data_CYT
#
_chem_comp.id CYT
_chem_comp.name 6-AMINOPYRIMIDIN-2(1H)-ONE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H5 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms CYTOSINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-01-29
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 111.102
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CYT
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2"
_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 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
CYT N3 N3 N 0 1 Y N N N N N 114.683 17.867 5.803 -0.356 -2.061 -3.112 N3 CYT 1
CYT C4 C4 C 0 1 Y N N N N N 113.623 18.547 5.241 0.341 -0.883 -3.202 C4 CYT 2
CYT N1 N1 N 0 1 Y N N N N N 115.137 16.765 3.744 -0.784 -1.739 -0.794 N1 CYT 3
CYT C2 C2 C 0 1 Y N N N N N 115.431 16.978 5.082 -0.931 -2.520 -1.928 C2 CYT 4
CYT O2 O2 O 0 1 N N N N N N 116.381 16.375 5.630 -1.546 -3.587 -1.909 O2 CYT 5
CYT N4 N4 N 0 1 N N N N N N 112.883 19.437 6.005 0.871 -0.510 -4.410 N4 CYT 6
CYT C5 C5 C 0 1 Y N N N N N 113.285 18.354 3.864 0.498 -0.109 -2.124 C5 CYT 7
CYT C6 C6 C 0 1 Y N N N N N 114.046 17.457 3.137 -0.124 -0.631 -0.895 C6 CYT 8
CYT HN3 HN3 H 0 1 N N N N N N 114.911 18.028 6.763 -0.452 -2.618 -3.955 HN3 CYT 9
CYT HN41 1HN4 H 0 0 N N N N N N 112.705 19.037 6.904 1.766 -0.078 -4.418 HN41 CYT 10
CYT HN42 2HN4 H 0 0 N N N N N N 113.396 20.288 6.115 0.341 -0.687 -5.232 HN42 CYT 11
CYT H5 H5 H 0 1 N N N N N N 112.465 18.890 3.409 1.030 0.832 -2.104 H5 CYT 12
CYT H6 H6 H 0 1 N N N N N N 113.812 17.278 2.098 0.001 -0.001 0.000 H6 CYT 13
#
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
CYT N3 C4 SING Y N 1
CYT N3 C2 SING Y N 2
CYT N3 HN3 SING N N 3
CYT C4 N4 SING N N 4
CYT C4 C5 DOUB Y N 5
CYT N1 C2 SING Y N 6
CYT N1 C6 DOUB Y N 7
CYT C2 O2 DOUB N N 8
CYT N4 HN41 SING N N 9
CYT N4 HN42 SING N N 10
CYT C5 C6 SING Y N 11
CYT C5 H5 SING N N 12
CYT C6 H6 SING N N 13
#
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
CYT SMILES ACDLabs 10.04 O=C1N=CC=C(N)N1
CYT SMILES_CANONICAL CACTVS 3.341 NC1=CC=NC(=O)N1
CYT SMILES CACTVS 3.341 NC1=CC=NC(=O)N1
CYT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=C(NC(=O)N=C1)N
CYT SMILES "OpenEye OEToolkits" 1.5.0 C1=C(NC(=O)N=C1)N
CYT InChI InChI 1.03 InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
CYT InChIKey InChI 1.03 OPTASPLRGRRNAP-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
CYT "SYSTEMATIC NAME" ACDLabs 10.04 6-aminopyrimidin-2(1H)-one
CYT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 4-amino-3H-pyrimidin-2-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CYT 'Create component' 2007-01-29 RCSB
CYT 'Modify descriptor' 2011-06-04 RCSB
CYT 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id CYT
_pdbx_chem_comp_synonyms.name CYTOSINE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id CYT
_pdbe_chem_comp_synonyms.name CYTOSINE
_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
CYT N3 N 6.404 -1.035 1
CYT C4 C 5.104 -0.285 2
CYT N1 N 7.702 1.215 3
CYT C2 C 7.702 -0.285 4
CYT O2 O 9.002 -1.035 5
CYT N4 N 3.805 -1.035 6
CYT C5 C 5.104 1.215 7
CYT C6 C 6.404 1.965 8
#
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
CYT N3 C4 SINGLE NONE 1
CYT N3 C2 SINGLE NONE 2
CYT C4 N4 SINGLE NONE 3
