data_OXY
#
_chem_comp.id OXY
_chem_comp.name 'OXYGEN MOLECULE'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 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 O2
_chem_comp.formula_weight 31.999
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code OXY
_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 1HMO
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm N
#
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
OXY O1 O1 O 0 1 N N N N N N 27.290 26.888 33.875 0.000 0.000 -0.501 O1 OXY 1
OXY O2 O2 O 0 1 N N N N N N 26.630 27.419 32.640 0.000 0.000 0.501 O2 OXY 2
#
_chem_comp_bond.comp_id OXY
_chem_comp_bond.atom_id_1 O1
_chem_comp_bond.atom_id_2 O2
_chem_comp_bond.value_order DOUB
_chem_comp_bond.pdbx_aromatic_flag N
_chem_comp_bond.pdbx_stereo_config N
_chem_comp_bond.pdbx_ordinal 1
#
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
OXY SMILES_CANONICAL CACTVS 3.341 O=O
OXY SMILES CACTVS 3.341 O=O
OXY SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 O=O
OXY SMILES 'OpenEye OEToolkits' 1.5.0 O=O
OXY InChI InChI 1.03 InChI=1S/O2/c1-2
OXY InChIKey InChI 1.03 MYMOFIZGZYHOMD-UHFFFAOYSA-N
#
_pdbx_chem_comp_identifier.comp_id OXY
_pdbx_chem_comp_identifier.type 'SYSTEMATIC NAME'
_pdbx_chem_comp_identifier.program 'OpenEye OEToolkits'
_pdbx_chem_comp_identifier.program_version 1.5.0
_pdbx_chem_comp_identifier.identifier 'molecular oxygen'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
OXY 'Create component' 1999-07-08 RCSB
OXY 'Modify descriptor' 2011-06-04 RCSB
OXY 'Modify PCM' 2024-09-27 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id OXY
_pdbe_chem_comp_drugbank_details.drugbank_id DB09140
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Oxygen
_pdbe_chem_comp_drugbank_details.description
"Oxygen is an element displayed by the symbol O, and atomic number 8.  It is an essential element for human survival. Decreased oxygen levels may be treated with medical oxygen therapy. Treatment with oxygen serves to increase blood oxygen levels and also exerts a secondary effect of decreasing blood flow resistance in the diseased lung, leading to decreased cardiovascular workload in an attempt to oxygenate the lungs. Oxygen therapy is used to treat emphysema, pneumonia, some heart disorders (congestive heart failure), some disorders that cause increased pulmonary artery pressure, and any disease that impairs the body's ability to take up and use gaseous oxygen. Higher level of oxygen than ambient air (hyperoxia) can be introduced under normobaric or hyperbaric conditions."
_pdbe_chem_comp_drugbank_details.cas_number 7782-44-7
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Oxygen therapy increases the arterial pressure of oxygen and is effective in improving gas exchange and oxygen delivery to tissues, provided that there are functional alveolar units. Oxygen plays a critical role as an electron acceptor during oxidative phosphorylation in the electron transport chain through activation of cytochrome c oxidase (terminal enzyme of the electron transport chain). This process achieves successful aerobic respiration in organisms to generate ATP molecules as an energy source in many tissues. Oxygen supplementation acts to restore normal cellular activity at the mitochondrial level and reduce metabolic acidosis. There is also evidence that oxygen may interact with O2-sensitive voltage-gated potassium channels in glomus cells and cause hyperpolarization of mitochondrial membrane [A19120].'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
OXY Oxygen ChEMBL 'International Nonproprietary Name'
OXY Dioxygen DrugBank ?
OXY 'Molecular oxygen' DrugBank ?
OXY Oxygen DrugBank ?
OXY 'Oxygen USP' DrugBank ?
OXY 'Pure oxygen' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id OXY
_pdbe_chem_comp_drugbank_classification.drugbank_id DB09140
_pdbe_chem_comp_drugbank_classification.parent 'Other non-metal oxides'
_pdbe_chem_comp_drugbank_classification.kingdom 'Inorganic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Other non-metal organides'
_pdbe_chem_comp_drugbank_classification.superclass 'Homogeneous non-metal compounds'
_pdbe_chem_comp_drugbank_classification.description
"This compound belongs to the class of inorganic compounds known as other non-metal oxides. These are inorganic compounds containing an oxygen atom of an oxidation state of -2, in which the heaviest atom bonded to the oxygen belongs to the class of 'other non-metals'."
