data_DUI
#
_chem_comp.id DUI
_chem_comp.name 4-amino-2-[(3R)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H11 N3 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-11-30
_chem_comp.pdbx_modified_date 2023-01-20
_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 273.244
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DUI
_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 7SZA
_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
DUI C1 C1 C 0 1 Y N N N N N -55.458 -11.474 26.945 4.571 0.373 -0.020 C1 DUI 1
DUI C2 C2 C 0 1 Y N N N N N -55.576 -10.885 25.684 4.172 1.688 -0.114 C2 DUI 2
DUI C3 C3 C 0 1 Y N N N N N -55.884 -11.667 24.550 2.824 2.016 -0.177 C3 DUI 3
DUI C4 C4 C 0 1 Y N N N N N -56.063 -13.029 24.748 1.868 1.016 -0.145 C4 DUI 4
DUI C5 C5 C 0 1 N N N N N N -56.378 -14.081 23.894 0.391 0.998 -0.190 C5 DUI 5
DUI C6 C6 C 0 1 N N R N N N -56.777 -16.588 23.951 -1.426 -0.700 -0.141 C6 DUI 6
DUI O1 O1 O 0 1 N N N N N N -57.320 -18.489 20.402 -5.353 0.340 -0.158 O1 DUI 7
DUI O2 O2 O 0 1 N N N N N N -58.964 -15.785 23.525 -1.543 0.127 2.057 O2 DUI 8
DUI N1 N1 N 0 1 N N N N N N -56.462 -15.258 24.501 -0.022 -0.281 -0.123 N1 DUI 9
DUI C7 C7 C 0 1 N N N N N N -55.596 -17.072 23.131 -2.084 -0.231 -1.443 C7 DUI 10
DUI C8 C8 C 0 1 N N N N N N -56.043 -18.330 22.406 -3.575 -0.581 -1.390 C8 DUI 11
DUI N2 N2 N 0 1 N N N N N N -58.075 -17.047 21.925 -3.452 0.226 0.956 N2 DUI 12
DUI N N3 N 0 1 N N N N N N -55.555 -13.446 28.350 4.026 -1.976 0.104 N DUI 13
DUI C C9 C 0 1 Y N N N N N -55.640 -12.846 27.115 3.622 -0.652 0.014 C DUI 14
DUI O O3 O 0 1 N N N N N N -56.557 -13.937 22.630 -0.329 1.973 -0.272 O DUI 15
DUI C10 C10 C 0 1 N N N N N N -58.020 -16.450 23.114 -2.149 -0.087 1.029 C10 DUI 16
DUI C11 C11 C 0 1 N N N N N N -56.219 -14.952 25.776 1.023 -1.123 -0.038 C11 DUI 17
DUI C12 C12 C 0 1 Y N N N N N -55.952 -13.608 26.009 2.266 -0.335 -0.048 C12 DUI 18
DUI C9 C13 C 0 1 N N N N N N -57.200 -17.962 21.500 -4.182 0.026 -0.153 C9 DUI 19
DUI O3 O4 O 0 1 N N N N N N -56.240 -15.844 26.682 0.952 -2.334 0.036 O3 DUI 20
DUI H1 H1 H 0 1 N N N N N N -55.222 -10.858 27.800 5.622 0.132 0.024 H1 DUI 21
DUI H2 H2 H 0 1 N N N N N N -55.430 -9.820 25.576 4.915 2.471 -0.139 H2 DUI 22
DUI H3 H3 H 0 1 N N N N N N -55.976 -11.224 23.569 2.522 3.050 -0.251 H3 DUI 23
DUI H4 H4 H 0 1 N N N N N N -56.965 -17.297 24.771 -1.482 -1.787 -0.075 H4 DUI 24
DUI H5 H5 H 0 1 N N N N N N -54.746 -17.299 23.791 -1.965 0.848 -1.545 H5 DUI 25
DUI H6 H6 H 0 1 N N N N N N -55.300 -16.302 22.403 -1.617 -0.733 -2.290 H6 DUI 26
DUI H7 H7 H 0 1 N N N N N N -56.367 -19.087 23.136 -4.074 -0.184 -2.273 H7 DUI 27
