data_ORO
#
_chem_comp.id ORO
_chem_comp.name "OROTIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H4 N2 O4"
_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 156.096
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ORO
_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 1D3G
_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
ORO N1 N1 N 0 1 Y N N N N N 41.864 32.767 4.711 1.126 0.005 0.042 N1 ORO 1
ORO C2 C2 C 0 1 Y N N N N N 40.857 33.656 5.061 1.193 -0.001 -1.299 C2 ORO 2
ORO O2 O2 O 0 1 N N N N N N 40.244 34.314 4.225 2.284 -0.001 -1.836 O2 ORO 3
ORO N3 N3 N 0 1 Y N N N N N 40.585 33.763 6.410 0.088 -0.000 -2.063 N3 ORO 4
ORO C4 C4 C 0 1 Y N N N N N 41.209 33.080 7.435 -1.135 -0.000 -1.495 C4 ORO 5
ORO O4 O4 O 0 1 N N N N N N 40.885 33.237 8.597 -2.138 0.000 -2.184 O4 ORO 6
ORO C5 C5 C 0 1 Y N N N N N 42.243 32.159 7.006 -1.236 -0.000 -0.030 C5 ORO 7
ORO C6 C6 C 0 1 Y N N N N N 42.525 32.066 5.699 -0.087 -0.000 0.695 C6 ORO 8
ORO C7 C7 C 0 1 N N N N N N 43.565 31.079 5.191 -0.139 -0.000 2.177 C7 ORO 9
ORO O71 O71 O 0 1 N N N N N N 44.647 30.922 5.742 -1.211 -0.000 2.746 O71 ORO 10
ORO O72 O72 O 0 1 N N N N N N 43.070 30.456 4.222 1.002 -0.000 2.891 O72 ORO 11
ORO HN1 HN1 H 0 1 N N N N N N 42.553 33.262 4.146 1.945 0.004 0.561 HN1 ORO 12
ORO HN3 HN3 H 0 1 N N N N N N 39.846 34.414 6.677 0.170 -0.000 -3.030 HN3 ORO 13
ORO H5 H5 H 0 1 N N N N N N 42.826 31.516 7.687 -2.199 -0.000 0.457 H5 ORO 14
ORO HO7 HO7 H 0 1 N N N N N N 43.719 29.839 3.904 0.968 -0.000 3.857 HO7 ORO 15
#
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
ORO N1 C2 SING Y N 1
ORO N1 C6 SING Y N 2
ORO N1 HN1 SING N N 3
ORO C2 O2 DOUB N N 4
ORO C2 N3 SING Y N 5
ORO N3 C4 SING Y N 6
ORO N3 HN3 SING N N 7
ORO C4 O4 DOUB N N 8
ORO C4 C5 SING Y N 9
ORO C5 C6 DOUB Y N 10
ORO C5 H5 SING N N 11
ORO C6 C7 SING N N 12
ORO C7 O71 DOUB N N 13
ORO C7 O72 SING N N 14
ORO O72 HO7 SING N N 15
#
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
ORO SMILES ACDLabs 10.04 O=C(O)C1=CC(=O)NC(=O)N1
ORO SMILES_CANONICAL CACTVS 3.341 OC(=O)C1=CC(=O)NC(=O)N1
ORO SMILES CACTVS 3.341 OC(=O)C1=CC(=O)NC(=O)N1
ORO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=C(NC(=O)NC1=O)C(=O)O
ORO SMILES "OpenEye OEToolkits" 1.5.0 C1=C(NC(=O)NC1=O)C(=O)O
ORO InChI InChI 1.03 InChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)
ORO InChIKey InChI 1.03 PXQPEWDEAKTCGB-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
ORO "SYSTEMATIC NAME" ACDLabs 10.04 "2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid"
ORO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2,6-dioxo-3H-pyrimidine-4-carboxylic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ORO 'Create component' 1999-07-08 RCSB
ORO 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id ORO
_pdbe_chem_comp_drugbank_details.drugbank_id DB02262
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Orotic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 65-86-1
_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
ORO 'Acidum oroticum' DrugBank ?
ORO 'Orotic acid' DrugBank ?
ORO 'Uracil-6-carboxylic acid' DrugBank ?
ORO 'Vitamin B13' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id ORO
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02262
_pdbe_chem_comp_drugbank_classification.parent 'Pyrimidinecarboxylic acids'
_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 pyrimidinecarboxylic acids. These are pyrimidines with a structure containing a carboxyl group attached to the pyrimidine ring.'
