data_LXP
#
_chem_comp.id LXP
_chem_comp.name "L-XYLITOL 5-PHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H13 O8 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-08-19
_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 232.126
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LXP
_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 1Q6Q
_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
LXP O8 O8 O 0 1 N N N N N N 40.638 5.045 13.019 -0.857 -0.405 -4.420 O8 LXP 1
LXP P P P 0 1 N N N N N N 40.606 5.354 11.521 0.112 -0.090 -3.174 P LXP 2
LXP O6 O6 O 0 1 N N N N N N 41.333 4.372 10.666 1.343 -0.903 -3.289 O6 LXP 3
LXP O7 O7 O 0 1 N N N N N N 39.164 5.578 11.074 0.498 1.472 -3.177 O7 LXP 4
LXP O5 O5 O 0 1 N N N N N N 41.371 6.777 11.279 -0.644 -0.452 -1.800 O5 LXP 5
LXP C5 C5 C 0 1 N N N N N N 40.927 7.999 11.823 0.262 -0.152 -0.737 C5 LXP 6
LXP C4 C4 C 0 1 N N S N N N 41.642 8.383 13.135 -0.398 -0.476 0.603 C4 LXP 7
LXP O4 O4 O 0 1 N N N N N N 41.066 9.608 13.625 -1.583 0.308 0.752 O4 LXP 8
LXP C3 C3 C 0 1 N N S N N N 43.151 8.416 12.900 0.573 -0.154 1.741 C3 LXP 9
LXP O3 O3 O 0 1 N N N N N N 43.480 9.383 11.876 0.912 1.232 1.700 O3 LXP 10
LXP C2 C2 C 0 1 N N R N N N 43.858 8.778 14.234 -0.087 -0.478 3.083 C2 LXP 11
LXP O2 O2 O 0 1 N N N N N N 43.985 10.206 14.318 -1.272 0.306 3.232 O2 LXP 12
LXP C1 C1 C 0 1 N N N N N N 45.216 8.117 14.293 0.883 -0.156 4.220 C1 LXP 13
LXP O1 O1 O 0 1 N N N N N N 45.920 8.636 15.445 0.266 -0.459 5.473 O1 LXP 14
LXP HO8 HO8 H 0 1 N N N N N N 40.174 5.670 13.563 -0.367 -0.175 -5.221 HO8 LXP 15
LXP HO7 HO7 H 0 1 N N N N N N 39.144 5.769 10.143 -0.329 1.965 -3.101 HO7 LXP 16
LXP H51 1H5 H 0 1 N N N N N N 41.011 8.819 11.072 0.521 0.905 -0.769 H51 LXP 17
LXP H52 2H5 H 0 1 N N N N N N 39.821 7.990 11.963 1.166 -0.751 -0.851 H52 LXP 18
LXP H4 H4 H 0 1 N N N N N N 41.491 7.626 13.940 -0.656 -1.534 0.635 H4 LXP 19
LXP HO4 HO4 H 0 1 N N N N N N 41.506 9.844 14.432 -1.310 1.235 0.719 HO4 LXP 20
LXP H3 H3 H 0 1 N N N N N N 43.498 7.414 12.553 1.476 -0.753 1.627 H3 LXP 21
LXP HO3 HO3 H 0 1 N N N N N N 44.418 9.403 11.729 0.086 1.725 1.804 HO3 LXP 22
LXP H2 H2 H 0 1 N N N N N N 43.255 8.410 15.097 -0.346 -1.536 3.114 H2 LXP 23
LXP HO2 HO2 H 0 1 N N N N N N 44.417 10.427 15.134 -0.999 1.233 3.198 HO2 LXP 24
LXP H11 1H1 H 0 1 N N N N N N 45.153 7.003 14.292 1.142 0.901 4.189 H11 LXP 25
LXP H12 2H1 H 0 1 N N N N N N 45.793 8.235 13.346 1.787 -0.755 4.107 H12 LXP 26
LXP HO1 HO1 H 0 1 N N N N N N 46.773 8.220 15.482 0.910 -0.242 6.161 HO1 LXP 27
#
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
LXP O8 P SING N N 1
LXP O8 HO8 SING N N 2
LXP P O6 DOUB N N 3
LXP P O7 SING N N 4
LXP P O5 SING N N 5
LXP O7 HO7 SING N N 6
LXP O5 C5 SING N N 7
LXP C5 C4 SING N N 8
LXP C5 H51 SING N N 9
LXP C5 H52 SING N N 10
LXP C4 O4 SING N N 11
LXP C4 C3 SING N N 12
