data_GOL
#
_chem_comp.id GOL
_chem_comp.name GLYCEROL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C3 H8 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "GLYCERIN; PROPANE-1,2,3-TRIOL"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2020-05-28
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces CRY
_chem_comp.formula_weight 92.094
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GOL
_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 1BXO
_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
GOL C1 C1 C 0 1 N N N N N N 29.490 2.376 31.160 -1.249 -0.665 0.295 C1 GOL 1
GOL O1 O1 O 0 1 N N N N N N 28.524 1.609 30.767 -2.413 -0.087 -0.300 O1 GOL 2
GOL C2 C2 C 0 1 N N N N N N 30.249 2.850 29.893 0.000 0.034 -0.245 C2 GOL 3
GOL O2 O2 O 0 1 N N N N N N 29.526 4.021 29.804 0.000 1.400 0.174 O2 GOL 4
GOL C3 C3 C 0 1 N N N N N N 31.780 2.780 29.785 1.249 -0.665 0.295 C3 GOL 5
GOL O3 O3 O 0 1 N N N N N N 32.215 4.129 29.472 2.413 -0.087 -0.300 O3 GOL 6
GOL H11 H11 H 0 1 N N N N N N 29.089 3.241 31.708 -1.295 -0.543 1.377 H11 GOL 7
GOL H12 H12 H 0 1 N N N N N N 30.169 1.821 31.824 -1.206 -1.727 0.051 H12 GOL 8
GOL HO1 HO1 H 0 1 N N N N N N 28.037 1.300 31.522 -3.244 -0.483 -0.003 HO1 GOL 9
GOL H2 H2 H 0 1 N N N N N N 30.271 2.201 29.005 -0.000 -0.012 -1.334 H2 GOL 10
GOL HO2 HO2 H 0 1 N N N N N N 29.825 4.522 29.054 0.000 1.517 1.134 HO2 GOL 11
GOL H31 H31 H 0 1 N N N N N N 32.222 2.438 30.733 1.295 -0.543 1.377 H31 GOL 12
GOL H32 H32 H 0 1 N N N N N N 32.083 2.080 28.993 1.206 -1.727 0.051 H32 GOL 13
GOL HO3 HO3 H 0 1 N N N N N N 33.162 4.147 29.393 3.244 -0.483 -0.003 HO3 GOL 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
GOL C1 O1 SING N N 1
GOL C1 C2 SING N N 2
GOL C1 H11 SING N N 3
GOL C1 H12 SING N N 4
GOL O1 HO1 SING N N 5
GOL C2 O2 SING N N 6
GOL C2 C3 SING N N 7
GOL C2 H2 SING N N 8
GOL O2 HO2 SING N N 9
GOL C3 O3 SING N N 10
GOL C3 H31 SING N N 11
GOL C3 H32 SING N N 12
GOL O3 HO3 SING N N 13
#
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
GOL SMILES ACDLabs 12.01 OCC(O)CO
GOL SMILES_CANONICAL CACTVS 3.370 OCC(O)CO
GOL SMILES CACTVS 3.370 OCC(O)CO
GOL SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C(C(CO)O)O
GOL SMILES "OpenEye OEToolkits" 1.7.0 C(C(CO)O)O
GOL InChI InChI 1.03 InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
GOL InChIKey InChI 1.03 PEDCQBHIVMGVHV-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
GOL "SYSTEMATIC NAME" ACDLabs 12.01 propane-1,2,3-triol
GOL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 propane-1,2,3-triol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GOL 'Create component' 1999-07-08 EBI
GOL 'Modify descriptor' 2011-06-04 RCSB
GOL 'Modify synonyms' 2020-05-28 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 GOL GLYCERIN ? ?
2 GOL PROPANE-1,2,3-TRIOL ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id GOL
_pdbe_chem_comp_drugbank_details.drugbank_id DB09462
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Glycerin
_pdbe_chem_comp_drugbank_details.description
'A trihydroxy sugar alcohol that is an intermediate in carbohydrate and lipid metabolism.'
