data_K66
#
_chem_comp.id K66
_chem_comp.name "[4,5,6,7-tetrabromo-2-(dimethylamino)-1H-benzimidazol-1-yl]acetic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H9 Br4 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-12-04
_chem_comp.pdbx_modified_date 2011-06-04
_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 534.824
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code K66
_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 3KXH
_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
K66 C1 C1 C 0 1 Y N N N N N 22.084 7.223 20.795 -0.942 -1.409 -0.012 C1 K66 1
K66 C2 C2 C 0 1 Y N N N N N 23.039 6.562 20.085 0.450 -1.408 -0.141 C2 K66 2
K66 C3 C3 C 0 1 Y N N N N N 23.318 7.098 18.813 1.133 -0.186 -0.248 C3 K66 3
K66 C4 C4 C 0 1 Y N N N N N 22.588 8.288 18.409 0.428 1.008 -0.225 C4 K66 4
K66 C5 C5 C 0 1 Y N N N N N 21.624 8.839 19.126 -0.948 0.991 -0.097 C5 K66 5
K66 C6 C6 C 0 1 Y N N N N N 21.340 8.320 20.361 -1.629 -0.214 0.003 C6 K66 6
K66 BR13 BR13 BR 0 0 N N N N N N 22.995 9.021 16.660 1.346 2.655 -0.369 BR13 K66 7
K66 BR15 BR15 BR 0 0 N N N N N N 20.639 10.232 18.445 -1.909 2.619 -0.066 BR15 K66 8
K66 BR17 BR17 BR 0 0 N N N N N N 19.980 9.123 21.486 -3.512 -0.216 0.178 BR17 K66 9
K66 BR19 BR19 BR 0 0 N N N N N N 21.957 6.453 22.561 -1.880 -3.045 0.134 BR19 K66 10
K66 N21 N21 N 0 1 Y N N N N N 23.792 5.514 20.364 1.383 -2.395 -0.191 N21 K66 11
K66 N23 N23 N 0 1 Y N N N N N 24.296 6.309 18.284 2.477 -0.505 -0.361 N23 K66 12
K66 C25 C25 C 0 1 Y N N N N N 24.582 5.425 19.266 2.575 -1.867 -0.321 C25 K66 13
K66 N28 N28 N 0 1 N N N N N N 25.471 4.369 19.159 3.753 -2.580 -0.403 N28 K66 14
K66 C30 C30 C 0 1 N N N N N N 25.894 3.562 20.306 3.904 -3.482 0.746 C30 K66 15
K66 C32 C32 C 0 1 N N N N N N 25.871 3.810 17.858 3.831 -3.322 -1.669 C32 K66 16
K66 C34 C34 C 0 1 N N N N N N 25.121 6.440 17.094 3.587 0.441 -0.498 C34 K66 17
K66 C36 C36 C 0 1 N N N N N N 24.621 6.255 15.728 4.013 0.917 0.867 C36 K66 18
K66 O38 O38 O 0 1 N N N N N N 23.541 5.698 15.650 5.020 1.796 0.988 O38 K66 19
K66 O40 O40 O 0 1 N N N N N N 25.347 6.630 14.768 3.447 0.507 1.853 O40 K66 20
K66 H30 H30 H 0 1 N N N N N N 26.600 2.788 19.970 3.071 -4.185 0.768 H30 K66 21
K66 H30A H30A H 0 0 N N N N N N 26.385 4.209 21.048 4.841 -4.032 0.655 H30A K66 22
K66 H30B H30B H 0 0 N N N N N N 25.015 3.084 20.762 3.912 -2.899 1.667 H30B K66 23
K66 H32 H32 H 0 1 N N N N N N 26.580 2.984 18.016 3.874 -2.618 -2.500 H32 K66 24
K66 H32A H32A H 0 0 N N N N N N 24.981 3.434 17.332 4.727 -3.942 -1.671 H32A K66 25
K66 H32B H32B H 0 0 N N N N N N 26.350 4.594 17.254 2.950 -3.955 -1.774 H32B K66 26
K66 H34 H34 H 0 1 N N N N N N 25.495 7.474 17.121 4.426 -0.051 -0.989 H34 K66 27
K66 H34A H34A H 0 0 N N N N N N 25.910 5.683 17.212 3.265 1.294 -1.096 H34A K66 28
K66 HO38 HO38 H 0 0 N N N N N N 23.311 5.580 14.736 5.257 2.072 1.884 HO38 K66 29