CYT C4 C5 DOUBLE NONE 4
CYT N1 C2 SINGLE NONE 5
CYT N1 C6 DOUBLE NONE 6
CYT C2 O2 DOUBLE NONE 7
CYT C5 C6 SINGLE NONE 8
#
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
CYT MurckoScaffold S1 scaffold 'O=c1nccc[nH]1' InChI=1S/C4H4N2O/c7-4-5-2-1-3-6-4/h1-3H,(H,5,6,7) VTGOHKSTWXHQJK-UHFFFAOYSA-N
CYT 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
CYT N3 S1 1
CYT C4 S1 1
CYT N1 S1 1
CYT C2 S1 1
CYT O2 S1 1
CYT C5 S1 1
CYT C6 S1 1
CYT C5 F1 1
CYT C4 F1 1
CYT N3 F1 1
CYT C2 F1 1
CYT N1 F1 1
CYT C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CYT
_pdbe_chem_comp_rdkit_properties.exactmw 111.043
_pdbe_chem_comp_rdkit_properties.amw 111.104
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 13
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_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 52.571
_pdbe_chem_comp_rdkit_properties.tpsa 71.770
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.129
_pdbe_chem_comp_rdkit_properties.CrippenMR 28.554
_pdbe_chem_comp_rdkit_properties.chi0v 3.750
_pdbe_chem_comp_rdkit_properties.chi1v 1.822
_pdbe_chem_comp_rdkit_properties.chi2v 0.521
_pdbe_chem_comp_rdkit_properties.chi3v 0.521
_pdbe_chem_comp_rdkit_properties.chi4v 0.269
_pdbe_chem_comp_rdkit_properties.chi0n 8.750
_pdbe_chem_comp_rdkit_properties.chi1n 4.164
_pdbe_chem_comp_rdkit_properties.chi2n 0.521
_pdbe_chem_comp_rdkit_properties.chi3n 0.521
_pdbe_chem_comp_rdkit_properties.chi4n 0.269
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.320
_pdbe_chem_comp_rdkit_properties.kappa1 1.580
_pdbe_chem_comp_rdkit_properties.kappa2 1.651
_pdbe_chem_comp_rdkit_properties.kappa3 0.841
_pdbe_chem_comp_rdkit_properties.Phi 0.326
#
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
CYT UniChem 'Guide to Pharmacology' 8490
CYT UniChem 'KEGG LIGAND' C00380
CYT UniChem ChEBI 16040
CYT UniChem ZINC ZINC000000895210
CYT UniChem eMolecules 1971016
CYT UniChem eMolecules 496404
CYT UniChem fdasrs 8J337D1HZY
CYT UniChem HMDB HMDB0000630
CYT UniChem NMRShiftDB 10016336
CYT UniChem NMRShiftDB 20096819
CYT UniChem ACTor 118511-36-7
CYT UniChem Recon csn
CYT UniChem Nikkaji J9.343B
CYT UniChem 'EPA CompTox Dashboard' DTXSID4044456
CYT UniChem MetaboLights MTBLC16040
CYT UniChem BRENDA 489
CYT UniChem Rhea 16040
CYT UniChem ChemicalBook CB3746093
CYT UniChem ClinicalTrials CYTOSINE
CYT UniChem rxnorm CYTOSINE
CYT UniChem MedChemExpress HY-I0626
CYT UniChem 'Probes And Drugs' PD013768
CYT UniChem CCDC CYTSIN
CYT UniChem eMolecules 7351983
CYT UniChem SureChEMBL SCHEMBL4059
CYT UniChem 'PubChem TPHARMA' 15297057
CYT UniChem 'PubChem TPHARMA' 15412737
CYT UniChem 'PubChem TPHARMA' 16918494
CYT UniChem PubChem 597
CYT UniChem Mcule MCULE-4426252594
#
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
CYT N3 -0.146 1.178 0.255 ETKDGv3 1
CYT C4 0.693 0.033 0.039 ETKDGv3 2
CYT N1 -2.112 -0.256 -0.154 ETKDGv3 3
CYT C2 -1.565 1.029 0.156 ETKDGv3 4
CYT O2 -2.326 2.015 0.340 ETKDGv3 5
CYT N4 2.113 0.163 0.134 ETKDGv3 6
CYT C5 0.136 -1.152 -0.250 ETKDGv3 7
CYT C6 -1.334 -1.281 -0.346 ETKDGv3 8
CYT HN3 0.273 2.108 0.481 ETKDGv3 9
CYT HN41 2.743 -0.657 -0.019 ETKDGv3 10
CYT HN42 2.543 1.087 0.359 ETKDGv3 11
CYT H5 0.754 -2.026 -0.415 ETKDGv3 12
CYT H6 -1.770 -2.243 -0.580 ETKDGv3 13
#