_pdbe_chem_comp_drugbank_details.cas_number 56-81-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'When administered rectally, glycerin exerts a hygroscopic and/or local irritant action, drawing water from the tissues into the feces and reflexively stimulating evacuation.  Glycerin decreases intraocular pressure by creating an osmotic gradient between the blood and intraocular fluid, causing fluid to move out of the aqueous and vitreous humors into the bloodstream.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
GOL Glycerin ChEMBL 'United States Accepted Names'
GOL Glycerol ChEMBL Tradename
GOL 'Monoctanoin Component D' ChEMBL 'United States Accepted Names'
GOL Optim ChEMBL Tradename
GOL Osmoglyn ChEMBL Tradename
GOL GLYCERIN wwPDB ?
GOL PROPANE-1,2,3-TRIOL wwPDB ?
GOL 1,2,3-propanetriol DrugBank ?
GOL 1,2,3-trihydroxypropane DrugBank ?
GOL Glycerin DrugBank ?
GOL 'Glycerin, anhydrous' DrugBank ?
GOL Glycerin,anhydrous DrugBank ?
GOL Glycerine DrugBank ?
GOL Glycerinum DrugBank ?
GOL Glycerol DrugBank ?
GOL 'Monoctanoin component D' DrugBank ?
GOL Propanetriol DrugBank ?
GOL Trihydroxypropane DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GOL
_pdbe_chem_comp_drugbank_classification.drugbank_id DB09462
_pdbe_chem_comp_drugbank_classification.parent 'Sugar 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 sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.'
#
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
GOL DB09462 'Peroxisome proliferator-activated receptor delta' Humans Q03181 yes 1
GOL DB09462 'Group IIE secretory phospholipase A2' Humans Q9NZK7 unknown 2
GOL DB09462 'Inositol-3-phosphate synthase 1' Humans Q9NPH2 unknown 3
GOL DB09462 'Alcohol dehydrogenase 1B' Humans P00325 unknown 4
GOL DB09462 'Inositol 1,4,5-trisphosphate receptor type 1' Humans Q14643 unknown 5
GOL DB09462 Glycodelin Humans P09466 unknown 6
GOL DB09462 Alpha-N-acetylgalactosaminidase Humans P17050 unknown 7
GOL DB09462 'ADP-ribosylation factor 1' Humans P84077 unknown 8
GOL DB09462 "Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1" Humans O43252 unknown 9
GOL DB09462 'DNA mismatch repair protein MutL' 'Escherichia coli (strain K12)' P23367 unknown 10
GOL DB09462 'Ribonucleoside-diphosphate reductase 1 subunit beta' 'Escherichia coli (strain K12)' P69924 unknown 11
GOL DB09462 'Adenine DNA glycosylase' 'Escherichia coli (strain K12)' P17802 unknown 12
GOL DB09462 'tRNA (cytosine(38)-C(5))-methyltransferase' Humans O14717 unknown 13
GOL DB09462 'Maleylacetoacetate isomerase' Humans O43708 unknown 14
#
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
GOL C1 C 7.702 1.357 1
GOL O1 O 9.002 0.608 2
GOL C2 C 6.404 0.608 3
GOL O2 O 6.404 -0.892 4
GOL C3 C 5.104 1.357 5
GOL O3 O 3.805 0.608 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
GOL C1 O1 SINGLE NONE 1
GOL C1 C2 SINGLE NONE 2
GOL C2 O2 SINGLE NONE 3
GOL C2 C3 SINGLE NONE 4
GOL C3 O3 SINGLE NONE 5
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id GOL
_pdbe_chem_comp_rdkit_properties.exactmw 92.047
