data_URE
#
_chem_comp.id URE
_chem_comp.name UREA
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C H4 N2 O"
_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 ?
_chem_comp.formula_weight 60.055
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code URE
_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 1BV3
_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
URE C C C 0 1 N N N N N N -4.578 0.646 15.273 0.052 -0.000 0.000 C URE 1
URE O O O 0 1 N N N N N N -4.217 1.786 15.701 1.267 0.000 0.000 O URE 2
URE N1 N1 N 0 1 N N N N N N -5.124 -0.322 16.018 -0.621 -0.000 1.167 N1 URE 3
URE N2 N2 N 0 1 N N N N N N -4.377 0.463 13.955 -0.621 0.000 -1.167 N2 URE 4
URE HN11 1HN1 H 0 0 N N N N N N -5.413 -1.237 15.674 -0.136 -0.000 2.007 HN11 URE 5
URE HN12 2HN1 H 0 0 N N N N N N -5.936 0.087 16.478 -1.591 0.003 1.167 HN12 URE 6
URE HN21 1HN2 H 0 0 N N N N N N -3.960 1.201 13.387 -0.136 0.000 -2.007 HN21 URE 7
URE HN22 2HN2 H 0 0 N N N N N N -4.666 -0.452 13.611 -1.591 -0.000 -1.167 HN22 URE 8
#
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
URE C O DOUB N N 1
URE C N1 SING N N 2
URE C N2 SING N N 3
URE N1 HN11 SING N N 4
URE N1 HN12 SING N N 5
URE N2 HN21 SING N N 6
URE N2 HN22 SING N N 7
#
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
URE SMILES ACDLabs 10.04 O=C(N)N
URE SMILES_CANONICAL CACTVS 3.341 NC(N)=O
URE SMILES CACTVS 3.341 NC(N)=O
URE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(=O)(N)N
URE SMILES "OpenEye OEToolkits" 1.5.0 C(=O)(N)N
URE InChI InChI 1.03 InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4)
URE InChIKey InChI 1.03 XSQUKJJJFZCRTK-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
URE "SYSTEMATIC NAME" ACDLabs 10.04 urea
URE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 urea
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
URE 'Create component' 1999-07-08 RCSB
URE 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id URE
_pdbe_chem_comp_drugbank_details.drugbank_id DB03904
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Urea
_pdbe_chem_comp_drugbank_details.description
'A compound formed in the liver from ammonia produced by the deamination of amino acids. It is the principal end product of protein catabolism and constitutes about one half of the total urinary solids.'
_pdbe_chem_comp_drugbank_details.cas_number 57-13-6
_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
URE 'Sterile Urea' ChEMBL Tradename
URE Urea ChEMBL 'United States Accepted Names'
URE Ureaphil ChEMBL Tradename
URE Carbamide DrugBank ?
URE Carbonyldiamide DrugBank ?
URE Urea DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id URE
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03904
_pdbe_chem_comp_drugbank_classification.parent Ureas
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organic carbonic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as ureas. These are compounds containing two amine groups joined by a carbonyl (C=O) functional 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
URE DB03904 'Dihydrofolate reductase' 'Gallus gallus' P00378 yes 1
URE DB03904 Arginase-1 Humans P05089 unknown 2
URE DB03904 'Carbonic anhydrase 2' Humans P00918 unknown 3
URE DB03904 'Catenin beta-1' Humans P35222 unknown 4
URE DB03904 'Sulfoxide reductase catalytic subunit YedY' 'Escherichia coli O157:H7' Q8XB74 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
URE C C 5.104 0.142 1
URE O O 6.404 0.892 2
URE N1 N 3.805 0.892 3
URE N2 N 5.104 -1.357 4
#
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
URE C O DOUBLE NONE 1
URE C N1 SINGLE NONE 2
URE C N2 SINGLE NONE 3
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id URE
_pdbe_chem_comp_rdkit_properties.exactmw 60.032
_pdbe_chem_comp_rdkit_properties.amw 60.056
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 4
_pdbe_chem_comp_rdkit_properties.NumAtoms 8
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_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 29.433
_pdbe_chem_comp_rdkit_properties.tpsa 69.110
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.976
_pdbe_chem_comp_rdkit_properties.CrippenMR 13.771
_pdbe_chem_comp_rdkit_properties.chi0v 1.803
_pdbe_chem_comp_rdkit_properties.chi1v 0.651
_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 5.803
_pdbe_chem_comp_rdkit_properties.chi1n 2.440
_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 -0.730
_pdbe_chem_comp_rdkit_properties.kappa1 0.429
_pdbe_chem_comp_rdkit_properties.kappa2 0.711
_pdbe_chem_comp_rdkit_properties.kappa3 0.174
_pdbe_chem_comp_rdkit_properties.Phi 0.076
#
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
URE UniChem ChEMBL CHEMBL985
URE UniChem DrugBank DB03904
URE UniChem PDBe URE
URE UniChem 'Guide to Pharmacology' 4539
URE UniChem 'KEGG LIGAND' C00086
URE UniChem ChEBI 16199
URE UniChem ChEBI 48376
URE UniChem ZINC ZINC000008214514
URE UniChem atlas Urea
URE UniChem fdasrs 8W8T17847W
URE UniChem PharmGKB PA451831
URE UniChem HMDB HMDB0000294
URE UniChem 'PubChem TPHARMA' 15146258
URE UniChem NMRShiftDB 10016903
URE UniChem LINCS LSM-45688
URE UniChem ACTor 30535-50-3
URE UniChem Recon urea
URE UniChem BindingDb 24961
URE UniChem DrugCentral 4264
URE UniChem MetaboLights MTBLC16199
URE UniChem MetaboLights MTBLC48376
URE UniChem BRENDA 210639
URE UniChem ChemicalBook CB11342474
URE UniChem ChemicalBook CB5853861
URE UniChem DailyMed UREA
URE UniChem ClinicalTrials 'UREA (13C)'
URE UniChem ClinicalTrials 'UREA 13 C'
URE UniChem ClinicalTrials 'UREA C 13'
URE UniChem ClinicalTrials 'UREA C-13'
URE UniChem rxnorm NUTRAPLUS
URE UniChem rxnorm UREA
URE UniChem rxnorm 'UREA C-13'
URE UniChem MedChemExpress HY-Y0271
URE UniChem 'Probes And Drugs' PD002093
URE UniChem Rhea 16199
URE UniChem eMolecules 10525132
URE UniChem eMolecules 475133
URE UniChem SureChEMBL SCHEMBL4441
URE UniChem PubChem 1176
URE UniChem Mcule MCULE-8513891094
URE UniChem ACTor 173144-80-4
URE UniChem ACTor 37955-36-5
URE UniChem ACTor 57-13-6
URE UniChem Nikkaji J2.322A
URE UniChem 'EPA CompTox Dashboard' DTXSID4021426
URE UniChem BRENDA 116
#
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
URE C -0.006 0.428 0.272 ETKDGv3 1
URE O -0.022 1.490 0.948 ETKDGv3 2
URE N1 -1.234 -0.211 -0.077 ETKDGv3 3
URE N2 1.239 -0.133 -0.142 ETKDGv3 4
URE HN11 -2.146 0.199 0.226 ETKDGv3 5
URE HN12 -1.233 -1.092 -0.636 ETKDGv3 6
URE HN21 2.138 0.333 0.112 ETKDGv3 7
URE HN22 1.263 -1.014 -0.703 ETKDGv3 8
#