#
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
K66 C2 C1 DOUB Y N 1
K66 C6 C1 SING Y N 2
K66 C1 BR19 SING N N 3
K66 C3 C2 SING Y N 4
K66 C2 N21 SING Y N 5
K66 N23 C3 SING Y N 6
K66 C4 C3 DOUB Y N 7
K66 BR13 C4 SING N N 8
K66 C4 C5 SING Y N 9
K66 BR15 C5 SING N N 10
K66 C5 C6 DOUB Y N 11
K66 C6 BR17 SING N N 12
K66 C25 N21 DOUB Y N 13
K66 C34 N23 SING N N 14
K66 N23 C25 SING Y N 15
K66 N28 C25 SING N N 16
K66 C32 N28 SING N N 17
K66 N28 C30 SING N N 18
K66 C30 H30 SING N N 19
K66 C30 H30A SING N N 20
K66 C30 H30B SING N N 21
K66 C32 H32 SING N N 22
K66 C32 H32A SING N N 23
K66 C32 H32B SING N N 24
K66 C36 C34 SING N N 25
K66 C34 H34 SING N N 26
K66 C34 H34A SING N N 27
K66 O40 C36 DOUB N N 28
K66 O38 C36 SING N N 29
K66 O38 HO38 SING N N 30
#
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
K66 SMILES_CANONICAL CACTVS 3.352 CN(C)c1nc2c(Br)c(Br)c(Br)c(Br)c2n1CC(O)=O
K66 SMILES CACTVS 3.352 CN(C)c1nc2c(Br)c(Br)c(Br)c(Br)c2n1CC(O)=O
K66 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 CN(C)c1nc2c(n1CC(=O)O)c(c(c(c2Br)Br)Br)Br
K66 SMILES "OpenEye OEToolkits" 1.7.0 CN(C)c1nc2c(n1CC(=O)O)c(c(c(c2Br)Br)Br)Br
K66 InChI InChI 1.03 InChI=1S/C11H9Br4N3O2/c1-17(2)11-16-9-7(14)5(12)6(13)8(15)10(9)18(11)3-4(19)20/h3H2,1-2H3,(H,19,20)
K66 InChIKey InChI 1.03 PHAOTASRLQMKBE-UHFFFAOYSA-N
#
_pdbx_chem_comp_identifier.comp_id K66
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.6.1
_pdbx_chem_comp_identifier.identifier "2-[4,5,6,7-tetrabromo-2-(dimethylamino)benzimidazol-1-yl]ethanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
K66 'Create component' 2009-12-04 RCSB
K66 'Modify aromatic_flag' 2011-06-04 RCSB
K66 'Modify descriptor' 2011-06-04 RCSB
#
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
K66 C1 C 5.598 -3.006 1
K66 C2 C 6.897 -2.256 2
K66 C3 C 6.897 -0.756 3
K66 C4 C 5.598 -0.006 4
K66 C5 C 4.299 -0.756 5
K66 C6 C 4.299 -2.256 6
K66 BR13 Br 4.848 1.293 7
K66 BR15 Br 3.000 -0.006 8
K66 BR17 Br 3.000 -3.006 9
K66 BR19 Br 5.598 -4.506 10
K66 N21 N 8.316 -2.713 11
K66 N23 N 8.316 -0.299 12
K66 C25 C 9.192 -1.506 13
K66 N28 N 10.692 -1.506 14
K66 C30 C 11.442 -0.207 15
K66 C32 C 11.442 -2.805 16
K66 C34 C 8.783 1.127 17
K66 C36 C 8.473 2.594 18
K66 O38 O 7.047 3.060 19
K66 O40 O 9.589 3.596 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
K66 C2 C1 DOUBLE NONE 1
K66 C6 C1 SINGLE NONE 2
K66 C1 BR19 SINGLE NONE 3
K66 C3 C2 SINGLE NONE 4
K66 C2 N21 SINGLE NONE 5
K66 N23 C3 SINGLE NONE 6
K66 C4 C3 DOUBLE NONE 7
K66 BR13 C4 SINGLE NONE 8
K66 C4 C5 SINGLE NONE 9
K66 BR15 C5 SINGLE NONE 10
K66 C5 C6 DOUBLE NONE 11
K66 C6 BR17 SINGLE NONE 12
K66 C25 N21 DOUBLE NONE 13
K66 C34 N23 SINGLE NONE 14
K66 N23 C25 SINGLE NONE 15
K66 N28 C25 SINGLE NONE 16
K66 C32 N28 SINGLE NONE 17
K66 N28 C30 SINGLE NONE 18
K66 C36 C34 SINGLE NONE 19
K66 O40 C36 DOUBLE NONE 20
K66 O38 C36 SINGLE NONE 21
#
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