DUI H8 H8 H 0 1 N N N N N N -55.212 -18.731 21.807 -3.694 -1.664 -1.360 H8 DUI 28
DUI H9 H9 H 0 1 N N N N N N -58.821 -16.793 21.309 -3.883 0.611 1.736 H9 DUI 29
DUI H10 H10 H 0 1 N N N N N N -55.322 -12.760 29.039 4.970 -2.193 0.143 H10 DUI 30
DUI H11 H11 H 0 1 N N N N N N -56.434 -13.863 28.579 3.364 -2.685 0.127 H11 DUI 31
#
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
DUI O1 C9 DOUB N N 1
DUI C9 N2 SING N N 2
DUI C9 C8 SING N N 3
DUI N2 C10 SING N N 4
DUI C8 C7 SING N N 5
DUI O C5 DOUB N N 6
DUI C10 O2 DOUB N N 7
DUI C10 C6 SING N N 8
DUI C7 C6 SING N N 9
DUI C5 N1 SING N N 10
DUI C5 C4 SING N N 11
DUI C6 N1 SING N N 12
DUI N1 C11 SING N N 13
DUI C3 C4 DOUB Y N 14
DUI C3 C2 SING Y N 15
DUI C4 C12 SING Y N 16
DUI C2 C1 DOUB Y N 17
DUI C11 C12 SING N N 18
DUI C11 O3 DOUB N N 19
DUI C12 C DOUB Y N 20
DUI C1 C SING Y N 21
DUI C N SING N N 22
DUI C1 H1 SING N N 23
DUI C2 H2 SING N N 24
DUI C3 H3 SING N N 25
DUI C6 H4 SING N N 26
DUI C7 H5 SING N N 27
DUI C7 H6 SING N N 28
DUI C8 H7 SING N N 29
DUI C8 H8 SING N N 30
DUI N2 H9 SING N N 31
DUI N H10 SING N N 32
DUI N H11 SING N N 33
#
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
DUI SMILES ACDLabs 12.01 O=C1NC(=O)CCC1N1C(=O)c2cccc(N)c2C1=O
DUI InChI InChI 1.03 InChI=1S/C13H11N3O4/c14-7-3-1-2-6-10(7)13(20)16(12(6)19)8-4-5-9(17)15-11(8)18/h1-3,8H,4-5,14H2,(H,15,17,18)/t8-/m1/s1
DUI InChIKey InChI 1.03 UVSMNLNDYGZFPF-MRVPVSSYSA-N
DUI SMILES_CANONICAL CACTVS 3.385 Nc1cccc2C(=O)N([C@@H]3CCC(=O)NC3=O)C(=O)c12
DUI SMILES CACTVS 3.385 Nc1cccc2C(=O)N([CH]3CCC(=O)NC3=O)C(=O)c12
DUI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc2c(c(c1)N)C(=O)N(C2=O)[C@@H]3CCC(=O)NC3=O
DUI SMILES "OpenEye OEToolkits" 2.0.7 c1cc2c(c(c1)N)C(=O)N(C2=O)C3CCC(=O)NC3=O
#
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
DUI "SYSTEMATIC NAME" ACDLabs 12.01 4-amino-2-[(3R)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione
DUI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 4-azanyl-2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]isoindole-1,3-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
DUI 'Create component' 2021-11-30 RCSB
DUI 'Initial release' 2023-01-25 RCSB
#
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
DUI C1 C 3.000 0.334 1
DUI C2 C 3.000 -1.166 2
DUI C3 C 4.299 -1.916 3
DUI C4 C 5.598 -1.166 4
DUI C5 C 7.018 -1.623 5
DUI C6 C 9.393 -0.416 6
DUI O1 O 13.893 -0.416 7
DUI O2 O 9.393 -3.014 8
DUI N1 N 7.893 -0.416 9
DUI C7 C 10.143 0.883 10
DUI C8 C 11.643 0.883 11
DUI N2 N 11.643 -1.715 12
DUI N N 4.299 2.584 13
DUI C C 4.299 1.084 14
DUI O O 7.483 -3.049 15
