data_JY6
#
_chem_comp.id JY6
_chem_comp.name (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H10 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms indirubin
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-05-16
_chem_comp.pdbx_modified_date 2022-11-18
_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 262.263
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code JY6
_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 7ZUB
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
JY6 N1 N1 N 0 1 N N N N N N 161.711 164.058 163.062 2.878 -1.832 -0.067 N1 JY6 1
JY6 C7 C1 C 0 1 N N N N N N 161.011 164.606 159.534 -0.438 -0.382 -0.004 C7 JY6 2
JY6 C8 C2 C 0 1 N N N N N N 160.175 164.206 158.512 -1.049 0.963 -0.123 C8 JY6 3
JY6 C9 C3 C 0 1 Y N N N N N 160.531 164.895 157.313 -2.504 0.734 -0.055 C9 JY6 4
JY6 O1 O1 O 0 1 N N N N N N 162.760 165.650 161.813 0.965 -3.074 -0.143 O1 JY6 5
JY6 C1 C4 C 0 1 Y N N N N N 159.207 161.323 163.314 4.497 1.542 0.102 C1 JY6 6
JY6 C5 C5 C 0 1 Y N N N N N 159.313 162.289 161.107 2.105 1.673 0.110 C5 JY6 7
JY6 C6 C6 C 0 1 N N N N N N 161.083 164.231 160.902 0.911 -0.672 -0.015 C6 JY6 8
JY6 C4 C7 C 0 1 Y N N N N N 160.302 163.172 161.535 2.036 0.283 0.038 C4 JY6 9
JY6 C3 C8 C 0 1 Y N N N N N 160.728 163.104 162.874 3.211 -0.483 0.001 C3 JY6 10
JY6 C2 C9 C 0 1 Y N N N N N 160.189 162.188 163.768 4.440 0.163 0.034 C2 JY6 11
JY6 N N2 N 0 1 N N N N N N 161.881 165.542 159.008 -1.465 -1.288 0.128 N JY6 12
JY6 C C10 C 0 1 Y N N N N N 158.775 161.373 161.997 3.336 2.296 0.139 C JY6 13
JY6 O O2 O 0 1 N N N N N N 159.233 163.383 158.586 -0.473 2.027 -0.250 O JY6 14
JY6 C10 C11 C 0 1 Y N N N N N 160.085 164.905 155.994 -3.602 1.593 -0.115 C10 JY6 15
JY6 C11 C12 C 0 1 Y N N N N N 160.707 165.721 155.062 -4.878 1.079 -0.028 C11 JY6 16
JY6 C12 C13 C 0 1 Y N N N N N 161.770 166.533 155.427 -5.070 -0.285 0.119 C12 JY6 17
JY6 C13 C14 C 0 1 Y N N N N N 162.233 166.547 156.733 -3.992 -1.145 0.179 C13 JY6 18
JY6 C14 C15 C 0 1 Y N N N N N 161.609 165.727 157.663 -2.696 -0.648 0.094 C14 JY6 19
JY6 C15 C16 C 0 1 N N N N N N 161.919 164.733 161.880 1.545 -2.008 -0.084 C15 JY6 20
JY6 H9 H1 H 0 1 N N N N N N 162.194 164.230 163.920 3.525 -2.554 -0.103 H9 JY6 21
JY6 H1 H2 H 0 1 N N N N N N 158.774 160.603 163.992 5.457 2.036 0.127 H1 JY6 22
JY6 H3 H3 H 0 1 N N N N N N 158.967 162.318 160.084 1.199 2.260 0.138 H3 JY6 23
