data_DIO
#
_chem_comp.id DIO
_chem_comp.name "1,4-DIETHYLENE DIOXIDE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H8 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 DOX
_chem_comp.formula_weight 88.105
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DIO
_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 1AF4
_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
DIO C1 C1 C 0 1 N N N N N N 4.027 34.555 4.863 -1.147 0.244 0.724 C1 DIO 1
DIO C2 C2 C 0 1 N N N N N N 2.539 32.753 5.104 1.147 0.244 0.724 C2 DIO 2
DIO "C1'" "C1'" C 0 1 N N N N N N 3.102 35.195 3.826 -1.147 -0.244 -0.724 "C1'" DIO 3
DIO "C2'" "C2'" C 0 1 N N N N N N 1.610 33.389 3.998 1.147 -0.244 -0.724 "C2'" DIO 4
DIO O1 O1 O 0 1 N N N N N N 3.263 33.778 5.797 0.000 -0.266 1.403 O1 DIO 5
DIO "O1'" "O1'" O 0 1 N N N N N N 2.385 34.171 3.094 0.000 0.266 -1.403 "O1'" DIO 6
DIO H11 1H1 H 0 1 N N N N N N 4.835 33.954 4.385 -1.123 1.334 0.739 H11 DIO 7
DIO H12 2H1 H 0 1 N N N N N N 4.665 35.312 5.375 -2.050 -0.104 1.225 H12 DIO 8
DIO H21 1H2 H 0 1 N N N N N N 1.965 32.103 5.805 2.050 -0.104 1.225 H21 DIO 9
DIO H22 2H2 H 0 1 N N N N N N 3.219 31.978 4.679 1.123 1.334 0.739 H22 DIO 10
DIO "H1'1" "1H1'" H 0 0 N N N N N N 2.410 35.938 4.287 -1.123 -1.334 -0.739 "H1'1" DIO 11
DIO "H1'2" "2H1'" H 0 0 N N N N N N 3.653 35.884 3.145 -2.050 0.104 -1.225 "H1'2" DIO 12
DIO "H2'1" "1H2'" H 0 0 N N N N N N 1.005 32.616 3.467 1.123 -1.334 -0.739 "H2'1" DIO 13
DIO "H2'2" "2H2'" H 0 0 N N N N N N 0.773 33.975 4.444 2.050 0.104 -1.225 "H2'2" DIO 14
#
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
DIO C1 "C1'" SING N N 1
DIO C1 O1 SING N N 2
DIO C1 H11 SING N N 3
DIO C1 H12 SING N N 4
DIO C2 "C2'" SING N N 5
DIO C2 O1 SING N N 6
DIO C2 H21 SING N N 7
DIO C2 H22 SING N N 8
DIO "C1'" "O1'" SING N N 9
DIO "C1'" "H1'1" SING N N 10
DIO "C1'" "H1'2" SING N N 11
DIO "C2'" "O1'" SING N N 12
DIO "C2'" "H2'1" SING N N 13
DIO "C2'" "H2'2" SING N N 14
#
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
DIO SMILES ACDLabs 10.04 O1CCOCC1
DIO SMILES_CANONICAL CACTVS 3.341 C1COCCO1
DIO SMILES CACTVS 3.341 C1COCCO1
DIO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1COCCO1
DIO SMILES "OpenEye OEToolkits" 1.5.0 C1COCCO1
DIO InChI InChI 1.03 InChI=1S/C4H8O2/c1-2-6-4-3-5-1/h1-4H2
DIO InChIKey InChI 1.03 RYHBNJHYFVUHQT-UHFFFAOYSA-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
DIO "SYSTEMATIC NAME" ACDLabs 10.04 1,4-dioxane
DIO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1,4-dioxane
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DIO 'Create component' 1999-07-08 RCSB
DIO 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id DIO
_pdbe_chem_comp_drugbank_details.drugbank_id DB03316
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 1,4-Dioxane
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 123-91-1
_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
DIO 1,4-dioxacyclohexane DrugBank ?
DIO 1,4-Dioxan DrugBank ?
DIO 1,4-Dioxane DrugBank ?
DIO 'di(ethylene oxide)' DrugBank ?
DIO Dioxan-1,4 DrugBank ?
DIO Dioxane-1,4 DrugBank ?
DIO 'glycol ethylene ether' DrugBank ?
DIO p-Dioxane DrugBank ?
DIO tetrahydro-1,4-dioxin DrugBank ?
DIO tetrahydro-p-dioxin DrugBank ?
