data_BDF
#
_chem_comp.id BDF
_chem_comp.name beta-D-fructopyranose
_chem_comp.type 'D-saccharide, beta linking'
_chem_comp.pdbx_type ATOMS
_chem_comp.formula 'C6 H12 O6'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 'beta-D-fructose; D-fructose; fructose'
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-11-01
_chem_comp.pdbx_modified_date 2024-09-27
_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 180.156
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code BDF
_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 1N3Q
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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 BDF beta-D-fructose PDB ?
2 BDF D-fructose PDB ?
3 BDF fructose 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
BDF C1 C1 C 0 1 N N N N N N -2.883 -16.858 -16.449 0.442 0.733 2.191 C1 BDF 1
BDF C2 C2 C 0 1 N N R N N N -1.962 -16.425 -17.579 0.031 -0.052 0.944 C2 BDF 2
BDF C3 C3 C 0 1 N N S N N N -1.942 -14.877 -17.738 0.910 0.369 -0.234 C3 BDF 3
BDF C4 C4 C 0 1 N N R N N N -1.212 -14.499 -19.032 0.515 -0.448 -1.469 C4 BDF 4
BDF C5 C5 C 0 1 N N R N N N -1.765 -15.228 -20.254 -0.993 -0.295 -1.694 C5 BDF 5
BDF C6 C6 C 0 1 N N N N N N -1.760 -16.721 -19.976 -1.730 -0.665 -0.405 C6 BDF 6
BDF O1 O1 O 0 1 N N N N N N -4.221 -16.413 -16.631 -0.376 0.338 3.294 O1 BDF 7
BDF O2 O2 O 0 1 N Y N N N N -0.634 -16.918 -17.382 0.199 -1.450 1.187 O2 BDF 8
BDF O3 O3 O 0 1 N N N N N N -1.250 -14.269 -16.633 2.282 0.124 0.080 O3 BDF 9
BDF O4 O4 O 0 1 N N N N N N -1.279 -13.085 -19.244 1.221 0.033 -2.614 O4 BDF 10
BDF O5 O5 O 0 1 N N N N N N -3.115 -14.805 -20.534 -1.292 1.057 -2.044 O5 BDF 11
BDF O6 O6 O 0 1 N N N N N N -2.518 -17.003 -18.769 -1.337 0.215 0.645 O6 BDF 12
BDF H11 H11 H 0 1 N N N N N N -2.845 -17.962 -16.303 0.314 1.800 2.007 H11 BDF 13
BDF H12 H12 H 0 1 N N N N N N -2.483 -16.531 -15.460 1.487 0.527 2.422 H12 BDF 14
BDF H3 H3 H 0 1 N N N N N N -2.995 -14.513 -17.767 0.766 1.430 -0.438 H3 BDF 15
BDF H4 H4 H 0 1 N N N N N N -0.150 -14.815 -18.906 0.755 -1.499 -1.306 H4 BDF 16
BDF H5 H5 H 0 1 N N N N N N -1.126 -14.990 -21.136 -1.311 -0.959 -2.499 H5 BDF 17
BDF H61 H61 H 0 1 N N N N N N -2.128 -17.310 -20.848 -1.484 -1.690 -0.128 H61 BDF 18
BDF H62 H62 H 0 1 N N N N N N -0.725 -17.133 -19.926 -2.805 -0.582 -0.565 H62 BDF 19
BDF HO1 HO1 H 0 1 N Y N N N N -4.796 -16.683 -15.925 -0.085 0.855 4.057 HO1 BDF 20
BDF HO2 HO2 H 0 1 N Y N N N N -0.058 -16.647 -18.087 -0.368 -1.674 1.936 HO2 BDF 21
BDF HO3 HO3 H 0 1 N Y N N N N -1.237 -13.324 -16.730 2.799 0.396 -0.690 HO3 BDF 22
BDF HO4 HO4 H 0 1 N Y N N N N -0.826 -12.850 -20.045 0.932 -0.500 -3.366 HO4 BDF 23
BDF HO5 HO5 H 0 1 N Y N N N N -3.459 -15.258 -21.294 -2.249 1.108 -2.170 HO5 BDF 24
#
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
BDF C1 C2 SING N N 1
BDF C1 O1 SING N N 2
BDF C1 H11 SING N N 3
BDF C1 H12 SING N N 4
BDF C2 C3 SING N N 5
BDF C2 O2 SING N N 6
BDF C2 O6 SING N N 7
BDF C3 C4 SING N N 8
BDF C3 O3 SING N N 9
BDF C3 H3 SING N N 10
