data_K17
#
_chem_comp.id K17
_chem_comp.name 4,5,6,7-TETRABROMO-BENZIMIDAZOLE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H2 Br4 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-03-12
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 433.720
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code K17
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye OEToolkits"
_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
K17 BR3 BR3 BR 0 0 N N N N N N 29.513 22.181 28.875 -1.773 -0.340 2.490 BR3 K17 1
K17 C3 C3 C 0 1 Y N N N N N 29.815 22.904 27.178 0.072 -0.534 2.083 C3 K17 2
K17 C2 C2 C 0 1 Y N N N N N 29.592 22.143 26.026 0.638 -0.311 0.823 C2 K17 3
K17 BR2 BR2 BR 0 0 N N N N N N 28.875 20.420 26.240 -0.519 0.236 -0.614 BR2 K17 4
K17 C7 C7 C 0 1 Y N N N N N 30.304 24.179 27.163 0.940 -0.931 3.100 C7 K17 5
K17 N8 N8 N 0 1 N N N N N N 30.605 25.077 28.168 0.736 -1.230 4.423 N8 K17 6
K17 C9 C9 C 0 1 N N N N N N 31.036 26.163 27.511 1.945 -1.563 4.967 C9 K17 7
K17 N5 N5 N 0 1 N N N N N N 31.028 25.933 26.150 2.915 -1.500 4.084 N5 K17 8
K17 C6 C6 C 0 1 Y N N N N N 30.576 24.695 25.920 2.308 -1.107 2.913 C6 K17 9
K17 C4 C4 C 0 1 Y N N N N N 30.360 23.938 24.762 2.860 -0.878 1.642 C4 K17 10
K17 BR4 BR4 BR 0 0 N N N N N N 30.781 24.710 23.123 4.735 -1.141 1.447 BR4 K17 11
K17 C1 C1 C 0 1 Y N N N N N 29.861 22.649 24.766 2.008 -0.479 0.605 C1 K17 12
K17 BR1 BR1 BR 0 0 N N N N N N 29.571 21.611 23.154 2.763 -0.167 -1.137 BR1 K17 13
K17 HN8 HN8 H 0 1 N N N N N N 30.521 24.947 29.156 -0.151 -1.208 4.909 HN8 K17 14
K17 H9 H9 H 0 1 N N N N N N 31.345 27.086 27.979 2.048 -1.842 6.006 H9 K17 15
#
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
K17 BR3 C3 SING N N 1
K17 C3 C2 DOUB Y N 2
K17 C3 C7 SING Y N 3
K17 C2 C1 SING Y N 4
K17 C2 BR2 SING N N 5
K17 C7 C6 DOUB Y N 6
K17 C7 N8 SING N N 7
K17 N8 C9 SING N N 8
K17 N8 HN8 SING N N 9
K17 C9 N5 DOUB N N 10
K17 C9 H9 SING N N 11
K17 N5 C6 SING N N 12
K17 C6 C4 SING Y N 13
K17 C4 BR4 SING N N 14
K17 C4 C1 DOUB Y N 15
K17 C1 BR1 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
K17 SMILES ACDLabs 10.04 Brc2c1c(ncn1)c(Br)c(Br)c2Br
K17 SMILES_CANONICAL CACTVS 3.341 Brc1c(Br)c(Br)c2nc[nH]c2c1Br
K17 SMILES CACTVS 3.341 Brc1c(Br)c(Br)c2nc[nH]c2c1Br
K17 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1[nH]c2c(n1)c(c(c(c2Br)Br)Br)Br
K17 SMILES "OpenEye OEToolkits" 1.5.0 c1[nH]c2c(n1)c(c(c(c2Br)Br)Br)Br
K17 InChI InChI 1.03 InChI=1S/C7H2Br4N2/c8-2-3(9)5(11)7-6(4(2)10)12-1-13-7/h1H,(H,12,13)
K17 InChIKey InChI 1.03 LOEIRDBRYBHAJB-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
K17 "SYSTEMATIC NAME" ACDLabs 10.04 4,5,6,7-tetrabromo-1H-benzimidazole
K17 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 4,5,6,7-tetrabromo-1H-benzimidazole
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
K17 'Create component' 2007-03-12 RCSB
K17 'Modify descriptor' 2011-06-04 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
K17 BR3 Br 5.598 3.000 1
K17 C3 C 5.598 1.500 2
K17 C2 C 4.299 0.750 3
K17 BR2 Br 3.000 1.500 4
K17 C7 C 6.897 0.750 5
K17 N8 N 8.316 1.207 6
K17 C9 C 9.192 0.000 7
K17 N5 N 8.316 -1.207 8
K17 C6 C 6.897 -0.750 9
K17 C4 C 5.598 -1.500 10
K17 BR4 Br 5.598 -3.000 11
K17 C1 C 4.299 -0.750 12