#
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
ORO DB02262 'Orotate phosphoribosyltransferase' 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)' P08870 unknown 1
ORO DB02262 'Dihydroorotate dehydrogenase (quinone), mitochondrial' Humans Q02127 unknown 2
ORO DB02262 'Dihydroorotate dehydrogenase (quinone)' 'Escherichia coli (strain K12)' P0A7E1 unknown 3
ORO DB02262 Dihydroorotase 'Escherichia coli (strain K12)' P05020 unknown 4
ORO DB02262 'Dihydroorotate dehydrogenase A (fumarate)' 'Lactococcus lactis subsp. cremoris' Q53ZE5 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
ORO N1 N 7.702 -1.500 1
ORO C2 C 9.002 -0.750 2
ORO O2 O 10.301 -1.500 3
ORO N3 N 9.002 0.750 4
ORO C4 C 7.702 1.500 5
ORO O4 O 7.702 3.000 6
ORO C5 C 6.404 0.750 7
ORO C6 C 6.404 -0.750 8
ORO C7 C 5.104 -1.500 9
ORO O71 O 3.805 -0.750 10
ORO O72 O 5.104 -3.000 11
#
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
ORO N1 C2 SINGLE NONE 1
ORO N1 C6 SINGLE NONE 2
ORO C2 O2 DOUBLE NONE 3
ORO C2 N3 SINGLE NONE 4
ORO N3 C4 SINGLE NONE 5
ORO C4 O4 DOUBLE NONE 6
ORO C4 C5 SINGLE NONE 7
ORO C5 C6 DOUBLE NONE 8
ORO C6 C7 SINGLE NONE 9
ORO C7 O71 DOUBLE NONE 10
ORO C7 O72 SINGLE NONE 11
#
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
ORO 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
ORO 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
ORO N1 S1 1
ORO C2 S1 1
ORO O2 S1 1
ORO N3 S1 1
ORO C4 S1 1
ORO O4 S1 1
ORO C5 S1 1
ORO C6 S1 1
ORO C5 F1 1
ORO C4 F1 1
ORO N3 F1 1
ORO C2 F1 1
ORO N1 F1 1
ORO C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ORO
_pdbe_chem_comp_rdkit_properties.exactmw 156.017
_pdbe_chem_comp_rdkit_properties.amw 156.097
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_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 65.337
_pdbe_chem_comp_rdkit_properties.tpsa 103.020
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.506
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.593
_pdbe_chem_comp_rdkit_properties.chi0v 5.027
_pdbe_chem_comp_rdkit_properties.chi1v 2.461
_pdbe_chem_comp_rdkit_properties.chi2v 0.823
_pdbe_chem_comp_rdkit_properties.chi3v 0.823
_pdbe_chem_comp_rdkit_properties.chi4v 0.461
_pdbe_chem_comp_rdkit_properties.chi0n 9.027
_pdbe_chem_comp_rdkit_properties.chi1n 4.264
_pdbe_chem_comp_rdkit_properties.chi2n 0.823
_pdbe_chem_comp_rdkit_properties.chi3n 0.823
_pdbe_chem_comp_rdkit_properties.chi4n 0.461
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.850
_pdbe_chem_comp_rdkit_properties.kappa1 3.515
_pdbe_chem_comp_rdkit_properties.kappa2 2.409
_pdbe_chem_comp_rdkit_properties.kappa3 1.540
_pdbe_chem_comp_rdkit_properties.Phi 0.770
#
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
ORO UniChem ChEMBL CHEMBL1235017
ORO UniChem DrugBank DB02262
ORO UniChem PDBe ORO
ORO UniChem 'Guide to Pharmacology' 4690
ORO UniChem 'KEGG LIGAND' C00295
ORO UniChem ChEBI 16742
ORO UniChem ZINC ZINC000001408068
ORO UniChem eMolecules 530220
ORO UniChem atlas 'orotic acid'
ORO UniChem fdasrs 61H4T033E5
ORO UniChem HMDB HMDB0000226
ORO UniChem Selleck Orotic-acid(6-Carboxyuracil)
ORO UniChem NMRShiftDB 20027358
ORO UniChem ACTor 68460-00-4
ORO UniChem DrugCentral 3402
ORO UniChem MetaboLights MTBLC16742
ORO UniChem BRENDA 12642
ORO UniChem BRENDA 163082
ORO UniChem BRENDA 446
ORO UniChem BRENDA 68893
ORO UniChem ChemicalBook CB34796962
ORO UniChem ChemicalBook CB5691265
ORO UniChem DailyMed 'OROTIC ACID'
ORO UniChem ClinicalTrials 'OROTIC ACID'
ORO UniChem rxnorm 'OROTIC ACID'
ORO UniChem MedChemExpress HY-N0157
ORO UniChem 'Probes And Drugs' PD001471
ORO UniChem 'EPA CompTox Dashboard' DTXSID0025814
ORO UniChem eMolecules 816071
ORO UniChem SureChEMBL SCHEMBL20865
ORO UniChem 'PubChem TPHARMA' 15120234
ORO UniChem 'PubChem TPHARMA' 16877294
ORO UniChem PubChem 967
ORO UniChem Mcule MCULE-1013719295
ORO UniChem Nikkaji J2.359K
#
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
ORO N1 -0.263 1.276 0.138 ETKDGv3 1
ORO C2 -1.675 1.101 0.296 ETKDGv3 2
ORO O2 -2.424 2.098 0.470 ETKDGv3 3
ORO N3 -2.227 -0.215 0.253 ETKDGv3 4
ORO C4 -1.350 -1.326 0.054 ETKDGv3 5
ORO O4 -1.814 -2.496 0.013 ETKDGv3 6
ORO C5 0.096 -1.100 -0.103 ETKDGv3 7
ORO C6 0.607 0.144 -0.062 ETKDGv3 8
ORO C7 2.062 0.360 -0.221 ETKDGv3 9
ORO O71 2.534 1.528 -0.181 ETKDGv3 10
ORO O72 2.922 -0.718 -0.415 ETKDGv3 11
ORO HN1 0.130 2.244 0.171 ETKDGv3 12
ORO HN3 -3.255 -0.363 0.366 ETKDGv3 13
ORO H5 0.738 -1.960 -0.253 ETKDGv3 14
ORO HO7 3.919 -0.575 -0.525 ETKDGv3 15
#