BDF C4 C5 SING N N 11
BDF C4 O4 SING N N 12
BDF C4 H4 SING N N 13
BDF C5 C6 SING N N 14
BDF C5 O5 SING N N 15
BDF C5 H5 SING N N 16
BDF C6 O6 SING N N 17
BDF C6 H61 SING N N 18
BDF C6 H62 SING N N 19
BDF O1 HO1 SING N N 20
BDF O2 HO2 SING N N 21
BDF O3 HO3 SING N N 22
BDF O4 HO4 SING N N 23
BDF O5 HO5 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
BDF SMILES ACDLabs 10.04 'OC1C(O)(OCC(O)C1O)CO'
BDF SMILES_CANONICAL CACTVS 3.341 'OC[C@@]1(O)OC[C@@H](O)[C@@H](O)[C@@H]1O'
BDF SMILES CACTVS 3.341 'OC[C]1(O)OC[CH](O)[CH](O)[CH]1O'
BDF SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C1[C@H]([C@H]([C@@H]([C@](O1)(CO)O)O)O)O'
BDF SMILES 'OpenEye OEToolkits' 1.5.0 'C1C(C(C(C(O1)(CO)O)O)O)O'
BDF InChI InChI 1.03 'InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3-,4-,5+,6-/m1/s1'
BDF InChIKey InChI 1.03 LKDRXBCSQODPBY-ARQDHWQXSA-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
BDF 'SYSTEMATIC NAME' ACDLabs 10.04 beta-D-fructopyranose
BDF 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2R,3S,4R,5R)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol'
BDF 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DFrupb
BDF 'COMMON NAME' GMML 1.0 b-D-fructopyranose
BDF 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-Frup
BDF 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Fru
#
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
BDF 'CARBOHYDRATE ISOMER' D PDB ?
BDF 'CARBOHYDRATE RING' pyranose PDB ?
BDF 'CARBOHYDRATE ANOMER' beta PDB ?
BDF 'CARBOHYDRATE PRIMARY CARBONYL GROUP' ketose 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
BDF 'Create component' 2002-11-01 RCSB
BDF 'Modify descriptor' 2011-06-04 RCSB
BDF 'Other modification' 2019-08-12 RCSB
BDF 'Other modification' 2019-12-19 RCSB
BDF 'Other modification' 2020-07-03 RCSB
BDF 'Modify name' 2020-07-17 RCSB
BDF 'Modify synonyms' 2020-07-17 RCSB
BDF 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id BDF
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category Carbohydrate
_pdbx_chem_comp_pcm.position 'Amino-acid backbone'
_pdbx_chem_comp_pcm.polypeptide_position N-terminal
_pdbx_chem_comp_pcm.comp_id_linking_atom C1
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom N
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
BDF beta-D-fructose wwPDB ?
BDF D-fructose wwPDB ?
BDF fructose 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
BDF C1 C 5.654 -2.080 1
BDF C2 C 6.404 -0.781 2
BDF C3 C 5.104 -0.031 3
BDF C4 C 5.104 1.469 4
BDF C5 C 6.404 2.219 5
BDF C6 C 7.702 1.469 6
BDF O1 O 6.404 -3.379 7
BDF O2 O 7.154 -2.080 8
BDF O3 O 3.805 -0.781 9
BDF O4 O 3.805 2.219 10
BDF O5 O 6.404 3.719 11
BDF O6 O 7.702 -0.031 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
BDF C1 C2 SINGLE NONE 1
BDF C1 O1 SINGLE NONE 2
BDF C2 C3 SINGLE NONE 3
BDF C2 O2 SINGLE BEGINWEDGE 4
BDF C2 O6 SINGLE NONE 5
BDF C3 C4 SINGLE NONE 6
BDF C3 O3 SINGLE BEGINWEDGE 7
BDF C4 C5 SINGLE NONE 8
BDF C4 O4 SINGLE BEGINDASH 9
BDF C5 C6 SINGLE NONE 10
BDF C5 O5 SINGLE BEGINDASH 11
