data_URC
#
_chem_comp.id URC
_chem_comp.name "URIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H4 N4 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-03-15
_chem_comp.pdbx_modified_date 2021-03-13
_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 168.110
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code URC
_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 1L5S
_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
URC N1 N1 N 0 1 Y N N N N N 38.217 -59.800 98.395 0.666 -0.000 -2.030 N1 URC 1
URC C2 C2 C 0 1 Y N N N N N 36.879 -59.858 98.272 -0.678 -0.001 -2.078 C2 URC 2
URC C6 C6 C 0 1 Y N N N N N 38.820 -59.260 99.467 1.311 0.000 -0.845 C6 URC 3
URC N3 N3 N 0 1 Y N N N N N 36.075 -59.372 99.225 -1.417 0.004 -0.953 N3 URC 4
URC O11 O11 O 0 1 N N N N N N 36.388 -60.365 97.276 -1.236 -0.001 -3.159 O11 URC 5
URC C4 C4 C 0 1 Y N N N N N 36.584 -58.819 100.325 -0.804 -0.000 0.278 C4 URC 6
URC C5 C5 C 0 1 Y N N N N N 37.918 -58.723 100.521 0.561 -0.000 0.347 C5 URC 7
URC N9 N9 N 0 1 Y N N N N N 36.036 -58.287 101.377 -1.282 -0.000 1.564 N9 URC 8
URC O13 O13 O 0 1 N N N N N N 40.032 -59.193 99.613 2.529 0.000 -0.807 O13 URC 9
URC N7 N7 N 0 1 Y N N N N N 38.101 -58.147 101.671 0.906 -0.000 1.703 N7 URC 10
URC C8 C8 C 0 1 Y N N N N N 36.945 -57.866 102.224 -0.238 -0.000 2.415 C8 URC 11
URC O24 O24 O 0 1 N N N N N N 36.753 -57.327 103.300 -0.316 -0.000 3.629 O24 URC 12
URC HN1 HN1 H 0 1 N N N N N N 38.797 -60.180 97.647 1.176 0.000 -2.855 HN1 URC 13
URC HN3 HN3 H 0 1 N N N N N N 35.063 -59.424 99.112 -2.385 0.004 -1.011 HN3 URC 14
URC HN9 HN9 H 0 1 N N N N N N 35.378 -58.927 101.821 -2.218 -0.000 1.819 HN9 URC 15
URC HN7 HN7 H 0 1 N N N N N N 39.014 -57.946 102.078 1.806 -0.000 2.065 HN7 URC 16
#
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
URC N1 C2 SING Y N 1
URC N1 C6 SING Y N 2
URC N1 HN1 SING N N 3
URC C2 N3 SING Y N 4
URC C2 O11 DOUB N N 5
URC C6 C5 SING Y N 6
URC C6 O13 DOUB N N 7
URC N3 C4 SING Y N 8
URC N3 HN3 SING N N 9
URC C4 C5 DOUB Y N 10
URC C4 N9 SING Y N 11
URC C5 N7 SING Y N 12
URC N9 C8 SING Y N 13
URC N9 HN9 SING N N 14
URC N7 C8 SING Y N 15
URC N7 HN7 SING N N 16
URC C8 O24 DOUB N N 17
#
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
URC SMILES ACDLabs 10.04 O=C1C2=C(NC(=O)N1)NC(=O)N2
URC SMILES_CANONICAL CACTVS 3.341 O=C1NC(=O)C2=C(N1)NC(=O)N2
URC SMILES CACTVS 3.341 O=C1NC(=O)C2=C(N1)NC(=O)N2
URC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C12=C(NC(=O)N1)NC(=O)NC2=O
URC SMILES "OpenEye OEToolkits" 1.5.0 C12=C(NC(=O)N1)NC(=O)NC2=O
URC InChI InChI 1.03 InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)
URC InChIKey InChI 1.03 LEHOTFFKMJEONL-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
URC "SYSTEMATIC NAME" ACDLabs 10.04 7,9-dihydro-1H-purine-2,6,8(3H)-trione
URC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 7,9-dihydro-3H-purine-2,6,8-trione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
URC 'Create component' 2002-03-15 RCSB
URC 'Modify descriptor' 2011-06-04 RCSB
URC 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id URC
_pdbx_chem_comp_synonyms.name 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id URC
_pdbe_chem_comp_drugbank_details.drugbank_id DB08844
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Uric acid'
_pdbe_chem_comp_drugbank_details.description
'Uric acid is the last product of purine metabolism in humans. The formation of uric acid is through the enzyme xanthine oxidase, which oxidizes oxypurines. Normally a small amount of uric acid is present in the body, but when there is an excess amount in the blood, called hyperuricemia, this can lead to gout and formation of kidney stones. As a therapeutic agent, it is known that uric acid is increased in response to oxidative stress, and as such, uric acid acts as an antioxidant. At present (August 2013), there is no approved formulation or indication for uric acid. In one country, Spain, uric acid is an investigational drug in a phase 3 trial studying its effects as an adjunct to alteplase in acute ischemic stroke.'