LXP C4 H4 SING N N 13
LXP O4 HO4 SING N N 14
LXP C3 O3 SING N N 15
LXP C3 C2 SING N N 16
LXP C3 H3 SING N N 17
LXP O3 HO3 SING N N 18
LXP C2 O2 SING N N 19
LXP C2 C1 SING N N 20
LXP C2 H2 SING N N 21
LXP O2 HO2 SING N N 22
LXP C1 O1 SING N N 23
LXP C1 H11 SING N N 24
LXP C1 H12 SING N N 25
LXP O1 HO1 SING N N 26
#
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
LXP SMILES ACDLabs 10.04 O=P(O)(O)OCC(O)C(O)C(O)CO
LXP SMILES_CANONICAL CACTVS 3.341 OC[C@@H](O)[C@H](O)[C@@H](O)CO[P](O)(O)=O
LXP SMILES CACTVS 3.341 OC[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O
LXP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@H]([C@@H]([C@H](COP(=O)(O)O)O)O)O)O
LXP SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(C(COP(=O)(O)O)O)O)O)O
LXP InChI InChI 1.03 InChI=1S/C5H13O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3-9H,1-2H2,(H2,10,11,12)/t3-,4+,5+/m1/s1
LXP InChIKey InChI 1.03 VJDOAZKNBQCAGE-WISUUJSJSA-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
LXP "SYSTEMATIC NAME" ACDLabs 10.04 1-O-phosphono-D-xylitol
LXP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl] dihydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LXP 'Create component' 2003-08-19 RCSB
LXP 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id LXP
_pdbe_chem_comp_drugbank_details.drugbank_id DB02630
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'L-xylitol 5-phosphate'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 64913-51-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
LXP 'Xylitol 5-P' DrugBank ?
LXP 'Xylitol 5-phosphate' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id LXP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02630
_pdbe_chem_comp_drugbank_classification.parent 'Monosaccharide phosphates'
_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 monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.'
#
_pdbe_chem_comp_drugbank_targets.comp_id LXP
_pdbe_chem_comp_drugbank_targets.drugbank_id DB02630
_pdbe_chem_comp_drugbank_targets.name '3-keto-L-gulonate-6-phosphate decarboxylase UlaD'
_pdbe_chem_comp_drugbank_targets.organism 'Escherichia coli (strain K12)'
_pdbe_chem_comp_drugbank_targets.uniprot_id P39304
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
LXP O8 O 14.198 -1.125 1
LXP P P 12.899 -0.375 2
LXP O6 O 13.649 0.924 3
LXP O7 O 12.149 -1.674 4
LXP O5 O 11.600 0.375 5
LXP C5 C 10.301 -0.375 6
LXP C4 C 9.002 0.375 7
LXP O4 O 9.002 1.875 8
LXP C3 C 7.702 -0.375 9
LXP O3 O 7.702 -1.875 10
LXP C2 C 6.404 0.375 11
LXP O2 O 6.404 1.875 12
LXP C1 C 5.104 -0.375 13
LXP O1 O 3.805 0.375 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
LXP O8 P SINGLE NONE 1
LXP P O6 DOUBLE NONE 2
LXP P O7 SINGLE NONE 3
LXP P O5 SINGLE NONE 4
LXP O5 C5 SINGLE NONE 5
LXP C5 C4 SINGLE NONE 6
LXP C4 O4 SINGLE BEGINWEDGE 7
LXP C4 C3 SINGLE NONE 8