BDF C6 O6 SINGLE NONE 12
#
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
BDF MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
BDF 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
BDF C2 S1 1
BDF C3 S1 1
BDF C4 S1 1
BDF C5 S1 1
BDF C6 S1 1
BDF O6 S1 1
BDF C5 F1 1
BDF C6 F1 1
BDF O6 F1 1
BDF C2 F1 1
BDF C3 F1 1
BDF C4 F1 1
BDF O2 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id BDF
_pdbe_chem_comp_rdkit_properties.exactmw 180.063
_pdbe_chem_comp_rdkit_properties.amw 180.156
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 85.936
_pdbe_chem_comp_rdkit_properties.tpsa 110.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.220
_pdbe_chem_comp_rdkit_properties.CrippenMR 36.008
_pdbe_chem_comp_rdkit_properties.chi0v 5.449
_pdbe_chem_comp_rdkit_properties.chi1v 2.679
_pdbe_chem_comp_rdkit_properties.chi2v 1.133
_pdbe_chem_comp_rdkit_properties.chi3v 1.133
_pdbe_chem_comp_rdkit_properties.chi4v 0.531
_pdbe_chem_comp_rdkit_properties.chi0n 17.449
_pdbe_chem_comp_rdkit_properties.chi1n 8.220
_pdbe_chem_comp_rdkit_properties.chi2n 1.133
_pdbe_chem_comp_rdkit_properties.chi3n 1.133
_pdbe_chem_comp_rdkit_properties.chi4n 0.531
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.240
_pdbe_chem_comp_rdkit_properties.kappa1 2.412
_pdbe_chem_comp_rdkit_properties.kappa2 3.250
_pdbe_chem_comp_rdkit_properties.kappa3 1.446
_pdbe_chem_comp_rdkit_properties.Phi 0.653
#
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
BDF UniChem ChEBI 41005
BDF UniChem ZINC ZINC000003861095
BDF UniChem fdasrs R73GS1TJE0
BDF UniChem 'EPA CompTox Dashboard' DTXSID0023082
BDF UniChem MetaboLights MTBLC41005
BDF UniChem ChemicalBook CB0875684
BDF UniChem MedChemExpress HY-N0395
BDF UniChem 'Probes And Drugs' PD062054
BDF UniChem CCDC FRUCTO
BDF UniChem Nikkaji J53.982A
BDF UniChem eMolecules 30316168
BDF UniChem SureChEMBL SCHEMBL366014
BDF UniChem 'PubChem TPHARMA' 14748353
BDF UniChem 'PubChem TPHARMA' 15487263
BDF UniChem PubChem 24310
BDF UniChem NMRShiftDB 60067455
BDF UniChem ACTor 7660-25-5
#
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
BDF C1 2.531 -0.099 0.184 ETKDGv3 1
BDF C2 1.057 -0.311 -0.230 ETKDGv3 2
BDF C3 0.317 1.066 -0.295 ETKDGv3 3
BDF C4 -1.169 0.939 0.119 ETKDGv3 4
BDF C5 -1.715 -0.436 -0.296 ETKDGv3 5
BDF C6 -0.868 -1.564 0.338 ETKDGv3 6
BDF O1 2.626 0.433 1.480 ETKDGv3 7
BDF O2 1.043 -0.921 -1.504 ETKDGv3 8
BDF O3 0.412 1.592 -1.596 ETKDGv3 9
BDF O4 -1.278 1.101 1.512 ETKDGv3 10
BDF O5 -3.059 -0.575 0.090 ETKDGv3 11
BDF O6 0.437 -1.156 0.733 ETKDGv3 12
BDF H11 3.018 0.604 -0.526 ETKDGv3 13
BDF H12 3.089 -1.062 0.127 ETKDGv3 14
BDF H3 0.797 1.785 0.412 ETKDGv3 15
BDF H4 -1.757 1.738 -0.392 ETKDGv3 16
BDF H5 -1.643 -0.527 -1.406 ETKDGv3 17
BDF H61 -1.384 -1.937 1.249 ETKDGv3 18
BDF H62 -0.800 -2.428 -0.359 ETKDGv3 19
BDF HO1 2.515 -0.326 2.111 ETKDGv3 20
BDF HO2 1.416 -1.836 -1.403 ETKDGv3 21
BDF HO3 0.228 2.566 -1.532 ETKDGv3 22
BDF HO4 -2.218 1.358 1.702 ETKDGv3 23
BDF HO5 -3.593 -0.002 -0.520 ETKDGv3 24
#