_pdbe_chem_comp_drugbank_details.cas_number 69-93-2
_pdbe_chem_comp_drugbank_details.mechanism_of_action
"The exact mechanism of action for uric acid's antioxidant effects have not yet been elucidated."
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
URC 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE wwPDB ?
URC 2,6,8-trihydroxypurine DrugBank ?
URC 2,6,8-trioxopurine DrugBank ?
URC 2,6,8-trioxypurine DrugBank ?
URC 7,9-dihydro-1H-purine-2,6,8(3H)-trione DrugBank ?
URC 'Lithic acid' DrugBank ?
URC Purine-2,6,8(1H,3H,9H)-trione DrugBank ?
URC Urate DrugBank ?
URC 'Uricum acidum' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id URC
_pdbe_chem_comp_drugbank_classification.drugbank_id DB08844
_pdbe_chem_comp_drugbank_classification.parent Xanthines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Imidazopyrimidines
_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 xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety.'
#
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
URC N1 N 4.299 -0.465 1
URC C2 C 4.299 1.035 2
URC C6 C 5.598 -1.215 3
URC N3 N 5.598 1.785 4
URC O11 O 3.000 1.785 5
URC C4 C 6.897 1.035 6
URC C5 C 6.897 -0.465 7
URC N9 N 8.316 1.492 8
URC O13 O 5.598 -2.715 9
URC N7 N 8.316 -0.922 10
URC C8 C 9.192 0.285 11
URC O24 O 10.692 0.285 12
#
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
URC N1 C2 SINGLE NONE 1
URC N1 C6 SINGLE NONE 2
URC C2 N3 SINGLE NONE 3
URC C2 O11 DOUBLE NONE 4
URC C6 C5 SINGLE NONE 5
URC C6 O13 DOUBLE NONE 6
URC N3 C4 SINGLE NONE 7
URC C4 C5 DOUBLE NONE 8
URC C4 N9 SINGLE NONE 9
URC C5 N7 SINGLE NONE 10
URC N9 C8 SINGLE NONE 11
URC N7 C8 SINGLE NONE 12
URC C8 O24 DOUBLE NONE 13
#
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
URC MurckoScaffold S1 scaffold 'O=c1[nH]c(=O)c2[nH]c(=O)[nH]c2[nH]1' InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12) LEHOTFFKMJEONL-UHFFFAOYSA-N
URC imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
URC purine F2 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
URC pyrimidine F3 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
URC N1 S1 1
URC C2 S1 1
URC C6 S1 1
URC N3 S1 1
URC O11 S1 1
URC C4 S1 1
URC C5 S1 1
URC N9 S1 1
URC O13 S1 1
URC N7 S1 1
URC C8 S1 1
URC O24 S1 1
URC C4 F1 1
URC C5 F1 1
URC N7 F1 1
URC C8 F1 1
URC N9 F1 1
URC N7 F2 1
URC C8 F2 1
URC N9 F2 1
URC C4 F2 1
URC C5 F2 1
URC C6 F2 1
URC N1 F2 1
URC C2 F2 1
URC N3 F2 1
URC C5 F3 1
URC C6 F3 1
URC N1 F3 1
URC C2 F3 1
URC N3 F3 1
URC C4 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id URC
_pdbe_chem_comp_rdkit_properties.exactmw 168.028
_pdbe_chem_comp_rdkit_properties.amw 168.112
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 16
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 69.318
_pdbe_chem_comp_rdkit_properties.tpsa 114.370
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.504
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.279