DUI C10 C 10.143 -1.715 16
DUI C11 C 7.018 0.791 17
DUI C12 C 5.598 0.334 18
DUI C9 C 12.393 -0.416 19
DUI O3 O 7.483 2.217 20
#
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
DUI O1 C9 DOUBLE NONE 1
DUI C9 N2 SINGLE NONE 2
DUI C9 C8 SINGLE NONE 3
DUI N2 C10 SINGLE NONE 4
DUI C8 C7 SINGLE NONE 5
DUI O C5 DOUBLE NONE 6
DUI C10 O2 DOUBLE NONE 7
DUI C10 C6 SINGLE NONE 8
DUI C7 C6 SINGLE NONE 9
DUI C5 N1 SINGLE NONE 10
DUI C5 C4 SINGLE NONE 11
DUI C6 N1 SINGLE BEGINDASH 12
DUI N1 C11 SINGLE NONE 13
DUI C3 C4 DOUBLE NONE 14
DUI C3 C2 SINGLE NONE 15
DUI C4 C12 SINGLE NONE 16
DUI C2 C1 DOUBLE NONE 17
DUI C11 C12 SINGLE NONE 18
DUI C11 O3 DOUBLE NONE 19
DUI C12 C DOUBLE NONE 20
DUI C1 C SINGLE NONE 21
DUI C N SINGLE NONE 22
#
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
DUI MurckoScaffold S1 scaffold 'O=C1CC[C@@H](N2C(=O)c3ccccc3C2=O)C(=O)N1' InChI=1S/C13H10N2O4/c16-10-6-5-9(11(17)14-10)15-12(18)7-3-1-2-4-8(7)13(15)19/h1-4,9H,5-6H2,(H,14,16,17)/t9-/m1/s1 UEJJHQNACJXSKW-SECBINFHSA-N
DUI amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
DUI peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
DUI phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
DUI Z2092370954 F4 fragment CCN(C)C(=O)c1cccc(N)c1 InChI=1S/C10H14N2O/c1-3-12(2)10(13)8-5-4-6-9(11)7-8/h4-7H,3,11H2,1-2H3 URNKFNQWYLXELN-UHFFFAOYSA-N
DUI Z56040660 F5 fragment CCC(C)NC(=O)c1ccccc1N InChI=1S/C11H16N2O/c1-3-8(2)13-11(14)9-6-4-5-7-10(9)12/h4-8H,3,12H2,1-2H3,(H,13,14) UOKULICTTSTSHO-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
DUI C1 S1 1
DUI C2 S1 1
DUI C3 S1 1
DUI C4 S1 1
DUI C5 S1 1
DUI C6 S1 1
DUI O1 S1 1
DUI O2 S1 1
DUI N1 S1 1
DUI C7 S1 1
DUI C8 S1 1
DUI N2 S1 1
DUI C S1 1
DUI O S1 1
DUI C10 S1 1
DUI C11 S1 1
DUI C12 S1 1
DUI C9 S1 1
DUI O3 S1 1
DUI N1 F1 1
DUI C5 F1 1
DUI O F1 1
DUI C4 F1 1
DUI N1 F1 2
DUI C11 F1 2
DUI O3 F1 2
DUI C12 F1 2
DUI N2 F1 3
DUI C9 F1 3
DUI O1 F1 3
DUI C8 F1 3
DUI N2 F1 4
DUI C10 F1 4
DUI O2 F1 4
DUI C6 F1 4
DUI O2 F2 1
DUI C10 F2 1
DUI C6 F2 1
DUI N1 F2 1
DUI C1 F3 1
DUI C2 F3 1
DUI C3 F3 1
DUI C4 F3 1
DUI C12 F3 1
DUI C F3 1
DUI C7 F4 1
DUI C6 F4 1
DUI N1 F4 1
DUI C11 F4 1
DUI C5 F4 1
DUI O F4 1
DUI C4 F4 1
DUI C3 F4 1
DUI C2 F4 1
DUI C1 F4 1
DUI C F4 1
DUI N F4 1
DUI C12 F4 1
DUI C10 F4 2
DUI C6 F4 2
DUI N1 F4 2
DUI C11 F4 2
DUI C5 F4 2
DUI O F4 2
DUI C4 F4 2
DUI C3 F4 2
DUI C2 F4 2
DUI C1 F4 2
DUI C F4 2
DUI N F4 2
DUI C12 F4 2
DUI C8 F5 1
DUI C7 F5 1
DUI C6 F5 1
DUI C10 F5 1
DUI N1 F5 1
DUI C11 F5 1
DUI O3 F5 1
DUI C12 F5 1
DUI C4 F5 1
DUI C3 F5 1
DUI C2 F5 1
DUI C1 F5 1
DUI C F5 1
DUI N F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DUI
