data_URA
#
_chem_comp.id URA
_chem_comp.name URACIL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H4 N2 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 ?
_chem_comp.formula_weight 112.087
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code URA
_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 5EUG
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
URA N1 N1 N 0 1 N N N N N N 11.108 1.891 16.998 0.994 0.000 -1.183 N1 URA 1
URA C2 C2 C 0 1 N N N N N N 11.695 3.129 17.208 -0.349 -0.001 -1.135 C2 URA 2
URA O2 O2 O 0 1 N N N N N N 12.704 3.566 16.668 -0.986 -0.001 -2.171 O2 URA 3
URA N3 N3 N 0 1 N N N N N N 11.057 3.877 18.176 -1.000 0.003 0.043 N3 URA 4
URA C4 C4 C 0 1 N N N N N N 9.905 3.568 18.878 -0.308 -0.001 1.200 C4 URA 5
URA O4 O4 O 0 1 N N N N N N 9.396 4.436 19.559 -0.896 -0.001 2.267 O4 URA 6
URA C5 C5 C 0 1 N N N N N N 9.353 2.263 18.597 1.106 -0.000 1.164 C5 URA 7
URA C6 C6 C 0 1 N N N N N N 9.960 1.507 17.663 1.733 0.000 -0.031 C6 URA 8
URA HN1 HN1 H 0 1 N N N N N N 11.817 1.177 17.163 1.445 0.000 -2.042 HN1 URA 9
URA HN3 HN3 H 0 1 N N N N N N 11.492 4.771 18.401 -1.969 0.003 0.059 HN3 URA 10
URA H5 H5 H 0 1 N N N N N N 8.464 1.842 19.097 1.677 -0.000 2.081 H5 URA 11
URA H6 H6 H 0 1 N N N N N N 9.497 0.532 17.433 2.812 0.000 -0.078 H6 URA 12
#
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
URA N1 C2 SING N N 1
URA N1 C6 SING N N 2
URA N1 HN1 SING N N 3
URA C2 O2 DOUB N N 4
URA C2 N3 SING N N 5
URA N3 C4 SING N N 6
URA N3 HN3 SING N N 7
URA C4 O4 DOUB N N 8
URA C4 C5 SING N N 9
URA C5 C6 DOUB N N 10
URA C5 H5 SING N N 11
URA C6 H6 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
URA SMILES ACDLabs 10.04 O=C1C=CNC(=O)N1
URA SMILES_CANONICAL CACTVS 3.341 O=C1NC=CC(=O)N1
URA SMILES CACTVS 3.341 O=C1NC=CC(=O)N1
URA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CNC(=O)NC1=O
URA SMILES "OpenEye OEToolkits" 1.5.0 C1=CNC(=O)NC1=O
URA InChI InChI 1.03 InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
URA InChIKey InChI 1.03 ISAKRJDGNUQOIC-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
URA "SYSTEMATIC NAME" ACDLabs 10.04 pyrimidine-2,4(1H,3H)-dione
URA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1H-pyrimidine-2,4-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
URA 'Create component' 1999-07-08 PDBJ
URA 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id URA
_pdbe_chem_comp_drugbank_details.drugbank_id DB03419
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Uracil
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 66-22-8
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id URA
_pdbe_chem_comp_synonyms.name Uracil
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id URA
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03419
_pdbe_chem_comp_drugbank_classification.parent Pyrimidones
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Diazines
_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 pyrimidones. These are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.'