JY6 H2 H4 H 0 1 N N N N N N 160.527 162.151 164.793 5.353 -0.413 0.006 H2 JY6 24
JY6 H8 H5 H 0 1 N N N N N N 162.598 166.014 159.521 -1.345 -2.246 0.227 H8 JY6 25
JY6 H H6 H 0 1 N N N N N N 158.010 160.689 161.661 3.394 3.373 0.195 H JY6 26
JY6 H4 H7 H 0 1 N N N N N N 159.257 164.279 155.698 -3.453 2.657 -0.229 H4 JY6 27
JY6 H5 H8 H 0 1 N N N N N N 160.360 165.724 154.039 -5.731 1.741 -0.075 H5 JY6 28
JY6 H6 H9 H 0 1 N N N N N N 162.242 167.161 154.686 -6.073 -0.680 0.187 H6 JY6 29
JY6 H7 H10 H 0 1 N N N N N N 163.059 167.180 157.020 -4.156 -2.207 0.294 H7 JY6 30
#
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
JY6 C11 C12 DOUB Y N 1
JY6 C11 C10 SING Y N 2
JY6 C12 C13 SING Y N 3
JY6 C10 C9 DOUB Y N 4
JY6 C13 C14 DOUB Y N 5
JY6 C9 C14 SING Y N 6
JY6 C9 C8 SING N N 7
JY6 C14 N SING N N 8
JY6 C8 O DOUB N N 9
JY6 C8 C7 SING N N 10
JY6 N C7 SING N N 11
JY6 C7 C6 DOUB N Z 12
JY6 C6 C4 SING N N 13
JY6 C6 C15 SING N N 14
JY6 C5 C4 DOUB Y N 15
JY6 C5 C SING Y N 16
JY6 C4 C3 SING Y N 17
JY6 O1 C15 DOUB N N 18
JY6 C15 N1 SING N N 19
JY6 C C1 DOUB Y N 20
JY6 C3 N1 SING N N 21
JY6 C3 C2 DOUB Y N 22
JY6 C1 C2 SING Y N 23
JY6 N1 H9 SING N N 24
JY6 C1 H1 SING N N 25
JY6 C5 H3 SING N N 26
JY6 C2 H2 SING N N 27
JY6 N H8 SING N N 28
JY6 C H SING N N 29
JY6 C10 H4 SING N N 30
JY6 C11 H5 SING N N 31
JY6 C12 H6 SING N N 32
JY6 C13 H7 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
JY6 InChI InChI 1.06 InChI=1S/C16H10N2O2/c19-15-10-6-2-4-8-12(10)17-14(15)13-9-5-1-3-7-11(9)18-16(13)20/h1-8,17H,(H,18,20)/b14-13-
JY6 InChIKey InChI 1.06 CRDNMYFJWFXOCH-YPKPFQOOSA-N
JY6 SMILES_CANONICAL CACTVS 3.385 O=C1Nc2ccccc2\C1=C/3Nc4ccccc4C/3=O
JY6 SMILES CACTVS 3.385 O=C1Nc2ccccc2C1=C3Nc4ccccc4C3=O
JY6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc2c(c1)/C(=C/3\C(=O)c4ccccc4N3)/C(=O)N2
JY6 SMILES "OpenEye OEToolkits" 2.0.7 c1ccc2c(c1)C(=C3C(=O)c4ccccc4N3)C(=O)N2
#
_pdbx_chem_comp_identifier.comp_id JY6
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id JY6
_pdbx_chem_comp_synonyms.name indirubin
_pdbx_chem_comp_synonyms.provenance AUTHOR
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
JY6 'Create component' 2022-05-16 PDBE
JY6 'Modify descriptor' 2022-08-22 RCSB
JY6 'Initial release' 2022-11-23 RCSB
#
_pdbe_chem_comp_synonyms.comp_id JY6
_pdbe_chem_comp_synonyms.name indirubin
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
JY6 N1 N 7.018 -3.920 1
