data_XLS
#
_chem_comp.id XLS
_chem_comp.name D-xylose
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C5 H10 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "D-XYLOSE (LINEAR FORM)"
_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 150.130
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XLS
_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 3XIS
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id XLS
_pdbx_chem_comp_synonyms.name "D-XYLOSE (LINEAR FORM)"
_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
XLS C1 C1 C 0 1 N N N N N N 10.368 33.903 47.391 0.359 0.090 -2.611 C1 XLS 1
XLS C2 C2 C 0 1 N N R N N N 11.506 34.167 46.413 -0.257 -0.408 -1.330 C2 XLS 2
XLS C3 C3 C 0 1 N N S N N N 12.131 32.856 45.937 0.602 0.033 -0.144 C3 XLS 3
XLS C4 C4 C 0 1 N N R N N N 13.647 32.959 45.869 -0.024 -0.472 1.156 C4 XLS 4
XLS C5 C5 C 0 1 N N N N N N 14.227 31.549 45.885 0.836 -0.031 2.341 C5 XLS 5
XLS O1 O1 O 0 1 N N N N N N 9.765 35.065 47.886 0.700 -0.695 -3.463 O1 XLS 6
XLS O2 O2 O 0 1 N N N N N N 11.287 35.112 45.370 -1.572 0.134 -1.192 O2 XLS 7
XLS O3 O3 O 0 1 N N N N N N 11.645 32.587 44.606 0.676 1.459 -0.114 O3 XLS 8
XLS O4 O4 O 0 1 N N N N N N 13.992 33.517 44.602 -1.339 0.069 1.293 O4 XLS 9
XLS O5 O5 O 0 1 N N N N N N 14.776 31.184 47.102 0.251 -0.504 3.556 O5 XLS 10
XLS H1 H1 H 0 1 N N N N N N 9.998 32.918 47.724 0.496 1.150 -2.768 H1 XLS 11
XLS H2 H2 H 0 1 N N N N N N 12.253 34.725 47.023 -0.314 -1.496 -1.353 H2 XLS 12
XLS H3 H3 H 0 1 N N N N N N 11.856 32.047 46.654 1.605 -0.380 -0.249 H3 XLS 13
XLS H4 H4 H 0 1 N N N N N N 14.028 33.572 46.718 -0.080 -1.561 1.133 H4 XLS 14
XLS H51 H51 H 0 1 N N N N N N 13.461 30.805 45.561 0.892 1.056 2.364 H51 XLS 15
XLS H52 H52 H 0 1 N N N N N N 14.971 31.421 45.064 1.839 -0.445 2.236 H52 XLS 16
XLS HO2 HO2 H 0 1 N N N N N N 11.996 35.276 44.760 -1.478 1.096 -1.176 HO2 XLS 17
XLS HO3 HO3 H 0 1 N N N N N N 12.033 31.772 44.310 -0.229 1.784 -0.020 HO3 XLS 18
XLS HO4 HO4 H 0 1 N N N N N N 14.938 33.581 44.559 -1.244 1.031 1.310 HO4 XLS 19
XLS HO5 HO5 H 0 1 N N N N N N 15.137 30.305 47.112 0.822 -0.205 4.277 HO5 XLS 20
#
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
XLS C1 C2 SING N N 1
XLS C1 O1 DOUB N N 2
XLS C1 H1 SING N N 3
XLS C2 C3 SING N N 4
XLS C2 O2 SING N N 5
XLS C2 H2 SING N N 6
XLS C3 C4 SING N N 7
XLS C3 O3 SING N N 8
XLS C3 H3 SING N N 9
XLS C4 C5 SING N N 10
XLS C4 O4 SING N N 11
XLS C4 H4 SING N N 12
XLS C5 O5 SING N N 13
XLS C5 H51 SING N N 14
XLS C5 H52 SING N N 15
XLS O2 HO2 SING N N 16
XLS O3 HO3 SING N N 17
XLS O4 HO4 SING N N 18
XLS O5 HO5 SING N N 19
#
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
XLS SMILES ACDLabs 10.04 O=CC(O)C(O)C(O)CO
XLS SMILES_CANONICAL CACTVS 3.341 OC[C@@H](O)[C@H](O)[C@@H](O)C=O
XLS SMILES CACTVS 3.341 OC[CH](O)[CH](O)[CH](O)C=O
XLS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@H]([C@@H]([C@H](C=O)O)O)O)O
XLS SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(C(C=O)O)O)O)O
XLS InChI InChI 1.03 InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5+/m0/s1
XLS InChIKey InChI 1.03 PYMYPHUHKUWMLA-VPENINKCSA-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
XLS "SYSTEMATIC NAME" ACDLabs 10.04 D-xylose
XLS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2R,3S,4R)-2,3,4,5-tetrahydroxypentanal
#
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
XLS "CARBOHYDRATE ISOMER" D PDB ?