DIO tetrahydro-para-dioxin DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id DIO
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03316
_pdbe_chem_comp_drugbank_classification.parent 1,4-dioxanes
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Dioxanes
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as 1,4-dioxanes. These are organic compounds containing 1,4-dioxane, an aliphatic six-member ring with two oxygen atoms in ring positions 1 and 4.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
DIO DB03316 'Subtilisin Carlsberg' 'Bacillus licheniformis' P00780 unknown 1
DIO DB03316 'Tumor necrosis factor ligand superfamily member 13B' Humans Q9Y275 unknown 2
DIO DB03316 Epsin-1 Humans Q9Y6I3 unknown 3
DIO DB03316 'Structural polyprotein' SINV P03316 unknown 4
DIO DB03316 'Transforming growth factor beta-3' Humans P10600 unknown 5
#
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
DIO C1 C 4.299 -1.500 1
DIO C2 C 5.598 0.750 2
DIO "C1'" C 3.000 -0.750 3
DIO "C2'" C 4.299 1.500 4
DIO O1 O 5.598 -0.750 5
DIO "O1'" O 3.000 0.750 6
#
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
DIO C1 "C1'" SINGLE NONE 1
DIO C1 O1 SINGLE NONE 2
DIO C2 "C2'" SINGLE NONE 3
DIO C2 O1 SINGLE NONE 4
DIO "C1'" "O1'" SINGLE NONE 5
DIO "C2'" "O1'" SINGLE NONE 6
#
_pdbe_chem_comp_substructure.comp_id DIO
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles C1COCCO1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C4H8O2/c1-2-6-4-3-5-1/h1-4H2
_pdbe_chem_comp_substructure.substructure_inchikeys RYHBNJHYFVUHQT-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
DIO C1 S1 1
DIO C2 S1 1
DIO "C1'" S1 1
DIO "C2'" S1 1
DIO O1 S1 1
DIO "O1'" S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DIO
_pdbe_chem_comp_rdkit_properties.exactmw 88.052
_pdbe_chem_comp_rdkit_properties.amw 88.106
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 6
_pdbe_chem_comp_rdkit_properties.NumAtoms 14
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 48.295
_pdbe_chem_comp_rdkit_properties.tpsa 18.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.033
_pdbe_chem_comp_rdkit_properties.CrippenMR 21.638
_pdbe_chem_comp_rdkit_properties.chi0v 2.816
_pdbe_chem_comp_rdkit_properties.chi1v 1.316
_pdbe_chem_comp_rdkit_properties.chi2v 0.287
_pdbe_chem_comp_rdkit_properties.chi3v 0.287
_pdbe_chem_comp_rdkit_properties.chi4v 0.134
_pdbe_chem_comp_rdkit_properties.chi0n 10.816
_pdbe_chem_comp_rdkit_properties.chi1n 5.316
_pdbe_chem_comp_rdkit_properties.chi2n 0.287
_pdbe_chem_comp_rdkit_properties.chi3n 0.287
_pdbe_chem_comp_rdkit_properties.chi4n 0.134
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.080
_pdbe_chem_comp_rdkit_properties.kappa1 0.740
_pdbe_chem_comp_rdkit_properties.kappa2 2.157
_pdbe_chem_comp_rdkit_properties.kappa3 0.954
_pdbe_chem_comp_rdkit_properties.Phi 0.266
#
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
DIO UniChem ChEMBL CHEMBL453716
DIO UniChem DrugBank DB03316
DIO UniChem PDBe DIO
DIO UniChem 'KEGG LIGAND' C14440
DIO UniChem ChEBI 47032
DIO UniChem ZINC ZINC000001648204
DIO UniChem eMolecules 483565
DIO UniChem fdasrs J8A3S10O7S
DIO UniChem HMDB HMDB0244216
DIO UniChem NMRShiftDB 10016061
DIO UniChem LINCS LSM-37087
DIO UniChem ACTor 123-91-1
DIO UniChem Nikkaji J2.502J
DIO UniChem MetaboLights MTBLC47032
DIO UniChem BRENDA 174397
DIO UniChem BRENDA 202494
DIO UniChem BRENDA 2960
DIO UniChem BRENDA 44647
DIO UniChem BRENDA 93221
DIO UniChem BRENDA 9759
DIO UniChem ChemicalBook CB6240532
DIO UniChem rxnorm DIOXANE
DIO UniChem 'Probes And Drugs' PD007092
DIO UniChem 'EPA CompTox Dashboard' DTXSID4020533
DIO UniChem SureChEMBL SCHEMBL284
DIO UniChem 'PubChem TPHARMA' 15146328
DIO UniChem PubChem 31275
DIO UniChem Mcule MCULE-5088019198
#
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
DIO C1 -1.199 0.613 0.293 ETKDGv3 1
DIO C2 1.020 0.909 -0.273 ETKDGv3 2
DIO "C1'" -1.020 -0.909 0.201 ETKDGv3 3
DIO "C2'" 1.199 -0.613 -0.365 ETKDGv3 4
DIO O1 -0.310 1.272 -0.587 ETKDGv3 5
DIO "O1'" 0.310 -1.272 0.515 ETKDGv3 6
DIO H11 -2.240 0.871 0.005 ETKDGv3 7
DIO H12 -1.045 0.960 1.340 ETKDGv3 8
DIO H21 1.702 1.396 -1.001 ETKDGv3 9
DIO H22 1.297 1.272 0.742 ETKDGv3 10
DIO "H1'1" -1.702 -1.396 0.929 ETKDGv3 11
DIO "H1'2" -1.297 -1.272 -0.814 ETKDGv3 12
DIO "H2'1" 1.045 -0.960 -1.412 ETKDGv3 13
DIO "H2'2" 2.240 -0.871 -0.077 ETKDGv3 14
#