data_URF
#
_chem_comp.id URF
_chem_comp.name 5-FLUOROURACIL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H3 F 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 130.077
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code URF
_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 1UPF
_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
URF N1 N1 N 0 1 N N N N N N -11.079 93.180 91.185 1.244 0.001 1.126 N1 URF 1
URF C2 C2 C 0 1 N N N N N N -11.885 92.455 90.307 -0.023 -0.000 1.576 C2 URF 2
URF N3 N3 N 0 1 N N N N N N -12.971 93.154 89.821 -1.062 -0.002 0.720 N3 URF 3
URF C4 C4 C 0 1 N N N N N N -13.340 94.440 90.119 -0.846 0.002 -0.610 C4 URF 4
URF C5 C5 C 0 1 N N N N N N -12.451 95.142 91.014 0.483 -0.001 -1.099 C5 URF 5
URF C6 C6 C 0 1 N N N N N N -11.404 94.494 91.544 1.507 0.000 -0.218 C6 URF 6
URF O2 O2 O 0 1 N N N N N N -11.634 91.310 89.946 -0.234 -0.000 2.774 O2 URF 7
URF O4 O4 O 0 1 N N N N N N -14.324 94.909 89.549 -1.786 0.001 -1.385 O4 URF 8
URF F5 F5 F 0 1 N N N N N N -12.772 96.329 91.457 0.724 -0.001 -2.428 F5 URF 9
URF HN1 HN1 H 0 1 N N N N N N -10.127 93.178 90.816 1.978 0.002 1.760 HN1 URF 10
URF HN3 HN3 H 0 1 N N N N N N -13.573 92.660 89.162 -1.970 -0.003 1.062 HN3 URF 11
URF H6 H6 H 0 1 N N N N N N -10.802 95.048 92.284 2.528 0.001 -0.571 H6 URF 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
URF N1 C2 SING N N 1
URF N1 C6 SING N N 2
URF N1 HN1 SING N N 3
URF C2 N3 SING N N 4
URF C2 O2 DOUB N N 5
URF N3 C4 SING N N 6
URF N3 HN3 SING N N 7
URF C4 C5 SING N N 8
URF C4 O4 DOUB N N 9
URF C5 C6 DOUB N N 10
URF C5 F5 SING N N 11
URF 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
URF SMILES ACDLabs 10.04 FC1=CNC(=O)NC1=O
URF SMILES_CANONICAL CACTVS 3.341 FC1=CNC(=O)NC1=O
URF SMILES CACTVS 3.341 FC1=CNC(=O)NC1=O
URF SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1)F
URF SMILES "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1)F
URF InChI InChI 1.03 InChI=1S/C4H3FN2O2/c5-2-1-6-4(9)7-3(2)8/h1H,(H2,6,7,8,9)
URF InChIKey InChI 1.03 GHASVSINZRGABV-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
URF "SYSTEMATIC NAME" ACDLabs 10.04 5-fluoropyrimidine-2,4(1H,3H)-dione
URF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 5-fluoro-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
URF 'Create component' 1999-07-08 RCSB
URF 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id URF
_pdbe_chem_comp_drugbank_details.drugbank_id DB00544
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Fluorouracil
_pdbe_chem_comp_drugbank_details.description
'A pyrimidine analog that is an antineoplastic antimetabolite. It interferes with DNA synthesis by blocking the thymidylate synthetase conversion of deoxyuridylic acid to thymidylic acid.'
_pdbe_chem_comp_drugbank_details.cas_number 51-21-8
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'The precise mechanism of action has not been fully determined, but the main mechanism of fluorouracil is thought to be the binding of the deoxyribonucleotide of the drug (FdUMP) and the folate cofactor, N5–10-methylenetetrahydrofolate, to thymidylate synthase (TS) to form a covalently bound ternary complex. This results in the inhibition of the formation of thymidylate from uracil, which leads to the inhibition of DNA and RNA synthesis and cell death. Fluorouracil can also be incorporated into RNA in place of uridine triphosphate (UTP), producing a fraudulent RNA and interfering with RNA processing and protein synthesis.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
URF '5 Fluorouracil' DrugBank ?
URF '5 FU' DrugBank ?
URF 5-Fluoropyrimidine-2,4-dione DrugBank ?
URF 5-Fluorouracil DrugBank ?
URF 5-Fluoruracil DrugBank ?
URF 5-Fluracil DrugBank ?
URF 5-FU DrugBank ?
URF 5Fluorouracil DrugBank ?
URF 5FU DrugBank ?
URF 'Fluoro Uracil' DrugBank ?
URF Fluorouracil DrugBank ?
URF Fluorouracilum DrugBank ?
URF Fluouracil DrugBank ?
URF flurouracil DrugBank ?
