data_HMU
#
_chem_comp.id HMU
_chem_comp.name "5-HYDROXYMETHYL URACIL"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H6 N2 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 5-(HYDROXYMETHYL)PYRIMIDINE-2,4(1H,3H)-DIONE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-03-19
_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 142.113
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HMU
_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 ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
HMU N1 N1 N 0 1 N N N N N N 4.328 20.980 42.926 1.402 -0.001 -1.017 N1 HMU 1
HMU C2 C2 C 0 1 N N N N N N 4.245 22.334 42.473 0.339 0.000 -1.842 C2 HMU 2
HMU O2 O2 O 0 1 N N N N N N 5.170 23.246 42.899 0.515 0.000 -3.045 O2 HMU 3
HMU N3 N3 N 0 1 N N N N N N 3.137 22.528 41.576 -0.914 0.002 -1.354 N3 HMU 4
HMU C4 C4 C 0 1 N N N N N N 2.248 21.500 41.163 -1.126 -0.002 -0.023 C4 HMU 5
HMU O3 O3 O 0 1 N N N N N N 1.211 18.816 39.902 1.042 -0.000 3.007 O3 HMU 6
HMU O4 O4 O 0 1 N N N N N N 1.326 21.668 40.316 -2.261 -0.001 0.419 O4 HMU 7
HMU C5 C5 C 0 1 N N N N N N 2.409 20.090 41.665 -0.017 0.001 0.856 C5 HMU 8
HMU CM5 CM5 C 0 1 N N N N N N 1.523 18.858 41.271 -0.226 0.001 2.349 CM5 HMU 9
HMU C6 C6 C 0 1 N N N N N N 3.480 19.923 42.592 1.230 -0.000 0.340 C6 HMU 10
HMU H1 H1 H 0 1 N N N N N N 4.332 21.025 43.945 2.298 -0.002 -1.387 H1 HMU 11
HMU H2 H2 H 0 1 N N N N N N 2.969 23.463 41.206 -1.669 0.003 -1.963 H2 HMU 12
HMU H3 H3 H 0 1 N N N N N N 1.144 17.873 39.607 0.863 -0.000 3.958 H3 HMU 13
HMU HM51 1HM5 H 0 0 N N N N N N 2.066 17.938 41.534 -0.786 -0.887 2.637 HM51 HMU 14
HMU HM52 2HM5 H 0 0 N N N N N N 0.574 18.949 41.820 -0.783 0.892 2.637 HM52 HMU 15
HMU H6 H6 H 0 1 N N N N N N 3.636 18.973 43.038 2.088 -0.001 0.996 H6 HMU 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
HMU N1 C2 SING N N 1
HMU N1 C6 SING N N 2
HMU N1 H1 SING N N 3
HMU C2 O2 DOUB N N 4
HMU C2 N3 SING N N 5
HMU N3 C4 SING N N 6
HMU N3 H2 SING N N 7
HMU C4 O4 DOUB N N 8
HMU C4 C5 SING N N 9
HMU O3 CM5 SING N N 10
HMU O3 H3 SING N N 11
HMU C5 CM5 SING N N 12
HMU C5 C6 DOUB N N 13
HMU CM5 HM51 SING N N 14
HMU CM5 HM52 SING N N 15
HMU C6 H6 SING N N 16
#
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
HMU SMILES ACDLabs 10.04 O=C1C(=CNC(=O)N1)CO
HMU SMILES_CANONICAL CACTVS 3.341 OCC1=CNC(=O)NC1=O
HMU SMILES CACTVS 3.341 OCC1=CNC(=O)NC1=O
HMU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1)CO
HMU SMILES "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1)CO
HMU InChI InChI 1.03 InChI=1S/C5H6N2O3/c8-2-3-1-6-5(10)7-4(3)9/h1,8H,2H2,(H2,6,7,9,10)
HMU InChIKey InChI 1.03 JDBGXEHEIRGOBU-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
HMU "SYSTEMATIC NAME" ACDLabs 10.04 5-(hydroxymethyl)pyrimidine-2,4(1H,3H)-dione
HMU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 5-(hydroxymethyl)-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
HMU 'Create component' 2003-03-19 EBI
HMU 'Modify descriptor' 2011-06-04 RCSB
HMU 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id HMU
_pdbx_chem_comp_synonyms.name 5-(HYDROXYMETHYL)PYRIMIDINE-2,4(1H,3H)-DIONE
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id HMU
_pdbe_chem_comp_synonyms.name 5-(HYDROXYMETHYL)PYRIMIDINE-2,4(1H,3H)-DIONE
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
HMU N1 N 7.702 0.233 1
HMU C2 C 7.702 -1.268 2
HMU O2 O 9.002 -2.018 3
HMU N3 N 6.404 -2.018 4
HMU C4 C 5.104 -1.268 5