#
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
URA DB03419 'Dihydropyrimidine dehydrogenase [NADP(+)]' Humans Q12882 yes 1
URA DB03419 'Uridine-cytidine kinase-like 1' Humans Q9NWZ5 unknown 2
URA DB03419 'Uracil-DNA glycosylase' HHV-1 P10186 unknown 3
URA DB03419 'Uracil-DNA glycosylase' 'Escherichia coli O157:H7' Q8X444 unknown 4
URA DB03419 'Ribosomal small subunit pseudouridine synthase A' 'Escherichia coli (strain K12)' P0AA43 unknown 5
URA DB03419 'Type-4 uracil-DNA glycosylase' 'Thermus thermophilus' Q5SKC5 unknown 6
URA DB03419 'Pyrimidine-nucleoside phosphorylase' 'Geobacillus stearothermophilus' P77836 unknown 7
#
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
URA N1 N 6.897 1.215 1
URA C2 C 6.897 -0.285 2
URA O2 O 8.196 -1.035 3
URA N3 N 5.598 -1.035 4
URA C4 C 4.299 -0.285 5
URA O4 O 3.000 -1.035 6
URA C5 C 4.299 1.215 7
URA C6 C 5.598 1.965 8
#
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
URA N1 C2 SINGLE NONE 1
URA N1 C6 SINGLE NONE 2
URA C2 O2 DOUBLE NONE 3
URA C2 N3 SINGLE NONE 4
URA N3 C4 SINGLE NONE 5
URA C4 O4 DOUBLE NONE 6
URA C4 C5 SINGLE NONE 7
URA C5 C6 DOUBLE NONE 8
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
URA MurckoScaffold S1 scaffold 'O=c1cc[nH]c(=O)[nH]1' InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) ISAKRJDGNUQOIC-UHFFFAOYSA-N
URA pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
URA N1 S1 1
URA C2 S1 1
URA O2 S1 1
URA N3 S1 1
URA C4 S1 1
URA O4 S1 1
URA C5 S1 1
URA C6 S1 1
URA C5 F1 1
URA C4 F1 1
URA N3 F1 1
URA C2 F1 1
URA N1 F1 1
URA C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id URA
_pdbe_chem_comp_rdkit_properties.exactmw 112.027
_pdbe_chem_comp_rdkit_properties.amw 112.088
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 12
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 49.930
_pdbe_chem_comp_rdkit_properties.tpsa 65.720
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.863
_pdbe_chem_comp_rdkit_properties.CrippenMR 27.899
_pdbe_chem_comp_rdkit_properties.chi0v 3.711
_pdbe_chem_comp_rdkit_properties.chi1v 1.803
_pdbe_chem_comp_rdkit_properties.chi2v 0.512
_pdbe_chem_comp_rdkit_properties.chi3v 0.512
_pdbe_chem_comp_rdkit_properties.chi4v 0.263
_pdbe_chem_comp_rdkit_properties.chi0n 7.711
_pdbe_chem_comp_rdkit_properties.chi1n 3.697
_pdbe_chem_comp_rdkit_properties.chi2n 0.512
_pdbe_chem_comp_rdkit_properties.chi3n 0.512
_pdbe_chem_comp_rdkit_properties.chi4n 0.263
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.320
_pdbe_chem_comp_rdkit_properties.kappa1 1.889
_pdbe_chem_comp_rdkit_properties.kappa2 1.651
_pdbe_chem_comp_rdkit_properties.kappa3 0.841
_pdbe_chem_comp_rdkit_properties.Phi 0.390
#
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
URA UniChem DrugBank DB03419
URA UniChem 'Guide to Pharmacology' 4560
URA UniChem 'KEGG LIGAND' C00106
URA UniChem ChEBI 17568
URA UniChem ZINC ZINC000000895045
URA UniChem fdasrs 56HH86ZVCT
URA UniChem HMDB HMDB0000300
URA UniChem Selleck uracil
URA UniChem PubChem 1174
URA UniChem NMRShiftDB 10016331
URA UniChem Recon ura
URA UniChem 'EPA CompTox Dashboard' DTXSID4021424
URA UniChem MetaboLights MTBLC17568
URA UniChem BRENDA 105212
URA UniChem BRENDA 334
URA UniChem Rhea 17568
URA UniChem ChemicalBook CB8376824
URA UniChem ClinicalTrials URACIL
URA UniChem rxnorm URACIL
URA UniChem MedChemExpress HY-I0960
URA UniChem 'Probes And Drugs' PD001670
URA UniChem CCDC URACIL
URA UniChem Nikkaji J4.842I
URA UniChem eMolecules 3726817
URA UniChem eMolecules 514222
URA UniChem SureChEMBL SCHEMBL8235
URA UniChem 'PubChem TPHARMA' 14747492
URA UniChem 'PubChem TPHARMA' 16250541
URA UniChem 'PubChem TPHARMA' 22425032
URA UniChem Mcule MCULE-1147953020
URA UniChem ACTor 138285-60-6
URA UniChem ACTor 16908-84-2
URA UniChem ACTor 24897-50-5
#
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
URA N1 1.206 0.734 0.039 ETKDGv3 1
URA C2 1.252 -0.697 0.027 ETKDGv3 2
URA O2 2.359 -1.298 0.050 ETKDGv3 3
URA N3 0.030 -1.436 -0.012 ETKDGv3 4
URA C4 -1.210 -0.723 -0.039 ETKDGv3 5
URA O4 -2.300 -1.353 -0.073 ETKDGv3 6
URA C5 -1.208 0.749 -0.025 ETKDGv3 7
URA C6 -0.053 1.423 0.012 ETKDGv3 8
URA HN1 2.093 1.285 0.067 ETKDGv3 9
URA HN3 0.042 -2.480 -0.022 ETKDGv3 10
URA H5 -2.146 1.290 -0.045 ETKDGv3 11
URA H6 -0.067 2.505 0.021 ETKDGv3 12
#