K17 BR1 Br 3.000 -1.500 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
K17 BR3 C3 SINGLE NONE 1
K17 C3 C2 DOUBLE NONE 2
K17 C3 C7 SINGLE NONE 3
K17 C2 C1 SINGLE NONE 4
K17 C2 BR2 SINGLE NONE 5
K17 C7 C6 DOUBLE NONE 6
K17 C7 N8 SINGLE NONE 7
K17 N8 C9 SINGLE NONE 8
K17 C9 N5 DOUBLE NONE 9
K17 N5 C6 SINGLE NONE 10
K17 C6 C4 SINGLE NONE 11
K17 C4 BR4 SINGLE NONE 12
K17 C4 C1 DOUBLE NONE 13
K17 C1 BR1 SINGLE NONE 14
#
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
K17 MurckoScaffold S1 scaffold 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
K17 benzimidazole F1 fragment 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
K17 imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
K17 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
K17 C3 S1 1
K17 C2 S1 1
K17 C7 S1 1
K17 N8 S1 1
K17 C9 S1 1
K17 N5 S1 1
K17 C6 S1 1
K17 C4 S1 1
K17 C1 S1 1
K17 C7 F1 1
K17 N8 F1 1
K17 C9 F1 1
K17 N5 F1 1
K17 C6 F1 1
K17 C4 F1 1
K17 C1 F1 1
K17 C2 F1 1
K17 C3 F1 1
K17 C7 F2 1
K17 C6 F2 1
K17 N5 F2 1
K17 C9 F2 1
K17 N8 F2 1
K17 C3 F3 1
K17 C2 F3 1
K17 C1 F3 1
K17 C4 F3 1
K17 C6 F3 1
K17 C7 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id K17
_pdbe_chem_comp_rdkit_properties.exactmw 429.695
_pdbe_chem_comp_rdkit_properties.amw 433.723
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 110.880
_pdbe_chem_comp_rdkit_properties.tpsa 28.680
_pdbe_chem_comp_rdkit_properties.CrippenClogP 4.184
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.688
_pdbe_chem_comp_rdkit_properties.chi0v 12.250
_pdbe_chem_comp_rdkit_properties.chi1v 6.322
_pdbe_chem_comp_rdkit_properties.chi2v 6.268
_pdbe_chem_comp_rdkit_properties.chi3v 6.268
_pdbe_chem_comp_rdkit_properties.chi4v 3.191
_pdbe_chem_comp_rdkit_properties.chi0n 7.906
_pdbe_chem_comp_rdkit_properties.chi1n 4.098
_pdbe_chem_comp_rdkit_properties.chi2n 1.542
_pdbe_chem_comp_rdkit_properties.chi3n 1.542
_pdbe_chem_comp_rdkit_properties.chi4n 0.938
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.610
_pdbe_chem_comp_rdkit_properties.kappa1 7.844
_pdbe_chem_comp_rdkit_properties.kappa2 3.640
_pdbe_chem_comp_rdkit_properties.kappa3 1.515
_pdbe_chem_comp_rdkit_properties.Phi 2.196
#
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
K17 UniChem ChEMBL CHEMBL373937
K17 UniChem PDBe K17
K17 UniChem ZINC ZINC000002528524
K17 UniChem eMolecules 8323381
K17 UniChem BindingDb 50156669
K17 UniChem BRENDA 135894
K17 UniChem BRENDA 61952
K17 UniChem 'Probes And Drugs' PD015419
K17 UniChem 'EPA CompTox Dashboard' DTXSID80408803
K17 UniChem SureChEMBL SCHEMBL406945
K17 UniChem 'PubChem TPHARMA' 15330121
K17 UniChem PubChem 5149739
K17 UniChem Nikkaji J1.930.031E
#
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
K17 BR3 -0.056 3.263 -0.356 ETKDGv3 1
K17 C3 0.420 1.417 -0.137 ETKDGv3 2
K17 C2 1.704 0.997 -0.039 ETKDGv3 3
K17 BR2 3.149 2.263 -0.117 ETKDGv3 4
K17 C7 -0.644 0.403 -0.070 ETKDGv3 5
K17 N8 -2.044 0.589 -0.147 ETKDGv3 6
K17 C9 -2.529 -0.750 -0.022 ETKDGv3 7
K17 N5 -1.585 -1.634 0.113 ETKDGv3 8
K17 C6 -0.382 -0.872 0.079 ETKDGv3 9
K17 C4 0.998 -1.370 0.189 ETKDGv3 10
K17 BR4 1.294 -3.252 0.405 ETKDGv3 11
K17 C1 2.008 -0.468 0.133 ETKDGv3 12
K17 BR1 3.836 -1.049 0.270 ETKDGv3 13
K17 HN8 -2.588 1.472 -0.265 ETKDGv3 14
K17 H9 -3.579 -1.009 -0.036 ETKDGv3 15
#