data_URI # _chem_comp.id URI _chem_comp.name URIDINE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H12 N2 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-03-08 _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 244.201 _chem_comp.one_letter_code ? _chem_comp.three_letter_code URI _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 1I5L _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 URI N1 N1 N 0 1 N N N N N N 13.859 6.258 12.518 -0.241 0.429 -1.029 N1 URI 1 URI C2 C2 C 0 1 N N N N N N 14.153 5.779 11.254 0.482 -0.634 -1.422 C2 URI 2 URI N3 N3 N 0 1 N N N N N N 13.320 6.227 10.257 0.743 -0.850 -2.725 N3 URI 3 URI C4 C4 C 0 1 N N N N N N 12.238 7.073 10.394 0.289 0.007 -3.661 C4 URI 4 URI C5 C5 C 0 1 N N N N N N 11.977 7.497 11.738 -0.468 1.134 -3.260 C5 URI 5 URI C6 C6 C 0 1 N N N N N N 12.771 7.080 12.731 -0.720 1.324 -1.947 C6 URI 6 URI O2 O2 O 0 1 N N N N N N 15.078 5.010 11.037 0.898 -1.416 -0.590 O2 URI 7 URI O4 O4 O 0 1 N N N N N N 11.593 7.395 9.395 0.529 -0.184 -4.839 O4 URI 8 URI "C1'" C1* C 0 1 N N R N N N 14.779 5.894 13.607 -0.513 0.636 0.394 "C1'" URI 9 URI "C2'" C2* C 0 1 N N R N N N 14.648 6.799 14.833 -1.204 -0.608 1.007 "C2'" URI 10 URI "C3'" C3* C 0 1 N N S N N N 14.868 5.842 16.003 -0.831 -0.481 2.508 "C3'" URI 11 URI "C4'" C4* C 0 1 N N R N N N 14.500 4.472 15.446 0.409 0.431 2.508 "C4'" URI 12 URI "O2'" O2* O 0 1 N N N N N N 15.597 7.844 14.783 -2.620 -0.546 0.828 "O2'" URI 13 URI "O3'" O3* O 0 1 N N N N N N 16.275 5.893 16.189 -1.901 0.117 3.240 "O3'" URI 14 URI "O4'" O4* O 0 1 N N N N N N 14.513 4.571 14.003 0.719 0.737 1.138 "O4'" URI 15 URI "C5'" C5* C 0 1 N N N N N N 13.181 3.891 15.891 1.589 -0.293 3.159 "C5'" URI 16 URI "O5'" O5* O 0 1 N N N N N N 13.240 3.291 17.191 2.736 0.558 3.148 "O5'" URI 17 URI H3 H3 H 0 1 N N N N N N 13.526 5.896 9.314 1.263 -1.624 -2.991 H3 URI 18 URI H5 H5 H 0 1 N N N N N N 11.142 8.162 12.015 -0.841 1.832 -3.995 H5 URI 19 URI H6 H6 H 0 1 N N N N N N 12.522 7.422 13.749 -1.296 2.178 -1.623 H6 URI 20 URI "H1'" H1* H 0 1 N N N N N N 15.815 6.011 13.212 -1.125 1.526 0.542 "H1'" URI 21 URI "H2'" H2* H 0 1 N N N N N N 13.665 7.320 14.910 -0.799 -1.527 0.581 "H2'" URI 22 URI "H3'" H3* H 0 1 N N N N N N 14.302 6.063 16.938 -0.585 -1.458 2.924 "H3'" URI 23 URI "H4'" H4* H 0 1 N N N N N N 15.258 3.764 15.855 0.193 1.350 3.053 "H4'" URI 24 URI "HO2'" *HO2 H 0 0 N N N N N N 15.515 8.406 15.544 -2.988 -1.345 1.229 "HO2'" URI 25 URI "HO3'" *HO3 H 0 0 N N N N N N 16.411 5.297 16.916 -1.614 0.170 4.162 "HO3'" URI 26 URI "H5'1" 1H5* H 0 0 N N N N N N 12.373 4.658 15.843 1.808 -1.204 2.602 "H5'1" URI 27 URI "H5'2" 2H5* H 0 0 N N N N N N 12.791 3.167 15.137 1.336 -0.548 4.188 "H5'2" URI 28 URI "HO5'" *HO5 H 0 0 N N N N N N 12.409 2.925 17.471 3.455 0.064 3.567 "HO5'" URI 29 # 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 URI N1 C2 SING N N 1 URI N1 C6 SING N