URF Carzonal DrugBank 'International brand'
URF Efudix DrugBank 'International brand'
URF Efurix DrugBank 'International brand'
URF Ftoruracil DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id URF
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00544
_pdbe_chem_comp_drugbank_classification.parent Halopyrimidines
_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 halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. 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
URF DB00544 'Thymidylate synthase' Humans P04818 yes 1
URF DB00544 'Telomerase reverse transcriptase' Humans O14746 unknown 2
URF DB00544 'Dihydropyrimidine dehydrogenase [NADP(+)]' Humans Q12882 unknown 3
URF DB00544 'Thymidylate synthase' Yeast P12461 unknown 4
#
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
URF N1 N 6.897 1.215 1
URF C2 C 6.897 -0.285 2
URF N3 N 5.598 -1.035 3
URF C4 C 4.299 -0.285 4
URF C5 C 4.299 1.215 5
URF C6 C 5.598 1.965 6
URF O2 O 8.196 -1.035 7
URF O4 O 3.000 -1.035 8
URF F5 F 3.000 1.965 9
#
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
URF N1 C2 SINGLE NONE 1
URF N1 C6 SINGLE NONE 2
URF C2 N3 SINGLE NONE 3
URF C2 O2 DOUBLE NONE 4
URF N3 C4 SINGLE NONE 5
URF C4 C5 SINGLE NONE 6
URF C4 O4 DOUBLE NONE 7
URF C5 C6 DOUBLE NONE 8
URF C5 F5 SINGLE NONE 9
#
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
URF 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
URF 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
URF N1 S1 1
URF C2 S1 1
URF N3 S1 1
URF C4 S1 1
URF C5 S1 1
URF C6 S1 1
URF O2 S1 1
URF O4 S1 1
URF C5 F1 1
URF C4 F1 1
URF N3 F1 1
URF C2 F1 1
URF N1 F1 1
URF C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id URF
_pdbe_chem_comp_rdkit_properties.exactmw 130.018
_pdbe_chem_comp_rdkit_properties.amw 130.078
_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 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 12
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 52.690
_pdbe_chem_comp_rdkit_properties.tpsa 65.720
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.002
_pdbe_chem_comp_rdkit_properties.CrippenMR 27.857
_pdbe_chem_comp_rdkit_properties.chi0v 4.089
_pdbe_chem_comp_rdkit_properties.chi1v 1.992
_pdbe_chem_comp_rdkit_properties.chi2v 0.635
_pdbe_chem_comp_rdkit_properties.chi3v 0.635
_pdbe_chem_comp_rdkit_properties.chi4v 0.306
_pdbe_chem_comp_rdkit_properties.chi0n 7.089
_pdbe_chem_comp_rdkit_properties.chi1n 3.386
_pdbe_chem_comp_rdkit_properties.chi2n 0.635
_pdbe_chem_comp_rdkit_properties.chi3n 0.635
_pdbe_chem_comp_rdkit_properties.chi4n 0.306
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.390
_pdbe_chem_comp_rdkit_properties.kappa1 2.954
_pdbe_chem_comp_rdkit_properties.kappa2 1.848
_pdbe_chem_comp_rdkit_properties.kappa3 1.042
_pdbe_chem_comp_rdkit_properties.Phi 0.606
#
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
URF UniChem DrugBank DB00544
URF UniChem 'Guide to Pharmacology' 4789
URF UniChem 'KEGG LIGAND' C07649
URF UniChem ChEBI 46345
URF UniChem NIH SAM002264615
URF UniChem ZINC ZINC000038212689
URF UniChem atlas 5-fluourouracil
URF UniChem fdasrs U3P01618RT
URF UniChem PharmGKB PA128406956
URF UniChem HMDB HMDB0014684
URF UniChem Selleck Adrucil(Fluorouracil)
URF UniChem PubChem 3385
URF UniChem NMRShiftDB 20027309
URF UniChem ACTor 1004-03-1
URF UniChem DrugCentral 26
URF UniChem BRENDA 155282
URF UniChem BRENDA 229064
URF UniChem BRENDA 229065
URF UniChem BRENDA 51649
URF UniChem ChemicalBook CB8162744
URF UniChem DailyMed FLUOROURACIL
URF UniChem ClinicalTrials ADRUCIL
URF UniChem ClinicalTrials CARAC
URF UniChem ClinicalTrials EFUDEX
URF UniChem ClinicalTrials FLUOROPLEX
URF UniChem ClinicalTrials FLUOROURACIL
URF UniChem ClinicalTrials NSC-19893
URF UniChem ClinicalTrials 'RO 2-9757'
URF UniChem ClinicalTrials RO-2-9757
URF UniChem rxnorm ADRUCIL
URF UniChem rxnorm CARAC
URF UniChem rxnorm EFUDEX
URF UniChem rxnorm FLUOROPLEX
URF UniChem rxnorm FLUOROURACIL
URF UniChem rxnorm TOLAK
URF UniChem MedChemExpress HY-90006
URF UniChem 'Probes And Drugs' PD002327
URF UniChem CCDC FURACL
URF UniChem BRENDA 812
URF UniChem eMolecules 13386136
URF UniChem eMolecules 512920
URF UniChem atlas 5-fluorouracil
URF UniChem SureChEMBL SCHEMBL3646
URF UniChem 'PubChem TPHARMA' 15218968
URF UniChem Mcule MCULE-6338086431
URF UniChem LINCS LSM-4261
URF UniChem Nikkaji J4.489J
URF UniChem BindingDb 50340677
URF UniChem 'EPA CompTox Dashboard' DTXSID2020634
#
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
URF N1 -1.382 0.342 0.004 ETKDGv3 1
URF C2 -1.017 -1.042 0.036 ETKDGv3 2
URF N3 0.366 -1.400 0.032 ETKDGv3 3
URF C4 1.352 -0.364 -0.004 ETKDGv3 4
URF C5 0.928 1.047 -0.035 ETKDGv3 5
URF C6 -0.372 1.362 -0.031 ETKDGv3 6
URF O2 -1.905 -1.934 0.067 ETKDGv3 7
URF O4 2.576 -0.658 -0.008 ETKDGv3 8
URF F5 1.860 2.033 -0.069 ETKDGv3 9
URF HN1 -2.389 0.617 0.007 ETKDGv3 10
URF HN3 0.653 -2.405 0.054 ETKDGv3 11
URF H6 -0.671 2.402 -0.054 ETKDGv3 12
#