data_PDO
#
_chem_comp.id PDO
_chem_comp.name 1,3-PROPANDIOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C3 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 2024-09-27
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces HPG
_chem_comp.formula_weight 76.094
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PDO
_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 1NAI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_chem_comp.pdbx_pcm Y
#
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
PDO C1 C1 C 0 1 N N N N N N 30.221 7.281 40.592 -1.249 -0.502 0.000 C1 PDO 1
PDO O1 O1 O 0 1 N N N N N N 31.364 7.997 41.091 -2.416 0.323 -0.000 O1 PDO 2
PDO C2 C2 C 0 1 N N N N N N 29.148 8.302 40.250 0.000 0.382 -0.000 C2 PDO 3
PDO C3 C3 C 0 1 N N N N N N 29.863 9.604 39.966 1.249 -0.502 0.000 C3 PDO 4
PDO O3 O3 O 0 1 N N N N N N 30.363 9.589 38.633 2.416 0.323 -0.000 O3 PDO 5
PDO H11 H11 H 0 1 N N N N N N 30.497 6.709 39.694 -1.249 -1.131 0.890 H11 PDO 6
PDO H12 H12 H 0 1 N N N N N N 29.849 6.584 41.358 -1.249 -1.131 -0.890 H12 PDO 7
PDO HO1 HO1 H 0 1 N N N N N N 32.052 7.381 41.313 -3.247 -0.171 0.000 HO1 PDO 8
PDO H21 H21 H 0 1 N N N N N N 28.577 7.978 39.368 -0.000 1.011 -0.890 H21 PDO 9
PDO H22 H22 H 0 1 N N N N N N 28.451 8.423 41.092 0.000 1.011 0.890 H22 PDO 10
PDO H31 H31 H 0 1 N N N N N N 29.160 10.442 40.085 1.249 -1.131 0.890 H31 PDO 11
PDO H32 H32 H 0 1 N N N N N N 30.699 9.724 40.670 1.249 -1.131 -0.890 H32 PDO 12
PDO HO3 HO3 H 0 1 N N N N N N 30.812 10.407 38.454 3.247 -0.171 0.000 HO3 PDO 13
#
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
PDO C1 O1 SING N N 1
PDO C1 C2 SING N N 2
PDO C1 H11 SING N N 3
PDO C1 H12 SING N N 4
PDO O1 HO1 SING N N 5
PDO C2 C3 SING N N 6
PDO C2 H21 SING N N 7
PDO C2 H22 SING N N 8
PDO C3 O3 SING N N 9
PDO C3 H31 SING N N 10
PDO C3 H32 SING N N 11
PDO O3 HO3 SING N N 12
#
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
PDO SMILES ACDLabs 11.02 OCCCO
PDO SMILES_CANONICAL CACTVS 3.352 OCCCO
PDO SMILES CACTVS 3.352 OCCCO
PDO SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 'C(CO)CO'
PDO SMILES 'OpenEye OEToolkits' 1.7.0 'C(CO)CO'
PDO InChI InChI 1.03 InChI=1S/C3H8O2/c4-2-1-3-5/h4-5H,1-3H2
PDO InChIKey InChI 1.03 YPFDHNVEDLHUCE-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
PDO 'SYSTEMATIC NAME' ACDLabs 11.02 propane-1,3-diol
PDO 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.6.1 propane-1,3-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PDO 'Create component' 1999-07-08 EBI
PDO 'Modify descriptor' 2011-06-04 RCSB
PDO 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PDO
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C2
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id PDO
_pdbe_chem_comp_drugbank_details.drugbank_id DB02774
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 1,3-Propanediol
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 504-63-2
_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
PDO 1,3-Dihydroxypropane DrugBank ?
PDO '1,3-propylene glycol' DrugBank ?
PDO 2-(hydroxymethyl)ethanol DrugBank ?
PDO 'beta-Propylene glycol' DrugBank ?
PDO Propane-1,3-diol DrugBank ?
PDO 'Trimethylene glycol' DrugBank ?
PDO 'β-propylene glycol' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id PDO
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02774
_pdbe_chem_comp_drugbank_classification.parent 'Primary alcohols'
_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 primary alcohols. These are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl).'