N 2 URI N1 "C1'" SING N N 3 URI C2 N3 SING N N 4 URI C2 O2 DOUB N N 5 URI N3 C4 SING N N 6 URI N3 H3 SING N N 7 URI C4 C5 SING N N 8 URI C4 O4 DOUB N N 9 URI C5 C6 DOUB N N 10 URI C5 H5 SING N N 11 URI C6 H6 SING N N 12 URI "C1'" "C2'" SING N N 13 URI "C1'" "O4'" SING N N 14 URI "C1'" "H1'" SING N N 15 URI "C2'" "C3'" SING N N 16 URI "C2'" "O2'" SING N N 17 URI "C2'" "H2'" SING N N 18 URI "C3'" "C4'" SING N N 19 URI "C3'" "O3'" SING N N 20 URI "C3'" "H3'" SING N N 21 URI "C4'" "O4'" SING N N 22 URI "C4'" "C5'" SING N N 23 URI "C4'" "H4'" SING N N 24 URI "O2'" "HO2'" SING N N 25 URI "O3'" "HO3'" SING N N 26 URI "C5'" "O5'" SING N N 27 URI "C5'" "H5'1" SING N N 28 URI "C5'" "H5'2" SING N N 29 URI "O5'" "HO5'" SING N N 30 # 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 URI SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)CO URI SMILES_CANONICAL CACTVS 3.341 OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O URI SMILES CACTVS 3.341 OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O URI SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O URI SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)O URI InChI InChI 1.03 InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1 URI InChIKey InChI 1.03 DRTQHJPVMGBUCF-XVFCMESISA-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 URI "SYSTEMATIC NAME" ACDLabs 10.04 uridine URI "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]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 URI 'Create component' 2001-03-08 RCSB URI 'Modify descriptor' 2011-06-04 RCSB # _pdbe_chem_comp_drugbank_details.comp_id URI _pdbe_chem_comp_drugbank_details.drugbank_id DB02745 _pdbe_chem_comp_drugbank_details.type 'small molecule' _pdbe_chem_comp_drugbank_details.name Uridine _pdbe_chem_comp_drugbank_details.description ? _pdbe_chem_comp_drugbank_details.cas_number 58-96-8 _pdbe_chem_comp_drugbank_details.mechanism_of_action ? # _pdbe_chem_comp_synonyms.comp_id URI _pdbe_chem_comp_synonyms.name Uridine _pdbe_chem_comp_synonyms.provenance DrugBank _pdbe_chem_comp_synonyms.type ? # _pdbe_chem_comp_drugbank_classification.comp_id URI _pdbe_chem_comp_drugbank_classification.drugbank_id DB02745 _pdbe_chem_comp_drugbank_classification.parent 'Pyrimidine nucleosides' _pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds' _pdbe_chem_comp_drugbank_classification.class 'Pyrimidine nucleosides' _pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues' _pdbe_chem_comp_drugbank_classification.description 'This compound belongs to the class of organic compounds known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.' # 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 URI DB02745 'Thymidine phosphorylase' Humans P19971 unknown 1 URI DB02745 'U6 snRNA-associated Sm-like protein LSm6' Humans P62312 unknown 2 URI DB02745 'Nucleoside-specific channel-forming protein tsx' 'Escherichia