data_5SP
#
_chem_comp.id 5SP
_chem_comp.name 5-O-phosphono-D-xylulose
_chem_comp.type saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C5 H11 O8 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "D-xylulose 5-phosphate"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-03-12
_chem_comp.pdbx_modified_date 2020-06-17
_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 230.110
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5SP
_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 3LQU
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
5SP O1 O1 O 0 1 N N N N N N -9.722 -21.772 20.480 5.076 1.358 0.057 O1 5SP 1
5SP C2 C2 C 0 1 N N N N N N -8.833 -22.674 21.065 3.802 1.179 -0.566 C2 5SP 2
5SP C3 C3 C 0 1 N N N N N N -8.005 -23.537 20.150 3.226 -0.153 -0.159 C3 5SP 3
5SP O4 O4 O 0 1 N N N N N N -8.222 -23.523 18.956 3.843 -0.875 0.587 O4 5SP 4
5SP C5 C5 C 0 1 N N S N N N -6.994 -24.521 20.709 1.881 -0.584 -0.683 C5 5SP 5
5SP C6 C6 C 0 1 N N R N N N -7.476 -25.291 21.937 0.779 0.191 0.042 C6 5SP 6
5SP C7 C7 C 0 1 N N N N N N -7.534 -26.781 21.671 -0.589 -0.334 -0.399 C7 5SP 7
5SP O8 O8 O 0 1 N N N N N N -7.304 -27.184 20.343 -1.618 0.465 0.188 O8 5SP 8
5SP P9 P9 P 0 1 N N N N N N -6.330 -28.399 20.084 -3.186 0.197 -0.061 P9 5SP 9
5SP O10 O10 O 0 1 N N N N N N -6.346 -29.216 21.361 -3.461 0.192 -1.515 O10 5SP 10
5SP O11 O11 O 0 1 N N N N N N -4.874 -27.894 19.838 -3.593 -1.229 0.567 O11 5SP 11
5SP O12 O12 O 0 1 N N N N N N -6.834 -29.231 18.837 -4.048 1.360 0.644 O12 5SP 12
5SP O13 O13 O 0 1 N N N N N N -5.687 -24.038 20.754 1.707 -1.984 -0.456 O13 5SP 13
5SP O14 O14 O 0 1 N N N N N N -6.888 -24.957 23.142 0.923 0.016 1.453 O14 5SP 14
5SP HO1 HO1 H 0 1 N N N N N N -9.705 -21.877 19.536 5.506 2.196 -0.161 HO1 5SP 15
5SP H2 H2 H 0 1 N N N N N N -8.128 -22.081 21.666 3.129 1.977 -0.251 H2 5SP 16
5SP H2A H2A H 0 1 N N N N N N -9.434 -23.355 21.686 3.919 1.209 -1.649 H2A 5SP 17
5SP H5 H5 H 0 1 N N N N N N -6.922 -25.316 19.952 1.825 -0.380 -1.753 H5 5SP 18
5SP H6 H6 H 0 1 N N N N N N -8.507 -24.942 22.095 0.858 1.250 -0.203 H6 5SP 19
5SP H7 H7 H 0 1 N N N N N N -6.762 -27.255 22.295 -0.664 -0.283 -1.485 H7 5SP 20
5SP H7A H7A H 0 1 N N N N N N -8.542 -27.123 21.947 -0.703 -1.368 -0.075 H7A 5SP 21
5SP HO11 HO11 H 0 0 N N N N N N -4.309 -28.203 20.536 -3.440 -1.297 1.519 HO11 5SP 22
5SP HO12 HO12 H 0 0 N N N N N N -7.062 -30.111 19.114 -5.003 1.262 0.535 HO12 5SP 23