JY6 C7 C 7.483 -0.080 2
JY6 C8 C 6.608 1.127 3
JY6 C9 C 7.483 2.334 4
JY6 O1 O 9.393 -2.713 5
JY6 C1 C 3.000 -3.463 6
JY6 C5 C 4.299 -1.213 7
JY6 C6 C 7.018 -1.506 8
JY6 C4 C 5.598 -1.963 9
JY6 C3 C 5.598 -3.463 10
JY6 C2 C 4.299 -4.213 11
JY6 N N 8.903 0.377 12
JY6 C C 3.000 -1.963 13
JY6 O O 5.108 1.127 14
JY6 C10 C 7.174 3.802 15
JY6 C11 C 8.290 4.804 16
JY6 C12 C 9.716 4.338 17
JY6 C13 C 10.026 2.870 18
JY6 C14 C 8.909 1.868 19
JY6 C15 C 7.893 -2.713 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
JY6 C11 C12 DOUBLE NONE 1
JY6 C11 C10 SINGLE NONE 2
JY6 C12 C13 SINGLE NONE 3
JY6 C10 C9 DOUBLE NONE 4
JY6 C13 C14 DOUBLE NONE 5
JY6 C9 C14 SINGLE NONE 6
JY6 C9 C8 SINGLE NONE 7
JY6 C14 N SINGLE NONE 8
JY6 C8 O DOUBLE NONE 9
JY6 C8 C7 SINGLE ENDUPRIGHT 10
JY6 N C7 SINGLE ENDDOWNRIGHT 11
JY6 C7 C6 DOUBLE NONE 12
JY6 C6 C4 SINGLE ENDDOWNRIGHT 13
JY6 C6 C15 SINGLE ENDUPRIGHT 14
JY6 C5 C4 DOUBLE NONE 15
JY6 C5 C SINGLE NONE 16
JY6 C4 C3 SINGLE NONE 17
JY6 O1 C15 DOUBLE NONE 18
JY6 C15 N1 SINGLE NONE 19
JY6 C C1 DOUBLE NONE 20
JY6 C3 N1 SINGLE NONE 21
JY6 C3 C2 DOUBLE NONE 22
JY6 C1 C2 SINGLE NONE 23
#
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
JY6 MurckoScaffold S1 scaffold O=C1Nc2ccccc2/C1=C1/Nc2ccccc2C1=O InChI=1S/C16H10N2O2/c19-15-10-6-2-4-8-12(10)17-14(15)13-9-5-1-3-7-11(9)18-16(13)20/h1-8,17H,(H,18,20)/b14-13- CRDNMYFJWFXOCH-YPKPFQOOSA-N
JY6 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
JY6 peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
JY6 phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
JY6 N1 S1 1
JY6 C7 S1 1
JY6 C8 S1 1
JY6 C9 S1 1
JY6 O1 S1 1
JY6 C1 S1 1
JY6 C5 S1 1
JY6 C6 S1 1
JY6 C4 S1 1
JY6 C3 S1 1
JY6 C2 S1 1
JY6 N S1 1
JY6 C S1 1
JY6 O S1 1
JY6 C10 S1 1
JY6 C11 S1 1
JY6 C12 S1 1
JY6 C13 S1 1
JY6 C14 S1 1
JY6 C15 S1 1
JY6 N1 F1 1
JY6 C15 F1 1
JY6 O1 F1 1
JY6 C6 F1 1
JY6 O F2 1
JY6 C8 F2 1
JY6 C7 F2 1
JY6 N F2 1
JY6 C9 F3 1
JY6 C10 F3 1
JY6 C11 F3 1
JY6 C12 F3 1
JY6 C13 F3 1
JY6 C14 F3 1
JY6 C1 F3 2
JY6 C F3 2
JY6 C5 F3 2
JY6 C4 F3 2
JY6 C3 F3 2
JY6 C2 F3 2
#
_pdbe_chem_comp_rdkit_properties.comp_id JY6
_pdbe_chem_comp_rdkit_properties.exactmw 262.074
_pdbe_chem_comp_rdkit_properties.amw 262.268
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 128.836
_pdbe_chem_comp_rdkit_properties.tpsa 58.200
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.788
_pdbe_chem_comp_rdkit_properties.CrippenMR 74.207
