data_LX5
#
_chem_comp.id LX5
_chem_comp.name "[(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl] hydrogen sulfate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H12 O7 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-09-26
_chem_comp.pdbx_modified_date 2020-02-21
_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 228.220
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LX5
_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 6SXU
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
LX5 C1 C1 C 0 1 N N S N N N 8.436 23.895 -36.236 0.040 0.013 0.363 C1 LX5 1
LX5 C2 C2 C 0 1 N N N N N N 6.999 23.626 -36.510 -0.485 1.418 0.726 C2 LX5 2
LX5 C6 C3 C 0 1 N N N N N N 8.874 25.269 -34.071 -1.409 -2.010 0.724 C6 LX5 3
LX5 C5 C4 C 0 1 N N S N N N 8.529 23.974 -34.738 -1.166 -0.785 -0.161 C5 LX5 4
LX5 C3 C5 C 0 1 N N S N N N 6.666 22.633 -35.428 -1.762 1.580 -0.136 C3 LX5 5
LX5 C4 C6 C 0 1 N N S N N N 7.382 23.138 -34.199 -2.382 0.162 -0.098 C4 LX5 6
LX5 O7 O1 O 0 1 N N N N N N 7.736 26.187 -34.083 -2.455 -2.804 0.162 O7 LX5 7
LX5 O8 O2 O 0 1 N N N N N N 7.652 22.228 -33.173 -3.234 -0.042 -1.228 O8 LX5 8
LX5 O9 O3 O 0 1 N N N N N N 5.304 22.279 -35.240 -2.648 2.537 0.448 O9 LX5 9
LX5 O10 O4 O 0 1 N N N N N N 9.074 22.815 -36.863 1.041 0.111 -0.652 O10 LX5 10
LX5 S11 S1 S 0 1 N N N N N N 10.488 22.874 -37.432 2.467 0.079 -0.122 S11 LX5 11
LX5 O12 O5 O 0 1 N N N N N N 11.263 23.510 -36.392 2.771 -1.362 0.266 O12 LX5 12
LX5 O13 O6 O 0 1 N N N N N N 10.430 23.785 -38.563 3.312 0.385 -1.222 O13 LX5 13
LX5 O14 O7 O 0 1 N N N N N N 10.746 21.352 -37.698 2.462 0.826 1.087 O14 LX5 14
LX5 H1 H1 H 0 1 N N N N N N 8.735 24.855 -36.683 0.453 -0.471 1.248 H1 LX5 15
LX5 H21 H2 H 0 1 N N N N N N 6.394 24.540 -36.416 -0.731 1.471 1.786 H21 LX5 16
LX5 H2 H3 H 0 1 N N N N N N 6.855 23.193 -37.511 0.251 2.179 0.466 H2 LX5 17
LX5 H6 H4 H 0 1 N N N N N N 9.164 25.070 -33.029 -0.496 -2.601 0.784 H6 LX5 18
LX5 H61 H5 H 0 1 N N N N N N 9.716 25.734 -34.604 -1.697 -1.684 1.724 H61 LX5 19
LX5 H5 H6 H 0 1 N N N N N N 9.406 23.347 -34.517 -0.989 -1.098 -1.190 H5 LX5 20
LX5 H3 H7 H 0 1 N N N N N N 7.190 21.708 -35.710 -1.505 1.865 -1.156 H3 LX5 21
LX5 H4 H8 H 0 1 N N N N N N 6.691 23.875 -33.764 -2.935 0.012 0.829 H4 LX5 22
LX5 HO7 H9 H 0 1 N N N N N N 7.979 26.999 -33.655 -2.663 -3.599 0.673 HO7 LX5 23
LX5 HO8 H10 H 0 1 N N N N N N 8.102 22.673 -32.465 -4.015 0.528 -1.240 HO8 LX5 24
LX5 HO9 H11 H 0 1 N N N N N N 5.235 21.650 -34.532 -2.275 3.426 0.521 HO9 LX5 25
LX5 H7 H12 H 0 1 N N N N N N 11.550 24.366 -36.689 3.661 -1.494 0.619 H7 LX5 26
