data_28Y
#
_chem_comp.id 28Y
_chem_comp.name 3H-imidazo[2,1-b]purin-4(5H)-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H5 N5 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms N2,3-ethenoguanine
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-09-11
_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 175.147
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 28Y
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 4MEJ
_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
28Y C4 C4 C 0 1 Y N N N N N 2.180 -4.540 -25.061 -0.422 0.875 -0.001 C4 28Y 1
28Y C5 C5 C 0 1 Y N N N N N 2.270 -5.823 -24.544 -1.314 -0.187 -0.001 C5 28Y 2
28Y C6 C6 C 0 1 N N N N N N 1.693 -6.133 -23.320 -0.823 -1.512 -0.000 C6 28Y 3
28Y C8 C8 C 0 1 Y N N N N N 3.287 -5.768 -26.441 -2.419 1.707 -0.001 C8 28Y 4
28Y N1 N1 N 0 1 N N N N N N 1.017 -5.147 -22.601 0.507 -1.730 0.001 N1 28Y 5
28Y N2 N2 N 0 1 Y N N N N N 0.364 -2.747 -22.680 2.711 -0.639 0.000 N2 28Y 6
28Y N3 N3 N 0 1 Y N N N N N 1.506 -3.548 -24.351 0.941 0.614 -0.000 N3 28Y 7
28Y O6 O6 O 0 1 N N N N N N 1.779 -7.275 -22.872 -1.598 -2.452 0.000 O6 28Y 8
28Y N7 N7 N 0 1 Y N N N N N 2.955 -6.550 -25.415 -2.578 0.370 -0.001 N7 28Y 9
28Y N9 N9 N 0 1 Y N N N N N 2.815 -4.540 -26.227 -1.144 2.000 0.004 N9 28Y 10
28Y CAD CAD C 0 1 Y N N N N N 1.261 -2.265 -24.594 2.043 1.435 -0.001 CAD 28Y 11
28Y CAB CAB C 0 1 Y N N N N N 0.569 -1.778 -23.567 3.126 0.637 -0.001 CAB 28Y 12
28Y C2 C2 C 0 1 Y N N N N N 0.928 -3.857 -23.125 1.396 -0.671 0.001 C2 28Y 13
28Y H1 H1 H 0 1 N N N N N N 3.849 -6.080 -27.309 -3.223 2.429 0.001 H1 28Y 14
28Y H2 H2 H 0 1 N N N N N N 0.600 -5.363 -21.718 0.844 -2.640 0.002 H2 28Y 15
28Y H3 H3 H 0 1 N N N N N N 3.183 -7.519 -25.319 -3.420 -0.112 -0.005 H3 28Y 16
28Y H5 H5 H 0 1 N N N N N N 1.569 -1.714 -25.471 2.040 2.515 -0.002 H5 28Y 17
28Y H6 H6 H 0 1 N N N N N N 0.228 -0.758 -23.469 4.154 0.967 -0.001 H6 28Y 18
#
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
28Y C8 N9 DOUB Y N 1
28Y C8 N7 SING Y N 2
28Y N9 C4 SING Y N 3
28Y N7 C5 SING Y N 4
28Y C4 C5 DOUB Y N 5
28Y C4 N3 SING N N 6
28Y CAD N3 SING Y N 7
28Y CAD CAB DOUB Y N 8
28Y C5 C6 SING N N 9
28Y N3 C2 SING Y N 10
28Y CAB N2 SING Y N 11
28Y C6 O6 DOUB N N 12
28Y C6 N1 SING N N 13
28Y C2 N2 DOUB Y N 14
28Y C2 N1 SING N N 15
28Y C8 H1 SING N N 16
28Y N1 H2 SING N N 17
28Y N7 H3 SING N N 18
28Y CAD H5 SING N N 19
28Y CAB H6 SING N N 20
#
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
28Y SMILES ACDLabs 12.01 O=C3c1c(ncn1)n2c(ncc2)N3
28Y InChI InChI 1.03 InChI=1S/C7H5N5O/c13-6-4-5(10-3-9-4)12-2-1-8-7(12)11-6/h1-3H,(H,9,10)(H,8,11,13)
28Y InChIKey InChI 1.03 OSXKHFTZRHDUJN-UHFFFAOYSA-N
28Y SMILES_CANONICAL CACTVS 3.385 O=C1Nc2nccn2c3nc[nH]c13
28Y SMILES CACTVS 3.385 O=C1Nc2nccn2c3nc[nH]c13
28Y SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1cn-2c(n1)NC(=O)c3c2nc[nH]3
28Y SMILES "OpenEye OEToolkits" 1.7.6 c1cn-2c(n1)NC(=O)c3c2nc[nH]3
#
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
28Y "SYSTEMATIC NAME" ACDLabs 12.01 3H-imidazo[2,1-b]purin-4(5H)-one
28Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 3,5-dihydroimidazo[2,1-b]purin-4-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
28Y 'Create component' 2013-09-11 RCSB
28Y 'Initial release' 2014-10-15 RCSB
28Y 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 28Y
_pdbx_chem_comp_synonyms.name N2,3-ethenoguanine
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id 28Y
_pdbe_chem_comp_synonyms.name N2,3-ethenoguanine
_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
28Y C4 C 5.295 -0.694 1
28Y C5 C 5.295 0.806 2
28Y C6 C 6.594 1.556 3
28Y C8 C 3.000 0.056 4
28Y N1 N 7.893 0.806 5
28Y N2 N 8.998 -1.694 6
28Y N3 N 6.594 -1.444 7
28Y O6 O 6.594 3.056 8