#
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
OXY DB09140 'Cytochrome c oxidase subunit 1' Humans P00395 unknown 1
OXY DB09140 'NADPH oxidase 1' Humans Q9Y5S8 unknown 2
#
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
OXY O1 O 3.000 0.000 1
OXY O2 O 4.500 0.000 2
#
_pdbe_chem_comp_bond_depiction.comp_id OXY
_pdbe_chem_comp_bond_depiction.atom_id_1 O1
_pdbe_chem_comp_bond_depiction.atom_id_2 O2
_pdbe_chem_comp_bond_depiction.value_order DOUBLE
_pdbe_chem_comp_bond_depiction.bond_dir NONE
_pdbe_chem_comp_bond_depiction.pdbx_ordinal 1
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id OXY
_pdbe_chem_comp_rdkit_properties.exactmw 31.990
_pdbe_chem_comp_rdkit_properties.amw 31.998
_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 2
_pdbe_chem_comp_rdkit_properties.NumAtoms 2
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_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 11.307
_pdbe_chem_comp_rdkit_properties.tpsa 34.140
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.067
_pdbe_chem_comp_rdkit_properties.CrippenMR 6.734
_pdbe_chem_comp_rdkit_properties.chi0v 0.816
_pdbe_chem_comp_rdkit_properties.chi1v 0.167
_pdbe_chem_comp_rdkit_properties.chi2v 0
_pdbe_chem_comp_rdkit_properties.chi3v 0
_pdbe_chem_comp_rdkit_properties.chi4v 0
_pdbe_chem_comp_rdkit_properties.chi0n 0.816
_pdbe_chem_comp_rdkit_properties.chi1n 0.167
_pdbe_chem_comp_rdkit_properties.chi2n 0
_pdbe_chem_comp_rdkit_properties.chi3n 0
_pdbe_chem_comp_rdkit_properties.chi4n 0
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.400
_pdbe_chem_comp_rdkit_properties.kappa1 1.600
_pdbe_chem_comp_rdkit_properties.kappa2 0.600
_pdbe_chem_comp_rdkit_properties.kappa3 -4.900
_pdbe_chem_comp_rdkit_properties.Phi 0.480
#
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
OXY UniChem ChEMBL CHEMBL1234886
OXY UniChem DrugBank DB09140
OXY UniChem PDBe OXY
OXY UniChem 'KEGG LIGAND' C00007
OXY UniChem ChEBI 15379
OXY UniChem ChEBI 26689
OXY UniChem ChEBI 27140
OXY UniChem eMolecules 474218
OXY UniChem atlas 'O2 2%'
OXY UniChem atlas 'O2 20%'
OXY UniChem fdasrs S88TT14065
OXY UniChem HMDB HMDB0001377
OXY UniChem 'PubChem TPHARMA' 15119552
OXY UniChem 'PubChem TPHARMA' 15218573
OXY UniChem NMRShiftDB 70128928
OXY UniChem ACTor 12185-07-8
OXY UniChem ACTor 1338-93-8
OXY UniChem ACTor 7782-44-7
OXY UniChem Recon o2
OXY UniChem Nikkaji J1.336.092H
OXY UniChem Nikkaji J415.761C
OXY UniChem 'EPA CompTox Dashboard' DTXSID2037681
OXY UniChem DrugCentral 4235
OXY UniChem MetaboLights MTBLC15379
OXY UniChem MetaboLights MTBLC26689
OXY UniChem MetaboLights MTBLC27140
OXY UniChem BRENDA 1180
OXY UniChem BRENDA 1403
OXY UniChem BRENDA 219467
OXY UniChem BRENDA 32877
OXY UniChem BRENDA 9
OXY UniChem Rhea 15379
OXY UniChem ChemicalBook CB5159244
OXY UniChem DailyMed OXYGEN
OXY UniChem ClinicalTrials OXYGEN
OXY UniChem rxnorm OXYGEN
OXY UniChem 'Probes And Drugs' PD009034
OXY UniChem SureChEMBL SCHEMBL821
OXY UniChem PubChem 977
#
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
OXY O1 0.575 0.000 0.000 ETKDGv3 1
OXY O2 -0.575 0.000 0.000 ETKDGv3 2
#