#
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
LX5 O13 S11 DOUB N N 1
LX5 O14 S11 DOUB N N 2
LX5 S11 O10 SING N N 3
LX5 S11 O12 SING N N 4
LX5 O10 C1 SING N N 5
LX5 C2 C1 SING N N 6
LX5 C2 C3 SING N N 7
LX5 C1 C5 SING N N 8
LX5 C3 O9 SING N N 9
LX5 C3 C4 SING N N 10
LX5 C5 C4 SING N N 11
LX5 C5 C6 SING N N 12
LX5 C4 O8 SING N N 13
LX5 O7 C6 SING N N 14
LX5 C1 H1 SING N N 15
LX5 C2 H21 SING N N 16
LX5 C2 H2 SING N N 17
LX5 C6 H6 SING N N 18
LX5 C6 H61 SING N N 19
LX5 C5 H5 SING N N 20
LX5 C3 H3 SING N N 21
LX5 C4 H4 SING N N 22
LX5 O7 HO7 SING N N 23
LX5 O8 HO8 SING N N 24
LX5 O9 HO9 SING N N 25
LX5 O12 H7 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
LX5 InChI InChI 1.03 InChI=1S/C6H12O7S/c7-2-3-5(13-14(10,11)12)1-4(8)6(3)9/h3-9H,1-2H2,(H,10,11,12)/t3-,4+,5+,6+/m1/s1
LX5 InChIKey InChI 1.03 WLWVVBPJYHXDMI-VANKVMQKSA-N
LX5 SMILES_CANONICAL CACTVS 3.385 OC[C@H]1[C@H](O)[C@@H](O)C[C@@H]1O[S](O)(=O)=O
LX5 SMILES CACTVS 3.385 OC[CH]1[CH](O)[CH](O)C[CH]1O[S](O)(=O)=O
LX5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C1[C@@H]([C@H]([C@@H]([C@H]1OS(=O)(=O)O)CO)O)O
LX5 SMILES "OpenEye OEToolkits" 2.0.7 C1C(C(C(C1OS(=O)(=O)O)CO)O)O
#
_pdbx_chem_comp_identifier.comp_id LX5
_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
"[(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl] hydrogen sulfate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LX5 'Create component' 2019-09-26 EBI
LX5 'Initial release' 2020-02-26 RCSB
#
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
LX5 C1 C 7.540 -0.286 1
LX5 C2 C 8.004 -1.712 2
LX5 C6 C 8.754 2.096 3
LX5 C5 C 8.754 0.596 4
LX5 C3 C 9.504 -1.712 5
LX5 C4 C 9.967 -0.286 6
LX5 O7 O 10.053 2.846 7
LX5 O8 O 11.394 0.178 8
LX5 O9 O 10.386 -2.926 9
LX5 O10 O 6.114 0.178 10
LX5 S11 S 4.999 -0.826 11
LX5 O12 O 6.003 -1.941 12
LX5 O13 O 3.884 -1.830 13
LX5 O14 O 3.995 0.289 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
LX5 O13 S11 DOUBLE NONE 1
LX5 O14 S11 DOUBLE NONE 2
LX5 S11 O10 SINGLE NONE 3
LX5 S11 O12 SINGLE NONE 4
LX5 C1 O10 SINGLE BEGINDASH 5
LX5 C2 C1 SINGLE NONE 6
LX5 C2 C3 SINGLE NONE 7
LX5 C1 C5 SINGLE NONE 8
LX5 C3 O9 SINGLE BEGINWEDGE 9
LX5 C3 C4 SINGLE NONE 10
LX5 C5 C4 SINGLE NONE 11
LX5 C5 C6 SINGLE BEGINWEDGE 12
LX5 C4 O8 SINGLE BEGINDASH 13
LX5 O7 C6 SINGLE NONE 14
#
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
LX5 MurckoScaffold S1 scaffold C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
LX5 cyclopentane F1 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-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