28Y N7 N 3.875 1.263 9
28Y N9 N 3.875 -1.151 10
28Y CAD C 6.908 -2.902 11
28Y CAB C 8.391 -3.056 12
28Y C2 C 7.893 -0.694 13
#
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
28Y C8 N9 DOUBLE NONE 1
28Y C8 N7 SINGLE NONE 2
28Y N9 C4 SINGLE NONE 3
28Y N7 C5 SINGLE NONE 4
28Y C4 C5 DOUBLE NONE 5
28Y C4 N3 SINGLE NONE 6
28Y CAD N3 SINGLE NONE 7
28Y CAD CAB DOUBLE NONE 8
28Y C5 C6 SINGLE NONE 9
28Y N3 C2 SINGLE NONE 10
28Y CAB N2 SINGLE NONE 11
28Y C6 O6 DOUBLE NONE 12
28Y C6 N1 SINGLE NONE 13
28Y C2 N2 DOUBLE NONE 14
28Y C2 N1 SINGLE NONE 15
#
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
28Y MurckoScaffold S1 scaffold 'O=c1[nH]c2nccn2c2nc[nH]c12' InChI=1S/C7H5N5O/c13-6-4-5(10-3-9-4)12-2-1-8-7(12)11-6/h1-3H,(H,9,10)(H,8,11,13) OSXKHFTZRHDUJN-UHFFFAOYSA-N
28Y imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
28Y 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
28Y 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
28Y C4 S1 1
28Y C5 S1 1
28Y C6 S1 1
28Y C8 S1 1
28Y N1 S1 1
28Y N2 S1 1
28Y N3 S1 1
28Y O6 S1 1
28Y N7 S1 1
28Y N9 S1 1
28Y CAD S1 1
28Y CAB S1 1
28Y C2 S1 1
28Y C4 F1 1
28Y C5 F1 1
28Y N7 F1 1
28Y C8 F1 1
28Y N9 F1 1
28Y CAD F1 2
28Y CAB F1 2
28Y N2 F1 2
28Y C2 F1 2
28Y N3 F1 2
28Y N7 F2 1
28Y C8 F2 1
28Y N9 F2 1
28Y C4 F2 1
28Y C5 F2 1
28Y C6 F2 1
28Y N1 F2 1
28Y C2 F2 1
28Y N3 F2 1
28Y C5 F3 1
28Y C4 F3 1
28Y N3 F3 1
28Y C2 F3 1
28Y N1 F3 1
28Y C6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 28Y
_pdbe_chem_comp_rdkit_properties.exactmw 175.049
_pdbe_chem_comp_rdkit_properties.amw 175.151
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_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 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 3
_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 78.402
_pdbe_chem_comp_rdkit_properties.tpsa 78.840
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.156
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.263
_pdbe_chem_comp_rdkit_properties.chi0v 6.144
_pdbe_chem_comp_rdkit_properties.chi1v 3.414
_pdbe_chem_comp_rdkit_properties.chi2v 1.663
_pdbe_chem_comp_rdkit_properties.chi3v 1.663
_pdbe_chem_comp_rdkit_properties.chi4v 1.116
_pdbe_chem_comp_rdkit_properties.chi0n 11.144
_pdbe_chem_comp_rdkit_properties.chi1n 5.808
_pdbe_chem_comp_rdkit_properties.chi2n 1.663
_pdbe_chem_comp_rdkit_properties.chi3n 1.663
_pdbe_chem_comp_rdkit_properties.chi4n 1.116
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.110
_pdbe_chem_comp_rdkit_properties.kappa1 3.328
_pdbe_chem_comp_rdkit_properties.kappa2 1.976
_pdbe_chem_comp_rdkit_properties.kappa3 0.689
_pdbe_chem_comp_rdkit_properties.Phi 0.506
#
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
28Y UniChem ChEBI 134095
28Y UniChem SureChEMBL SCHEMBL232090
28Y UniChem SureChEMBL SCHEMBL24681154
28Y UniChem ACTor 62962-42-9
28Y UniChem Nikkaji J272.506A
28Y UniChem 'EPA CompTox Dashboard' DTXSID80212164
28Y UniChem BRENDA 252840
28Y UniChem PubChem 176480
28Y UniChem 'PubChem TPHARMA' 16410800
#
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
28Y C4 0.557 -0.630 -0.064 ETKDGv3 1
28Y C5 1.338 0.421 -0.002 ETKDGv3 2
28Y C6 0.798 1.795 0.120 ETKDGv3 3
28Y C8 2.538 -1.430 -0.179 ETKDGv3 4
28Y N1 -0.636 1.969 0.172 ETKDGv3 5
28Y N2 -2.741 0.760 0.132 ETKDGv3 6
28Y N3 -0.858 -0.487 -0.016 ETKDGv3 7
28Y O6 1.568 2.790 0.178 ETKDGv3 8
28Y N7 2.684 -0.007 -0.071 ETKDGv3 9
28Y N9 1.301 -1.835 -0.179 ETKDGv3 10
28Y CAD -1.952 -1.377 -0.057 ETKDGv3 11
28Y CAB -3.058 -0.640 0.030 ETKDGv3 12
28Y C2 -1.449 0.787 0.100 ETKDGv3 13
28Y H1 3.377 -2.109 -0.255 ETKDGv3 14
28Y H2 -1.066 2.917 0.258 ETKDGv3 15
28Y H3 3.558 0.563 -0.049 ETKDGv3 16
28Y H5 -1.892 -2.454 -0.144 ETKDGv3 17
28Y H6 -4.065 -1.034 0.025 ETKDGv3 18
#