LXP C3 O3 SINGLE BEGINWEDGE 9
LXP C3 C2 SINGLE NONE 10
LXP C2 O2 SINGLE BEGINWEDGE 11
LXP C2 C1 SINGLE NONE 12
LXP C1 O1 SINGLE NONE 13
#
_pdbe_chem_comp_substructure.comp_id LXP
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-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
LXP O8 F1 1
LXP P F1 1
LXP O6 F1 1
LXP O7 F1 1
LXP O5 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LXP
_pdbe_chem_comp_rdkit_properties.exactmw 232.035
_pdbe_chem_comp_rdkit_properties.amw 232.125
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 98.412
_pdbe_chem_comp_rdkit_properties.tpsa 147.680
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.829
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.102
_pdbe_chem_comp_rdkit_properties.chi0v 7.108
_pdbe_chem_comp_rdkit_properties.chi1v 4.212
_pdbe_chem_comp_rdkit_properties.chi2v 1.070
_pdbe_chem_comp_rdkit_properties.chi3v 1.070
_pdbe_chem_comp_rdkit_properties.chi4v 0.488
_pdbe_chem_comp_rdkit_properties.chi0n 19.213
_pdbe_chem_comp_rdkit_properties.chi1n 8.700
_pdbe_chem_comp_rdkit_properties.chi2n 0.755
_pdbe_chem_comp_rdkit_properties.chi3n 0.755
_pdbe_chem_comp_rdkit_properties.chi4n 0.293
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.050
_pdbe_chem_comp_rdkit_properties.kappa1 3.474
_pdbe_chem_comp_rdkit_properties.kappa2 5.740
_pdbe_chem_comp_rdkit_properties.kappa3 5.632
_pdbe_chem_comp_rdkit_properties.Phi 1.424
#
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
LXP UniChem DrugBank DB02630
LXP UniChem PDBe LXP
LXP UniChem SureChEMBL SCHEMBL21610
LXP UniChem 'PubChem TPHARMA' 14773838
LXP UniChem PubChem 448027
LXP UniChem ACTor 64913-51-5
LXP UniChem BRENDA 125197
LXP UniChem BRENDA 145789
LXP UniChem 'Probes And Drugs' PD007275
LXP UniChem 'EPA CompTox Dashboard' DTXSID70215225
#
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
LXP O8 3.974 1.603 -0.604 ETKDGv3 1
LXP P 3.956 0.286 0.460 ETKDGv3 2
LXP O6 3.958 0.786 1.887 ETKDGv3 3
LXP O7 5.341 -0.651 0.205 ETKDGv3 4
LXP O5 2.577 -0.680 0.182 ETKDGv3 5
LXP C5 1.433 0.131 0.308 ETKDGv3 6
LXP C4 0.177 -0.729 0.079 ETKDGv3 7
LXP O4 0.215 -1.364 -1.178 ETKDGv3 8
LXP C3 -1.128 0.090 0.271 ETKDGv3 9
LXP O3 -1.190 1.195 -0.600 ETKDGv3 10
LXP C2 -2.403 -0.795 0.187 ETKDGv3 11
LXP O2 -2.578 -1.353 -1.094 ETKDGv3 12
LXP C1 -3.672 -0.057 0.658 ETKDGv3 13
LXP O1 -3.943 1.049 -0.159 ETKDGv3 14
LXP HO8 4.835 2.060 -0.425 ETKDGv3 15
LXP HO7 5.275 -0.944 -0.739 ETKDGv3 16
LXP H51 1.449 0.954 -0.442 ETKDGv3 17
LXP H52 1.375 0.568 1.332 ETKDGv3 18
LXP H4 0.188 -1.528 0.853 ETKDGv3 19
LXP HO4 0.435 -0.682 -1.864 ETKDGv3 20
LXP H3 -1.093 0.498 1.306 ETKDGv3 21
LXP HO3 -1.192 0.858 -1.531 ETKDGv3 22
LXP H2 -2.262 -1.643 0.893 ETKDGv3 23
LXP HO2 -2.892 -0.639 -1.705 ETKDGv3 24
LXP H11 -3.535 0.279 1.711 ETKDGv3 25
LXP H12 -4.532 -0.762 0.627 ETKDGv3 26
LXP HO1 -4.765 1.467 0.207 ETKDGv3 27
#