_pdbe_chem_comp_rdkit_properties.amw 92.094
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 6
_pdbe_chem_comp_rdkit_properties.NumAtoms 14
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_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 47.352
_pdbe_chem_comp_rdkit_properties.tpsa 60.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.668
_pdbe_chem_comp_rdkit_properties.CrippenMR 20.178
_pdbe_chem_comp_rdkit_properties.chi0v 2.725
_pdbe_chem_comp_rdkit_properties.chi1v 1.112
_pdbe_chem_comp_rdkit_properties.chi2v 0.185
_pdbe_chem_comp_rdkit_properties.chi3v 0.185
_pdbe_chem_comp_rdkit_properties.chi4v 0.021
_pdbe_chem_comp_rdkit_properties.chi0n 10.725
_pdbe_chem_comp_rdkit_properties.chi1n 4.837
_pdbe_chem_comp_rdkit_properties.chi2n 0.185
_pdbe_chem_comp_rdkit_properties.chi3n 0.185
_pdbe_chem_comp_rdkit_properties.chi4n 0.021
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.120
_pdbe_chem_comp_rdkit_properties.kappa1 0.844
_pdbe_chem_comp_rdkit_properties.kappa2 3.085
_pdbe_chem_comp_rdkit_properties.kappa3 2.138
_pdbe_chem_comp_rdkit_properties.Phi 0.434
#
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
GOL UniChem ChEMBL CHEMBL692
GOL UniChem DrugBank DB09462
GOL UniChem PDBe GOL
GOL UniChem 'Guide to Pharmacology' 5195
GOL UniChem 'KEGG LIGAND' C00116
GOL UniChem ChEBI 17754
GOL UniChem ZINC ZINC000000895048
GOL UniChem eMolecules 476493
GOL UniChem fdasrs PDC6A3C0OX
GOL UniChem HMDB HMDB0000131
GOL UniChem NMRShiftDB 10005613
GOL UniChem LINCS LSM-37180
GOL UniChem ACTor 175385-78-1
GOL UniChem ACTor 8043-29-6
GOL UniChem Recon glyc
GOL UniChem Nikkaji J1.916J
GOL UniChem 'EPA CompTox Dashboard' DTXSID9020663
GOL UniChem DrugCentral 1316
GOL UniChem MetaboLights MTBLC17754
GOL UniChem BRENDA 106408
GOL UniChem BRENDA 107129
GOL UniChem BRENDA 135
GOL UniChem BRENDA 161944
GOL UniChem BRENDA 164880
GOL UniChem BRENDA 166157
GOL UniChem BRENDA 183683
GOL UniChem BRENDA 234046
GOL UniChem BRENDA 49999
GOL UniChem Rhea 17754
GOL UniChem ChemicalBook CB51261492
GOL UniChem ChemicalBook CB5339206
GOL UniChem ChemicalBook CB8398945
GOL UniChem DailyMed GLYCERIN
GOL UniChem rxnorm GLYCERIN
GOL UniChem MedChemExpress HY-B1659
GOL UniChem 'Probes And Drugs' PD006499
GOL UniChem SureChEMBL SCHEMBL797
GOL UniChem 'PubChem TPHARMA' 14747384
GOL UniChem PubChem 753
GOL UniChem Mcule MCULE-6349111826
GOL UniChem ACTor 29796-42-7
GOL UniChem ACTor 56-81-5
#
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
GOL C1 1.300 -0.145 -0.352 ETKDGv3 1
GOL O1 1.512 1.119 -0.918 ETKDGv3 2
GOL C2 -0.171 -0.557 -0.500 ETKDGv3 3
GOL O2 -0.303 -1.897 -0.103 ETKDGv3 4
GOL C3 -1.100 0.323 0.358 ETKDGv3 5
GOL O3 -1.092 1.653 -0.088 ETKDGv3 6
GOL H11 1.586 -0.136 0.724 ETKDGv3 7
GOL H12 1.937 -0.892 -0.878 ETKDGv3 8
GOL HO1 2.473 1.325 -0.778 ETKDGv3 9
GOL H2 -0.456 -0.458 -1.574 ETKDGv3 10
GOL HO2 -1.156 -2.229 -0.488 ETKDGv3 11
GOL H31 -0.771 0.297 1.418 ETKDGv3 12
GOL H32 -2.139 -0.079 0.323 ETKDGv3 13
GOL HO3 -1.620 1.674 -0.928 ETKDGv3 14
#