5SP HO13 HO13 H 0 0 N N N N N N -5.114 -24.706 21.113 1.745 -2.239 0.476 HO13 5SP 24
5SP HO14 HO14 H 0 0 N N N N N N -7.258 -25.492 23.834 0.864 -0.904 1.743 HO14 5SP 25
#
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
5SP O1 C2 SING N N 1
5SP C2 C3 SING N N 2
5SP C3 O4 DOUB N N 3
5SP C3 C5 SING N N 4
5SP C5 C6 SING N N 5
5SP C5 O13 SING N N 6
5SP C6 C7 SING N N 7
5SP C6 O14 SING N N 8
5SP C7 O8 SING N N 9
5SP O8 P9 SING N N 10
5SP P9 O10 DOUB N N 11
5SP P9 O11 SING N N 12
5SP P9 O12 SING N N 13
5SP O1 HO1 SING N N 14
5SP C2 H2 SING N N 15
5SP C2 H2A SING N N 16
5SP C5 H5 SING N N 17
5SP C6 H6 SING N N 18
5SP C7 H7 SING N N 19
5SP C7 H7A SING N N 20
5SP O11 HO11 SING N N 21
5SP O12 HO12 SING N N 22
5SP O13 HO13 SING N N 23
5SP O14 HO14 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
5SP SMILES ACDLabs 12.01 O=P(OCC(O)C(O)C(=O)CO)(O)O
5SP SMILES_CANONICAL CACTVS 3.370 OCC(=O)[C@@H](O)[C@H](O)CO[P](O)(O)=O
5SP SMILES CACTVS 3.370 OCC(=O)[CH](O)[CH](O)CO[P](O)(O)=O
5SP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C([C@H]([C@@H](C(=O)CO)O)O)OP(=O)(O)O
5SP SMILES "OpenEye OEToolkits" 1.7.0 C(C(C(C(=O)CO)O)O)OP(=O)(O)O
5SP InChI InChI 1.03 InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5-/m1/s1
5SP InChIKey InChI 1.03 FNZLKVNUWIIPSJ-RFZPGFLSSA-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
5SP "SYSTEMATIC NAME" ACDLabs 12.01 5-O-phosphono-D-xylulose
5SP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S)-2,3,5-trihydroxy-4-oxo-pentyl] 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
5SP 'Create component' 2010-03-12 PDBJ
5SP 'Modify synonyms' 2010-10-28 PDBJ
5SP 'Modify descriptor' 2011-06-04 RCSB
5SP 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 5SP
_pdbx_chem_comp_synonyms.name "D-xylulose 5-phosphate"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id 5SP
_pdbe_chem_comp_drugbank_details.drugbank_id DB04034
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Ribulose-5-Phosphate
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id 5SP
_pdbe_chem_comp_synonyms.name 'D-xylulose 5-phosphate'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id 5SP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04034
_pdbe_chem_comp_drugbank_classification.parent 'Pentose 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 pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.'