HMU O3 O 3.805 2.482 6
HMU O4 O 3.805 -2.018 7
HMU C5 C 5.104 0.233 8
HMU CM5 C 3.805 0.983 9
HMU C6 C 6.404 0.983 10
#
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
HMU N1 C2 SINGLE NONE 1
HMU N1 C6 SINGLE NONE 2
HMU C2 O2 DOUBLE NONE 3
HMU C2 N3 SINGLE NONE 4
HMU N3 C4 SINGLE NONE 5
HMU C4 O4 DOUBLE NONE 6
HMU C4 C5 SINGLE NONE 7
HMU O3 CM5 SINGLE NONE 8
HMU C5 CM5 SINGLE NONE 9
HMU C5 C6 DOUBLE NONE 10
#
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
HMU 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
HMU 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
HMU N1 S1 1
HMU C2 S1 1
HMU O2 S1 1
HMU N3 S1 1
HMU C4 S1 1
HMU O4 S1 1
HMU C5 S1 1
HMU C6 S1 1
HMU C5 F1 1
HMU C4 F1 1
HMU N3 F1 1
HMU C2 F1 1
HMU N1 F1 1
HMU C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HMU
_pdbe_chem_comp_rdkit_properties.exactmw 142.038
_pdbe_chem_comp_rdkit_properties.amw 142.114
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 16
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.200
_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 63.986
_pdbe_chem_comp_rdkit_properties.tpsa 85.950
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.301
_pdbe_chem_comp_rdkit_properties.CrippenMR 33.556
_pdbe_chem_comp_rdkit_properties.chi0v 4.619
_pdbe_chem_comp_rdkit_properties.chi1v 2.257
_pdbe_chem_comp_rdkit_properties.chi2v 0.776
_pdbe_chem_comp_rdkit_properties.chi3v 0.776
_pdbe_chem_comp_rdkit_properties.chi4v 0.386
_pdbe_chem_comp_rdkit_properties.chi0n 10.619
_pdbe_chem_comp_rdkit_properties.chi1n 5.059
_pdbe_chem_comp_rdkit_properties.chi2n 0.776
_pdbe_chem_comp_rdkit_properties.chi3n 0.776
_pdbe_chem_comp_rdkit_properties.chi4n 0.386
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.360
_pdbe_chem_comp_rdkit_properties.kappa1 2.353
_pdbe_chem_comp_rdkit_properties.kappa2 2.486
_pdbe_chem_comp_rdkit_properties.kappa3 1.135
_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
HMU UniChem 'KEGG LIGAND' C03088
HMU UniChem ChEBI 16964
HMU UniChem ZINC ZINC000000114121
HMU UniChem fdasrs 590TQ3GL34
HMU UniChem SureChEMBL SCHEMBL44459
HMU UniChem HMDB HMDB0000469
HMU UniChem 'PubChem TPHARMA' 15363635
HMU UniChem NMRShiftDB 60022167
HMU UniChem ACTor 4433-40-3
HMU UniChem 'EPA CompTox Dashboard' DTXSID9063455
HMU UniChem MetaboLights MTBLC16964
HMU UniChem BRENDA 227080
HMU UniChem BRENDA 43547
HMU UniChem BRENDA 5919
HMU UniChem Rhea 16964
HMU UniChem ChemicalBook CB7122987
HMU UniChem MedChemExpress HY-W004924
HMU UniChem 'Probes And Drugs' PD020630
HMU UniChem CCDC IKIYOS
HMU UniChem BindingDb 50106411
HMU UniChem eMolecules 601500
HMU UniChem eMolecules 888696
HMU UniChem 'PubChem TPHARMA' 15321509
HMU UniChem PubChem 78168
HMU UniChem Mcule MCULE-2866555326
HMU UniChem Nikkaji J58.058I
#
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
HMU N1 -1.370 1.378 -0.124 ETKDGv3 1
HMU C2 -2.239 0.355 0.367 ETKDGv3 2
HMU O2 -3.444 0.612 0.625 ETKDGv3 3
HMU N3 -1.725 -0.962 0.565 ETKDGv3 4
HMU C4 -0.351 -1.227 0.265 ETKDGv3 5
HMU O3 2.711 -0.354 0.633 ETKDGv3 6
HMU O4 0.116 -2.382 0.454 ETKDGv3 7
HMU C5 0.512 -0.143 -0.263 ETKDGv3 8
HMU CM5 1.967 -0.405 -0.553 ETKDGv3 9
HMU C6 0.004 1.092 -0.421 ETKDGv3 10
HMU H1 -1.734 2.347 -0.266 ETKDGv3 11
HMU H2 -2.343 -1.721 0.930 ETKDGv3 12
HMU H3 2.807 0.606 0.866 ETKDGv3 13
HMU HM51 2.082 -1.414 -1.003 ETKDGv3 14
HMU HM52 2.371 0.322 -1.295 ETKDGv3 15
HMU H6 0.635 1.896 -0.780 ETKDGv3 16
#