XLS "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
XLS 'Create component' 1999-07-08 RCSB
XLS 'Modify descriptor' 2011-06-04 RCSB
XLS 'Other modification' 2020-07-03 RCSB
XLS 'Modify name' 2020-07-17 RCSB
XLS 'Modify synonyms' 2020-07-17 RCSB
XLS 'Modify linking type' 2020-07-17 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id XLS
_pdbe_chem_comp_drugbank_details.drugbank_id DB09419
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Xylose
_pdbe_chem_comp_drugbank_details.description
'Xylose is a monosaccharide of the aldopentose type consisted of five carbon atoms and an aldehyde functional group. Xylose is a sugar isolated from wood. D-Xylose is a sugar widely used as a diabetic sweetener in food and beverage. Xylose has also been used as a diagnostic agent to observe malabsorption. Reduction of xylose by catalytic hydrogenation produces the common food additive sweetener substitute xylitol [DB11195].  The dextrorotary form of xylose, D-xylose, refers usually to the endogenously occurring form of the sugar in living things. The levorotary form, L-xylose, can refer to the form that is synthesized. Nevertheless, xylose by itself may not necessarily serve many purposes immediately - but its metabolism results in a variety of substrates that can serve important nutritional and biological purposes.'
_pdbe_chem_comp_drugbank_details.cas_number 58-86-6
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Xylose is metabolized into various chemical intermediates that can play critical functions in the biological homeostasis of the human body. Via the oxido-reductase metabolism pathway of xylose in eukaryotic organisms, xylose is ultimately catabolized into (D)-xylulose-5-phosphate, which functions as an intermediate in the pentose phosphate pathway [A32666]. Within the pentose phosphate pathway, NADPH, pentose 5-carbon sugars, and ribose 5-phosphate are generated as materials and precursors for the synthesis of nucleotides [A32666]. In particular, xylulose-5-phosphate can be used to directly generate glycerinaldehyde-3-phosphate in the pathway [A32666]. Other studies have also demonstrated that xylulose-5-phosphate may also play a role in gene expression, perhaps by promoting ChREBP transcription factor in the well-fed state [A32668].'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
XLS 'D-XYLOSE (LINEAR FORM)' wwPDB ?
XLS (+)-Xylose DrugBank ?
XLS aldehydo-D-xylose DrugBank ?
XLS D-Xylose DrugBank ?
XLS 'Wood sugar' DrugBank ?
XLS Xylose DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id XLS
_pdbe_chem_comp_drugbank_classification.drugbank_id DB09419
_pdbe_chem_comp_drugbank_classification.parent Pentoses
_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 pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.'