coli (strain K12)' P0A927 unknown 3 # 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 URI N1 N 6.331 0.686 1 URI C2 C 7.630 1.436 2 URI N3 N 7.630 2.936 3 URI C4 C 6.331 3.686 4 URI C5 C 5.032 2.936 5 URI C6 C 5.032 1.436 6 URI O2 O 8.929 0.686 7 URI O4 O 6.331 5.186 8 URI "C1'" C 6.331 -0.814 9 URI "C2'" C 5.118 -1.696 10 URI "C3'" C 5.581 -3.123 11 URI "C4'" C 7.081 -3.123 12 URI "O2'" O 3.691 -1.232 13 URI "O3'" O 4.699 -4.336 14 URI "O4'" O 7.545 -1.696 15 URI "C5'" C 7.963 -4.336 16 URI "O5'" O 9.455 -4.179 17 # 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 URI N1 C2 SINGLE NONE 1 URI N1 C6 SINGLE NONE 2 URI "C1'" N1 SINGLE BEGINDASH 3 URI C2 N3 SINGLE NONE 4 URI C2 O2 DOUBLE NONE 5 URI N3 C4 SINGLE NONE 6 URI C4 C5 SINGLE NONE 7 URI C4 O4 DOUBLE NONE 8 URI C5 C6 DOUBLE NONE 9 URI "C1'" "C2'" SINGLE NONE 10 URI "C1'" "O4'" SINGLE NONE 11 URI "C2'" "C3'" SINGLE NONE 12 URI "C2'" "O2'" SINGLE BEGINWEDGE 13 URI "C3'" "C4'" SINGLE NONE 14 URI "C3'" "O3'" SINGLE BEGINWEDGE 15 URI "C4'" "O4'" SINGLE NONE 16 URI "C4'" "C5'" SINGLE BEGINDASH 17 URI "C5'" "O5'" SINGLE NONE 18 # 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 URI MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CCCO2)c(=O)[nH]1' InChI=1S/C8H10N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h3-4,7H,1-2,5H2,(H,9,11,12)/t7-/m1/s1 CWWIKVUHBBTKHC-SSDOTTSWSA-N URI pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N URI ribose F2 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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 URI N1 S1 1 URI C2 S1 1 URI N3 S1 1 URI C4 S1 1 URI C5 S1 1 URI C6 S1 1 URI O2 S1 1 URI O4 S1 1 URI "C1'" S1 1 URI "C2'" S1 1 URI "C3'" S1 1 URI "C4'" S1 1 URI "O4'" S1 1 URI C5 F1 1 URI C4 F1 1 URI N3 F1 1 URI C2 F1 1 URI N1 F1 1 URI C6 F1 1 URI "C2'" F2 1 URI "C3'" F2 1 URI "C4'" F2 1 URI "O4'" F2 1 URI "C1'" F2 1 URI "C5'" F2 1 URI "O5'" F2 1 URI "O3'" F2 1 URI "O2'" F2 1 # _pdbe_chem_comp_rdkit_properties.comp_id URI _pdbe_chem_comp_rdkit_properties.exactmw 244.070 _pdbe_chem_comp_rdkit_properties.amw 244.203 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 8 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 4 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5 _pdbe_chem_comp_rdkit_properties.NumHBD 4 _pdbe_chem_comp_rdkit_properties.NumHBA 7 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17 _pdbe_chem_comp_rdkit_properties.NumAtoms 29 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556 _pdbe_chem_comp_rdkit_properties.NumRings 2 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 111.897 _pdbe_chem_comp_rdkit_properties.tpsa 124.780 _pdbe_chem_comp_rdkit_properties.CrippenClogP -1.052 _pdbe_chem_comp_rdkit_properties.CrippenMR 54.548 _pdbe_chem_comp_rdkit_properties.chi0v 7.844 _pdbe_chem_comp_rdkit_properties.chi1v 4.047 _pdbe_chem_comp_rdkit_properties.chi2v 1.764 _pdbe_chem_comp_rdkit_properties.chi3v 1.764 _pdbe_chem_comp_rdkit_properties.chi4v 1.058 _pdbe_chem_comp_rdkit_properties.chi0n 19.844 _pdbe_chem_comp_rdkit_properties.chi1n 9.719 _pdbe_chem_comp_rdkit_properties.chi2n 1.764 _pdbe_chem_comp_rdkit_properties.chi3n 1.764 _pdbe_chem_comp_rdkit_properties.chi4n 1.058 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.480 _pdbe_chem_comp_rdkit_properties.kappa1 4.023 _pdbe_chem_comp_rdkit_properties.kappa2 4.414 _pdbe_chem_comp_rdkit_properties.kappa3 2.026 _pdbe_chem_comp_rdkit_properties.Phi 1.045 # 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 URI UniChem DrugBank DB02745 URI UniChem 'Guide to Pharmacology' 4566 URI UniChem 'KEGG LIGAND' C00299 URI UniChem ChEBI 16704 URI UniChem ZINC ZINC000002583633 URI UniChem fdasrs WHI7HQ7H85 URI UniChem PharmGKB PA130230921 URI UniChem HMDB HMDB0000296 URI UniChem Selleck uridine URI UniChem NMRShiftDB 60021002 URI UniChem Recon uri URI UniChem 'EPA CompTox Dashboard' DTXSID40891555 URI UniChem BRENDA 113278 URI UniChem BRENDA 144373 URI UniChem BRENDA 261 URI UniChem BRENDA 30495 URI UniChem BRENDA 90609 URI UniChem Rhea 16704 URI UniChem ChemicalBook CB0330400 URI UniChem ClinicalTrials URIDINE URI UniChem rxnorm URIDINE URI UniChem MedChemExpress HY-B1449 URI UniChem 'Probes And Drugs' PD000785 URI UniChem CCDC BEURID URI UniChem DailyMed URIDINE URI UniChem eMolecules 533118 URI UniChem SureChEMBL SCHEMBL20667 URI UniChem 'PubChem TPHARMA' 14847540 URI UniChem 'PubChem TPHARMA' 15221017 URI UniChem PubChem 6029 URI UniChem ACTor 12693-39-9 URI UniChem ACTor 21231-59-4 URI UniChem Nikkaji J4.593D URI UniChem BindingDb 50088517 URI UniChem MetaboLights MTBLC16704 # 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 URI N1 1.327 -0.145 0.315 ETKDGv3 1 URI C2 2.319 -0.395 1.332 ETKDGv3 2 URI N3 3.518 0.382 1.354 ETKDGv3 3 URI C4 3.697 1.418 0.388 ETKDGv3 4 URI C5 2.647 1.675 -0.605 ETKDGv3 5 URI C6 1.534 0.936 -0.622 ETKDGv3 6 URI O2 2.142 -1.289 2.203 ETKDGv3 7 URI O4 4.748 2.112 0.391 ETKDGv3 8 URI "C1'" 0.063 -0.899 0.301 ETKDGv3 9 URI "C2'" -1.021 -0.154 1.060 ETKDGv3 10 URI "C3'" -2.278 -0.634 0.375 ETKDGv3 11 URI "C4'" -1.784 -0.944 -1.042 ETKDGv3 12 URI "O2'" -0.993 -0.478 2.426 ETKDGv3 13 URI "O3'" -2.757 -1.814 0.972 ETKDGv3 14 URI "O4'" -0.379 -1.105 -1.024 ETKDGv3 15 URI "C5'" -2.158 0.175 -2.027 ETKDGv3 16 URI "O5'" -1.717 -0.143 -3.320 ETKDGv3 17 URI H3 4.253 0.200 2.074 ETKDGv3 18 URI H5 2.772 2.475 -1.325 ETKDGv3 19 URI H6 0.776 1.163 -1.361 ETKDGv3 20 URI "H1'" 0.214 -1.906 0.754 ETKDGv3 21 URI "H2'" -0.909 0.946 0.914 ETKDGv3 22 URI "H3'" -3.066 0.157 0.388 ETKDGv3 23 URI "H4'" -2.246 -1.889 -1.407 ETKDGv3 24 URI "HO2'" -1.609 0.157 2.876 ETKDGv3 25 URI "HO3'" -3.343 -1.539 1.725 ETKDGv3 26 URI "H5'1" -1.728 1.148 -1.695 ETKDGv3 27 URI "H5'2" -3.263 0.285 -2.054 ETKDGv3 28 URI "HO5'" -0.757 0.106 -3.364 ETKDGv3 29 #