_pdbe_chem_comp_rdkit_properties.chi0v 9.711
_pdbe_chem_comp_rdkit_properties.chi1v 5.553
_pdbe_chem_comp_rdkit_properties.chi2v 2.915
_pdbe_chem_comp_rdkit_properties.chi3v 2.915
_pdbe_chem_comp_rdkit_properties.chi4v 2.059
_pdbe_chem_comp_rdkit_properties.chi0n 19.711
_pdbe_chem_comp_rdkit_properties.chi1n 10.447
_pdbe_chem_comp_rdkit_properties.chi2n 2.915
_pdbe_chem_comp_rdkit_properties.chi3n 2.915
_pdbe_chem_comp_rdkit_properties.chi4n 2.059
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.880
_pdbe_chem_comp_rdkit_properties.kappa1 4.904
_pdbe_chem_comp_rdkit_properties.kappa2 3.805
_pdbe_chem_comp_rdkit_properties.kappa3 1.358
_pdbe_chem_comp_rdkit_properties.Phi 0.933
#
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
JY6 UniChem ChEMBL CHEMBL1276127
JY6 UniChem PDBe JY6
JY6 UniChem ZINC ZINC000018825333
JY6 UniChem fdasrs V86L8P74GI
JY6 UniChem 'PubChem TPHARMA' 15189132
JY6 UniChem NMRShiftDB 60072478
JY6 UniChem LINCS LSM-42899
JY6 UniChem ACTor 479-41-4
JY6 UniChem BindingDb 7392
JY6 UniChem BRENDA 192444
JY6 UniChem BRENDA 39848
JY6 UniChem ClinicalTrials INDIRUBIN
JY6 UniChem 'Probes And Drugs' PD010731
JY6 UniChem eMolecules 1934365
JY6 UniChem SureChEMBL SCHEMBL9899338
#
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
JY6 N1 2.753 -0.759 2.164 ETKDGv3 1
JY6 C7 -0.434 -0.169 0.382 ETKDGv3 2
JY6 C8 -0.958 0.714 -0.683 ETKDGv3 3
JY6 C9 -2.400 0.551 -0.695 ETKDGv3 4
JY6 O1 0.613 -1.345 2.949 ETKDGv3 5
JY6 C1 4.740 0.374 -0.834 ETKDGv3 6
JY6 C5 2.319 0.302 -1.268 ETKDGv3 7
JY6 C6 0.855 -0.354 0.737 ETKDGv3 8
JY6 C4 2.088 0.041 0.028 ETKDGv3 9
JY6 C3 3.200 -0.197 0.941 ETKDGv3 10
JY6 C2 4.472 -0.047 0.563 ETKDGv3 11
JY6 N -1.541 -0.800 1.051 ETKDGv3 12
JY6 C 3.722 0.526 -1.704 ETKDGv3 13
JY6 O -0.327 1.600 -1.316 ETKDGv3 14
JY6 C10 -3.344 1.109 -1.456 ETKDGv3 15
JY6 C11 -4.757 0.731 -1.187 ETKDGv3 16
JY6 C12 -5.056 -0.140 -0.198 ETKDGv3 17
JY6 C13 -3.975 -0.729 0.638 ETKDGv3 18
JY6 C14 -2.717 -0.371 0.373 ETKDGv3 19
JY6 C15 1.340 -0.884 2.030 ETKDGv3 20
JY6 H9 3.341 -1.079 2.966 ETKDGv3 21
JY6 H1 5.760 0.524 -1.162 ETKDGv3 22
JY6 H3 1.533 0.288 -2.006 ETKDGv3 23
JY6 H2 5.286 -0.272 1.241 ETKDGv3 24
JY6 H8 -1.508 -1.547 1.778 ETKDGv3 25
JY6 H 3.926 0.796 -2.732 ETKDGv3 26
JY6 H4 -3.092 1.809 -2.242 ETKDGv3 27
JY6 H5 -5.549 1.158 -1.789 ETKDGv3 28
JY6 H6 -6.086 -0.410 -0.008 ETKDGv3 29
JY6 H7 -4.204 -1.421 1.439 ETKDGv3 30
#