#
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
XLS C1 C 9.495 -0.375 1
XLS C2 C 8.196 0.375 2
XLS C3 C 6.897 -0.375 3
XLS C4 C 5.598 0.375 4
XLS C5 C 4.299 -0.375 5
XLS O1 O 10.794 0.375 6
XLS O2 O 8.196 1.875 7
XLS O3 O 6.897 -1.875 8
XLS O4 O 5.598 1.875 9
XLS O5 O 3.000 0.375 10
#
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
XLS C1 C2 SINGLE NONE 1
XLS C1 O1 DOUBLE NONE 2
XLS C2 C3 SINGLE NONE 3
XLS C2 O2 SINGLE BEGINWEDGE 4
XLS C3 C4 SINGLE NONE 5
XLS C3 O3 SINGLE BEGINWEDGE 6
XLS C4 C5 SINGLE NONE 7
XLS C4 O4 SINGLE BEGINWEDGE 8
XLS C5 O5 SINGLE NONE 9
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id XLS
_pdbe_chem_comp_rdkit_properties.exactmw 150.053
_pdbe_chem_comp_rdkit_properties.amw 150.130
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 20
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 71.934
_pdbe_chem_comp_rdkit_properties.tpsa 97.990
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.740
_pdbe_chem_comp_rdkit_properties.CrippenMR 31.170
_pdbe_chem_comp_rdkit_properties.chi0v 4.541
_pdbe_chem_comp_rdkit_properties.chi1v 2.021
_pdbe_chem_comp_rdkit_properties.chi2v 0.598
_pdbe_chem_comp_rdkit_properties.chi3v 0.598
_pdbe_chem_comp_rdkit_properties.chi4v 0.196
_pdbe_chem_comp_rdkit_properties.chi0n 14.541
_pdbe_chem_comp_rdkit_properties.chi1n 6.654
_pdbe_chem_comp_rdkit_properties.chi2n 0.598
_pdbe_chem_comp_rdkit_properties.chi3n 0.598
_pdbe_chem_comp_rdkit_properties.chi4n 0.196
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.490
_pdbe_chem_comp_rdkit_properties.kappa1 2.010
_pdbe_chem_comp_rdkit_properties.kappa2 4.345
_pdbe_chem_comp_rdkit_properties.kappa3 2.402
_pdbe_chem_comp_rdkit_properties.Phi 0.873
#
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
XLS UniChem DrugBank DB09419
XLS UniChem 'Guide to Pharmacology' 4724
XLS UniChem ChEBI 15936
XLS UniChem Selleck Xylose
XLS UniChem NMRShiftDB 60019461
XLS UniChem ChemicalBook CB2389952
XLS UniChem MedChemExpress HY-N0537
XLS UniChem 'Probes And Drugs' PD010855
XLS UniChem ZINC ZINC000018168715
XLS UniChem eMolecules 1938508
XLS UniChem fdasrs A1TA934AKO
XLS UniChem SureChEMBL SCHEMBL15776
XLS UniChem 'PubChem TPHARMA' 15995355
XLS UniChem PubChem 644160
XLS UniChem Recon 'xyl_D'
XLS UniChem Nikkaji J2.806A
XLS UniChem MetaboLights MTBLC15936
XLS UniChem ChemicalBook CB1686052
XLS UniChem ChemicalBook CB4686053
XLS UniChem ChemicalBook CB52130508
#
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
XLS C1 2.745 0.343 0.419 ETKDGv3 1
XLS C2 1.367 -0.265 0.499 ETKDGv3 2
XLS C3 0.362 0.473 -0.427 ETKDGv3 3
XLS C4 -1.055 -0.170 -0.446 ETKDGv3 4
XLS C5 -1.750 -0.118 0.929 ETKDGv3 5
XLS O1 2.927 1.504 0.750 ETKDGv3 6
XLS O2 1.416 -1.644 0.222 ETKDGv3 7
XLS O3 0.874 0.579 -1.735 ETKDGv3 8
XLS O4 -1.856 0.459 -1.416 ETKDGv3 9
XLS O5 -3.046 -0.649 0.842 ETKDGv3 10
XLS H1 3.589 -0.249 0.078 ETKDGv3 11
XLS H2 1.033 -0.147 1.551 ETKDGv3 12
XLS H3 0.254 1.510 -0.038 ETKDGv3 13
XLS H4 -0.960 -1.238 -0.738 ETKDGv3 14
XLS H51 -1.780 0.927 1.315 ETKDGv3 15
XLS H52 -1.184 -0.732 1.659 ETKDGv3 16
XLS HO2 1.818 -1.763 -0.678 ETKDGv3 17
XLS HO3 0.827 -0.318 -2.156 ETKDGv3 18
XLS HO4 -1.947 1.414 -1.156 ETKDGv3 19
XLS HO5 -3.636 0.084 0.527 ETKDGv3 20
#