#
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
PDO DB02774 'Haloalkane dehalogenase' 'Sphingobium indicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S)' D4Z2G1 unknown 1
PDO DB02774 'ADP-ribosylation factor 1' Humans P84077 unknown 2
#
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
PDO C1 C 7.702 0.375 1
PDO O1 O 9.002 -0.375 2
PDO C2 C 6.404 -0.375 3
PDO C3 C 5.104 0.375 4
PDO O3 O 3.805 -0.375 5
#
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
PDO C1 O1 SINGLE NONE 1
PDO C1 C2 SINGLE NONE 2
PDO C2 C3 SINGLE NONE 3
PDO C3 O3 SINGLE NONE 4
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id PDO
_pdbe_chem_comp_rdkit_properties.exactmw 76.052
_pdbe_chem_comp_rdkit_properties.amw 76.095
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 5
_pdbe_chem_comp_rdkit_properties.NumAtoms 13
_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 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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 42.471
_pdbe_chem_comp_rdkit_properties.tpsa 40.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.639
_pdbe_chem_comp_rdkit_properties.CrippenMR 18.789
_pdbe_chem_comp_rdkit_properties.chi0v 2.316
_pdbe_chem_comp_rdkit_properties.chi1v 0.908
_pdbe_chem_comp_rdkit_properties.chi2v 0.102
_pdbe_chem_comp_rdkit_properties.chi3v 0.102
_pdbe_chem_comp_rdkit_properties.chi4v 0.021
_pdbe_chem_comp_rdkit_properties.chi0n 10.316
_pdbe_chem_comp_rdkit_properties.chi1n 4.725
_pdbe_chem_comp_rdkit_properties.chi2n 0.102
_pdbe_chem_comp_rdkit_properties.chi3n 0.102
_pdbe_chem_comp_rdkit_properties.chi4n 0.021
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.080
_pdbe_chem_comp_rdkit_properties.kappa1 0.532
_pdbe_chem_comp_rdkit_properties.kappa2 3.920
_pdbe_chem_comp_rdkit_properties.kappa3 3.920
_pdbe_chem_comp_rdkit_properties.Phi 0.417
#
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
PDO UniChem DrugBank DB02774
PDO UniChem 'KEGG LIGAND' C02457
PDO UniChem ChEBI 16109
PDO UniChem ZINC ZINC000001529437
PDO UniChem eMolecules 514561
PDO UniChem fdasrs 5965N8W85T
PDO UniChem NMRShiftDB 10016663
PDO UniChem Nikkaji J2.606I
PDO UniChem 'EPA CompTox Dashboard' DTXSID8041246
PDO UniChem MetaboLights MTBLC16109
PDO UniChem BRENDA 2925
PDO UniChem BRENDA 3664
PDO UniChem BRENDA 43125
PDO UniChem BRENDA 44730
PDO UniChem BRENDA 90129
PDO UniChem Rhea 16109
PDO UniChem ChemicalBook CB5853689
PDO UniChem rxnorm 1,3-PROPANEDIOL
PDO UniChem MedChemExpress HY-W017758
PDO UniChem 'Probes And Drugs' PD007650
PDO UniChem CCDC QATTEK
PDO UniChem SureChEMBL SCHEMBL15135
PDO UniChem 'PubChem TPHARMA' 15461782
PDO UniChem PubChem 10442
PDO UniChem Mcule MCULE-5166824786
PDO UniChem ACTor 504-63-2
#
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
PDO C1 1.072 -0.697 -0.512 ETKDGv3 1
PDO O1 2.244 -0.188 -1.086 ETKDGv3 2
PDO C2 0.024 0.412 -0.378 ETKDGv3 3
PDO C3 -1.279 -0.127 0.217 ETKDGv3 4
PDO O3 -2.232 0.898 0.303 ETKDGv3 5
PDO H11 1.292 -1.143 0.485 ETKDGv3 6
PDO H12 0.679 -1.501 -1.170 ETKDGv3 7
PDO HO1 2.712 0.321 -0.374 ETKDGv3 8
PDO H21 0.423 1.216 0.277 ETKDGv3 9
PDO H22 -0.182 0.844 -1.382 ETKDGv3 10
PDO H31 -1.093 -0.565 1.225 ETKDGv3 11
PDO H32 -1.683 -0.928 -0.437 ETKDGv3 12
PDO HO3 -1.978 1.458 1.082 ETKDGv3 13
#