_pdbe_chem_comp_rdkit_properties.exactmw 273.075
_pdbe_chem_comp_rdkit_properties.amw 273.248
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 4
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.231
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 128.899
_pdbe_chem_comp_rdkit_properties.tpsa 109.570
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.820
_pdbe_chem_comp_rdkit_properties.CrippenMR 66.170
_pdbe_chem_comp_rdkit_properties.chi0v 9.475
_pdbe_chem_comp_rdkit_properties.chi1v 5.158
_pdbe_chem_comp_rdkit_properties.chi2v 2.606
_pdbe_chem_comp_rdkit_properties.chi3v 2.606
_pdbe_chem_comp_rdkit_properties.chi4v 1.775
_pdbe_chem_comp_rdkit_properties.chi0n 20.475
_pdbe_chem_comp_rdkit_properties.chi1n 10.500
_pdbe_chem_comp_rdkit_properties.chi2n 2.606
_pdbe_chem_comp_rdkit_properties.chi3n 2.606
_pdbe_chem_comp_rdkit_properties.chi4n 1.775
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.700
_pdbe_chem_comp_rdkit_properties.kappa1 5.007
_pdbe_chem_comp_rdkit_properties.kappa2 4.156
_pdbe_chem_comp_rdkit_properties.kappa3 1.594
_pdbe_chem_comp_rdkit_properties.Phi 1.040
#
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
DUI UniChem ChEMBL CHEMBL1788309
DUI UniChem PDBe DUI
DUI UniChem ZINC ZINC000001997125
DUI UniChem fdasrs X9549G9WCL
DUI UniChem SureChEMBL SCHEMBL931134
DUI UniChem Nikkaji J1.121.695A
DUI UniChem PubChem 15479857
#
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
DUI C1 -4.364 0.045 0.218 ETKDGv3 1
DUI C2 -4.378 -0.359 -1.069 ETKDGv3 2
DUI C3 -3.113 -0.468 -1.839 ETKDGv3 3
DUI C4 -1.978 -0.150 -1.215 ETKDGv3 4
DUI C5 -0.601 -0.164 -1.689 ETKDGv3 5
DUI C6 1.750 0.134 -0.679 ETKDGv3 6
DUI O1 5.375 -0.168 1.407 ETKDGv3 7
DUI O2 1.922 2.489 -0.237 ETKDGv3 8
DUI N1 0.289 0.271 -0.657 ETKDGv3 9
DUI C7 2.167 -1.158 0.048 ETKDGv3 10
DUI C8 3.691 -1.287 0.130 ETKDGv3 11
DUI N2 3.655 1.204 0.640 ETKDGv3 12
DUI N -3.084 0.815 2.262 ETKDGv3 13
DUI C -3.080 0.390 0.895 ETKDGv3 14
DUI O -0.230 -0.526 -2.837 ETKDGv3 15
DUI C10 2.417 1.342 -0.067 ETKDGv3 16
DUI C11 -0.537 0.518 0.491 ETKDGv3 17
DUI C12 -1.950 0.285 0.173 ETKDGv3 18
DUI C9 4.288 -0.072 0.779 ETKDGv3 19
DUI O3 -0.083 0.860 1.615 ETKDGv3 20
DUI H1 -5.296 0.118 0.765 ETKDGv3 21
DUI H2 -5.317 -0.608 -1.548 ETKDGv3 22
DUI H3 -3.114 -0.795 -2.870 ETKDGv3 23
DUI H4 2.095 0.070 -1.735 ETKDGv3 24
DUI H5 1.757 -2.036 -0.496 ETKDGv3 25
DUI H6 1.747 -1.168 1.078 ETKDGv3 26
DUI H7 3.950 -2.194 0.717 ETKDGv3 27
DUI H8 4.115 -1.396 -0.892 ETKDGv3 28
DUI H9 4.104 2.049 1.060 ETKDGv3 29
DUI H10 -2.213 1.082 2.766 ETKDGv3 30
DUI H11 -3.985 0.875 2.786 ETKDGv3 31
#