#
_pdbe_chem_comp_drugbank_targets.comp_id 5SP
_pdbe_chem_comp_drugbank_targets.drugbank_id DB04034
_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
5SP O1 O 3.805 0.375 1
5SP C2 C 5.104 -0.375 2
5SP C3 C 6.404 0.375 3
5SP O4 O 6.404 1.875 4
5SP C5 C 7.702 -0.375 5
5SP C6 C 9.002 0.375 6
5SP C7 C 10.301 -0.375 7
5SP O8 O 11.600 0.375 8
5SP P9 P 12.899 -0.375 9
5SP O10 O 14.198 -1.125 10
5SP O11 O 13.649 0.924 11
5SP O12 O 12.149 -1.674 12
5SP O13 O 7.702 -1.875 13
5SP O14 O 9.002 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
5SP O1 C2 SINGLE NONE 1
5SP C2 C3 SINGLE NONE 2
5SP C3 O4 DOUBLE NONE 3
5SP C3 C5 SINGLE NONE 4
5SP C5 C6 SINGLE NONE 5
5SP C5 O13 SINGLE BEGINDASH 6
5SP C6 C7 SINGLE NONE 7
5SP C6 O14 SINGLE BEGINDASH 8
5SP C7 O8 SINGLE NONE 9
5SP O8 P9 SINGLE NONE 10
5SP P9 O10 DOUBLE NONE 11
5SP P9 O11 SINGLE NONE 12
5SP P9 O12 SINGLE NONE 13
#
_pdbe_chem_comp_substructure.comp_id 5SP
_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
5SP O8 F1 1
5SP P9 F1 1
5SP O10 F1 1
5SP O11 F1 1
5SP O12 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 5SP
_pdbe_chem_comp_rdkit_properties.exactmw 230.019
_pdbe_chem_comp_rdkit_properties.amw 230.109
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 94.883
_pdbe_chem_comp_rdkit_properties.tpsa 144.520
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.621
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.103
_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 17.213
_pdbe_chem_comp_rdkit_properties.chi1n 7.792
_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 -0.340
_pdbe_chem_comp_rdkit_properties.kappa1 3.911
_pdbe_chem_comp_rdkit_properties.kappa2 5.519
_pdbe_chem_comp_rdkit_properties.kappa3 5.403
_pdbe_chem_comp_rdkit_properties.Phi 1.542
#
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
5SP UniChem DrugBank DB04034
5SP UniChem PDBe 5SP
5SP UniChem 'KEGG LIGAND' C00231
5SP UniChem ChEBI 16332
5SP UniChem ZINC ZINC000030320708
5SP UniChem SureChEMBL SCHEMBL50220
5SP UniChem HMDB HMDB0000868
5SP UniChem 'PubChem TPHARMA' 15172367
5SP UniChem NMRShiftDB 60020764
5SP UniChem Nikkaji J652.282C
5SP UniChem MetaboLights MTBLC16332
5SP UniChem BRENDA 182224
5SP UniChem BRENDA 5631
5SP UniChem BRENDA 644
5SP UniChem 'Probes And Drugs' PD006540
5SP UniChem PubChem 439190
#
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
5SP O1 -2.911 0.994 1.229 ETKDGv3 1
5SP C2 -2.759 -0.398 1.216 ETKDGv3 2
5SP C3 -2.069 -0.872 -0.039 ETKDGv3 3
5SP O4 -1.944 -2.075 -0.210 ETKDGv3 4
5SP C5 -1.499 0.074 -1.081 ETKDGv3 5
5SP C6 -0.257 0.834 -0.557 ETKDGv3 6
5SP C7 0.892 -0.124 -0.212 ETKDGv3 7
5SP O8 2.001 0.625 0.229 ETKDGv3 8
5SP P9 3.259 -0.456 0.627 ETKDGv3 9
5SP O10 2.851 -1.311 1.806 ETKDGv3 10
5SP O11 4.635 0.435 1.043 ETKDGv3 11
5SP O12 3.621 -1.449 -0.696 ETKDGv3 12
5SP O13 -2.483 0.993 -1.481 ETKDGv3 13
5SP O14 0.191 1.732 -1.541 ETKDGv3 14
5SP HO1 -3.358 1.215 2.087 ETKDGv3 15
5SP H2 -2.157 -0.717 2.095 ETKDGv3 16
5SP H2A -3.761 -0.878 1.274 ETKDGv3 17
5SP H5 -1.181 -0.517 -1.973 ETKDGv3 18
5SP H6 -0.521 1.394 0.370 ETKDGv3 19
5SP H7 0.553 -0.817 0.590 ETKDGv3 20
5SP H7A 1.152 -0.709 -1.125 ETKDGv3 21
5SP HO11 4.843 0.968 0.235 ETKDGv3 22
5SP HO12 4.401 -1.985 -0.403 ETKDGv3 23
5SP HO13 -3.141 0.489 -2.029 ETKDGv3 24
5SP HO14 -0.356 2.556 -1.453 ETKDGv3 25
#