid" PUBCHEM ?
4 TK8 "xylonic acid" PUBCHEM ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
TK8 'Create component' 2020-12-23 PDBE
TK8 'Initial release' 2021-04-14 RCSB
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
TK8 '(2~{R},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentanoic acid' wwPDB ?
TK8 6602431 wwPDB ?
TK8 '(2R,3S,4R)-2,3,4,5-tetrahydroxypentanoic acid' wwPDB ?
TK8 'xylonic acid' wwPDB ?
#
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
TK8 C02 C 5.104 -0.375 1
TK8 C03 C 6.404 0.375 2
TK8 C04 C 7.702 -0.375 3
TK8 C05 C 9.002 0.375 4
TK8 C06 C 10.301 -0.375 5
TK8 O01 O 3.805 0.375 6
TK8 O07 O 10.301 -1.875 7
TK8 O08 O 11.600 0.375 8
TK8 O09 O 9.002 1.875 9
TK8 O10 O 7.702 -1.875 10
TK8 O11 O 6.404 1.875 11
#
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
TK8 C04 O10 SINGLE BEGINWEDGE 1
TK8 C05 O09 SINGLE BEGINWEDGE 2
TK8 C05 C04 SINGLE NONE 3
TK8 C05 C06 SINGLE NONE 4
TK8 C03 O11 SINGLE BEGINWEDGE 5
TK8 C04 C03 SINGLE NONE 6
TK8 C03 C02 SINGLE NONE 7
TK8 C06 O08 DOUBLE NONE 8
TK8 C06 O07 SINGLE NONE 9
TK8 C02 O01 SINGLE NONE 10
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id TK8
_pdbe_chem_comp_rdkit_properties.exactmw 166.048
_pdbe_chem_comp_rdkit_properties.amw 166.129
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 76.815
_pdbe_chem_comp_rdkit_properties.tpsa 118.220
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.854
_pdbe_chem_comp_rdkit_properties.CrippenMR 32.742
_pdbe_chem_comp_rdkit_properties.chi0v 4.949
_pdbe_chem_comp_rdkit_properties.chi1v 2.225
_pdbe_chem_comp_rdkit_properties.chi2v 0.691
_pdbe_chem_comp_rdkit_properties.chi3v 0.691
_pdbe_chem_comp_rdkit_properties.chi4v 0.242
_pdbe_chem_comp_rdkit_properties.chi0n 14.949
_pdbe_chem_comp_rdkit_properties.chi1n 6.766
_pdbe_chem_comp_rdkit_properties.chi2n 0.691
_pdbe_chem_comp_rdkit_properties.chi3n 0.691
_pdbe_chem_comp_rdkit_properties.chi4n 0.242
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.690
_pdbe_chem_comp_rdkit_properties.kappa1 2.397
_pdbe_chem_comp_rdkit_properties.kappa2 4.243
_pdbe_chem_comp_rdkit_properties.kappa3 2.808
_pdbe_chem_comp_rdkit_properties.Phi 0.924
#
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
TK8 UniChem ChEBI 48093
TK8 UniChem ZINC ZINC000008551175
TK8 UniChem fdasrs DA38Q87GYH
TK8 UniChem fdasrs OCI0V55QO1
TK8 UniChem HMDB HMDB0059750
TK8 UniChem BRENDA 179704
TK8 UniChem BRENDA 44010
TK8 UniChem BRENDA 5539
TK8 UniChem ChemicalBook CB82671442
TK8 UniChem Nikkaji J387.172J
TK8 UniChem SureChEMBL SCHEMBL15186907
TK8 UniChem 'PubChem TPHARMA' 16851816
TK8 UniChem PubChem 6602431
#
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
TK8 C02 -2.084 -0.407 -0.748 ETKDGv3 1
TK8 C03 -0.845 0.415 -0.355 ETKDGv3 2
TK8 C04 0.170 -0.421 0.466 ETKDGv3 3
TK8 C05 1.488 0.350 0.718 ETKDGv3 4
TK8 C06 2.208 0.638 -0.567 ETKDGv3 5
TK8 O01 -2.877 -0.676 0.375 ETKDGv3 6
TK8 O07 2.746 -0.406 -1.313 ETKDGv3 7
TK8 O08 2.314 1.824 -0.980 ETKDGv3 8
TK8 O09 2.339 -0.415 1.533 ETKDGv3 9
TK8 O10 -0.396 -0.765 1.708 ETKDGv3 10
TK8 O11 -1.232 1.551 0.376 ETKDGv3 11
TK8 H1 -1.768 -1.360 -1.230 ETKDGv3 12
TK8 H2 -2.680 0.172 -1.489 ETKDGv3 13
TK8 H031 -0.351 0.733 -1.303 ETKDGv3 14
TK8 H041 0.425 -1.343 -0.112 ETKDGv3 15
TK8 H051 1.259 1.319 1.224 ETKDGv3 16
TK8 H3 -3.644 -1.215 0.048 ETKDGv3 17
TK8 H4 3.228 -0.227 -2.186 ETKDGv3 18
TK8 H5 2.062 -0.258 2.474 ETKDGv3 19
TK8 H6 -0.732 -1.696 1.633 ETKDGv3 20
TK8 H7 -1.632 2.188 -0.272 ETKDGv3 21
#