LX5 C1 S1 1
LX5 C2 S1 1
LX5 C5 S1 1
LX5 C3 S1 1
LX5 C4 S1 1
LX5 C1 F1 1
LX5 C2 F1 1
LX5 C3 F1 1
LX5 C4 F1 1
LX5 C5 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LX5
_pdbe_chem_comp_rdkit_properties.exactmw 228.030
_pdbe_chem_comp_rdkit_properties.amw 228.222
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_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 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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 98.098
_pdbe_chem_comp_rdkit_properties.tpsa 124.290
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.092
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.628
_pdbe_chem_comp_rdkit_properties.chi0v 7.082
_pdbe_chem_comp_rdkit_properties.chi1v 4.316
_pdbe_chem_comp_rdkit_properties.chi2v 1.546
_pdbe_chem_comp_rdkit_properties.chi3v 1.546
_pdbe_chem_comp_rdkit_properties.chi4v 1.025
_pdbe_chem_comp_rdkit_properties.chi0n 18.266
_pdbe_chem_comp_rdkit_properties.chi1n 8.616
_pdbe_chem_comp_rdkit_properties.chi2n 1.175
_pdbe_chem_comp_rdkit_properties.chi3n 1.175
_pdbe_chem_comp_rdkit_properties.chi4n 0.696
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.250
_pdbe_chem_comp_rdkit_properties.kappa1 3.371
_pdbe_chem_comp_rdkit_properties.kappa2 4.088
_pdbe_chem_comp_rdkit_properties.kappa3 2.624
_pdbe_chem_comp_rdkit_properties.Phi 0.984
#
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
LX5 UniChem PDBe LX5
LX5 UniChem PubChem 145946074
#
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
LX5 C1 0.547 -0.270 -0.115 ETKDGv3 1
LX5 C2 0.125 -1.532 0.638 ETKDGv3 2
LX5 C6 -0.554 1.953 -0.681 ETKDGv3 3
LX5 C5 -0.445 0.804 0.333 ETKDGv3 4
LX5 C3 -1.353 -1.347 1.013 ETKDGv3 5
LX5 C4 -1.763 0.054 0.530 ETKDGv3 6
LX5 O7 -1.430 2.934 -0.198 ETKDGv3 7
LX5 O8 -2.560 0.705 1.485 ETKDGv3 8
LX5 O9 -2.167 -2.346 0.449 ETKDGv3 9
LX5 O10 1.860 0.118 0.236 ETKDGv3 10
LX5 S11 2.968 -0.541 -0.866 ETKDGv3 11
LX5 O12 4.527 -0.190 -0.344 ETKDGv3 12
LX5 O13 2.762 0.056 -2.231 ETKDGv3 13
LX5 O14 2.810 -2.034 -0.939 ETKDGv3 14
LX5 H1 0.412 -0.439 -1.211 ETKDGv3 15
LX5 H21 0.284 -2.434 0.007 ETKDGv3 16
LX5 H2 0.731 -1.647 1.565 ETKDGv3 17
LX5 H6 0.454 2.402 -0.832 ETKDGv3 18
LX5 H61 -0.919 1.571 -1.661 ETKDGv3 19
LX5 H5 -0.111 1.217 1.313 ETKDGv3 20
LX5 H3 -1.448 -1.404 2.120 ETKDGv3 21
LX5 H4 -2.305 -0.011 -0.443 ETKDGv3 22
LX5 HO7 -1.459 3.643 -0.892 ETKDGv3 23
LX5 HO8 -3.453 0.275 1.445 ETKDGv3 24
LX5 HO9 -2.038 -2.324 -0.536 ETKDGv3 25
LX5 H7 4.526 0.788 -0.184 ETKDGv3 26
#