_pdbe_chem_comp_rdkit_properties.chi0v 5.514
_pdbe_chem_comp_rdkit_properties.chi1v 2.901
_pdbe_chem_comp_rdkit_properties.chi2v 1.222
_pdbe_chem_comp_rdkit_properties.chi3v 1.222
_pdbe_chem_comp_rdkit_properties.chi4v 0.791
_pdbe_chem_comp_rdkit_properties.chi0n 9.514
_pdbe_chem_comp_rdkit_properties.chi1n 4.690
_pdbe_chem_comp_rdkit_properties.chi2n 1.222
_pdbe_chem_comp_rdkit_properties.chi3n 1.222
_pdbe_chem_comp_rdkit_properties.chi4n 0.791
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.050
_pdbe_chem_comp_rdkit_properties.kappa1 3.566
_pdbe_chem_comp_rdkit_properties.kappa2 1.969
_pdbe_chem_comp_rdkit_properties.kappa3 0.797
_pdbe_chem_comp_rdkit_properties.Phi 0.585
#
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
URC UniChem ChEMBL CHEMBL792
URC UniChem DrugBank DB08844
URC UniChem PDBe 8HX
URC UniChem PDBe URC
URC UniChem 'Guide to Pharmacology' 4731
URC UniChem 'KEGG LIGAND' C00366
URC UniChem ChEBI 17775
URC UniChem ChEBI 46811
URC UniChem ChEBI 46814
URC UniChem ChEBI 46817
URC UniChem ChEBI 46823
URC UniChem ChEBI 62589
URC UniChem ZINC ZINC000002041003
URC UniChem fdasrs 268B43MJ25
URC UniChem HMDB HMDB0000289
URC UniChem Recon urate
URC UniChem Nikkaji J2.372H
URC UniChem BindingDb 50325824
URC UniChem MetaboLights MTBLC17775
URC UniChem MetaboLights MTBLC46811
URC UniChem MetaboLights MTBLC46814
URC UniChem MetaboLights MTBLC46817
URC UniChem MetaboLights MTBLC46823
URC UniChem MetaboLights MTBLC62589
URC UniChem BRENDA 1421
URC UniChem BRENDA 153417
URC UniChem BRENDA 154402
URC UniChem BRENDA 163088
URC UniChem BRENDA 166682
URC UniChem BRENDA 710
URC UniChem Rhea 17775
URC UniChem DailyMed 'URIC ACID'
URC UniChem ClinicalTrials 'URIC ACID'
URC UniChem rxnorm 'URIC ACID'
URC UniChem MedChemExpress HY-B2130
URC UniChem 'Probes And Drugs' PD008492
URC UniChem 'EPA CompTox Dashboard' DTXSID3042508
URC UniChem eMolecules 31240396
URC UniChem eMolecules 516211
URC UniChem eMolecules 884300
URC UniChem SureChEMBL SCHEMBL17081907
URC UniChem SureChEMBL SCHEMBL7933
URC UniChem 'PubChem TPHARMA' 15219467
URC UniChem 'PubChem TPHARMA' 15321837
URC UniChem PubChem 1175
URC UniChem Mcule MCULE-3320087210
URC UniChem NMRShiftDB 10016335
URC UniChem ACTor 13154-20-6
#
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
URC N1 -2.142 0.735 -0.014 ETKDGv3 1
URC C2 -2.141 -0.704 -0.036 ETKDGv3 2
URC C6 -0.894 1.443 0.012 ETKDGv3 3
URC N3 -0.891 -1.416 -0.032 ETKDGv3 4
URC O11 -3.229 -1.338 -0.058 ETKDGv3 5
URC C4 0.325 -0.661 -0.006 ETKDGv3 6
URC C5 0.345 0.661 0.014 ETKDGv3 7
URC N9 1.636 -1.211 0.000 ETKDGv3 8
URC O13 -0.868 2.702 0.031 ETKDGv3 9
URC N7 1.679 1.158 0.037 ETKDGv3 10
URC C8 2.448 -0.041 0.028 ETKDGv3 11
URC O24 3.706 -0.064 0.042 ETKDGv3 12
URC HN1 -3.045 1.260 -0.016 ETKDGv3 13
URC HN3 -0.868 -2.459 -0.048 ETKDGv3 14
URC HN9 1.928 -2.213 -0.011 ETKDGv3 15
URC HN7 2.010 2.148 0.056 ETKDGv3 16
#