K66 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
K66 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
K66 imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
K66 peptide F3 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
K66 phenyl F4 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
K66 C1 S1 1
K66 C2 S1 1
K66 C3 S1 1
K66 C4 S1 1
K66 C5 S1 1
K66 C6 S1 1
K66 N21 S1 1
K66 N23 S1 1
K66 C25 S1 1
K66 C2 F1 1
K66 N21 F1 1
K66 C25 F1 1
K66 N23 F1 1
K66 C3 F1 1
K66 C4 F1 1
K66 C5 F1 1
K66 C6 F1 1
K66 C1 F1 1
K66 C2 F2 1
K66 C3 F2 1
K66 N23 F2 1
K66 C25 F2 1
K66 N21 F2 1
K66 O40 F3 1
K66 C36 F3 1
K66 C34 F3 1
K66 N23 F3 1
K66 C1 F4 1
K66 C2 F4 1
K66 C3 F4 1
K66 C4 F4 1
K66 C5 F4 1
K66 C6 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id K66
_pdbe_chem_comp_rdkit_properties.exactmw 530.743
_pdbe_chem_comp_rdkit_properties.amw 534.828
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.273
_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 161.129
_pdbe_chem_comp_rdkit_properties.tpsa 58.360
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.428
_pdbe_chem_comp_rdkit_properties.CrippenMR 89.466
_pdbe_chem_comp_rdkit_properties.chi0v 15.514
_pdbe_chem_comp_rdkit_properties.chi1v 7.875
_pdbe_chem_comp_rdkit_properties.chi2v 6.983
_pdbe_chem_comp_rdkit_properties.chi3v 6.983
_pdbe_chem_comp_rdkit_properties.chi4v 3.854
_pdbe_chem_comp_rdkit_properties.chi0n 18.170
_pdbe_chem_comp_rdkit_properties.chi1n 9.111
_pdbe_chem_comp_rdkit_properties.chi2n 2.257
_pdbe_chem_comp_rdkit_properties.chi3n 2.257
_pdbe_chem_comp_rdkit_properties.chi4n 1.512
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.120
_pdbe_chem_comp_rdkit_properties.kappa1 7.937
_pdbe_chem_comp_rdkit_properties.kappa2 5.939
_pdbe_chem_comp_rdkit_properties.kappa3 2.646
_pdbe_chem_comp_rdkit_properties.Phi 2.357
#
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
K66 UniChem 'Guide to Pharmacology' 8140
K66 UniChem ZINC ZINC000058638742
K66 UniChem eMolecules 29806684
K66 UniChem BindingDb 50359846
K66 UniChem 'EPA CompTox Dashboard' DTXSID50677589
K66 UniChem MedChemExpress HY-135906
K66 UniChem 'Probes And Drugs' PD050716
K66 UniChem SureChEMBL SCHEMBL1759230
K66 UniChem 'PubChem TPHARMA' 136367060
K66 UniChem PubChem 46943415
#
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
K66 C1 3.017 -0.670 0.097 ETKDGv3 1
K66 C2 1.693 -0.546 0.169 ETKDGv3 2
K66 C3 1.041 0.687 0.492 ETKDGv3 3
K66 C4 1.739 1.797 0.792 ETKDGv3 4
K66 C5 3.234 1.719 0.696 ETKDGv3 5
K66 C6 3.840 0.547 0.361 ETKDGv3 6
K66 BR13 0.905 3.404 1.429 ETKDGv3 7
K66 BR15 4.279 3.297 1.047 ETKDGv3 8
K66 BR17 5.755 0.421 0.229 ETKDGv3 9
K66 BR19 3.807 -2.367 -0.313 ETKDGv3 10
K66 N21 0.720 -1.563 0.015 ETKDGv3 11
K66 N23 -0.370 0.439 0.497 ETKDGv3 12
K66 C25 -0.429 -0.982 0.219 ETKDGv3 13
K66 N28 -1.659 -1.725 0.181 ETKDGv3 14
K66 C30 -2.701 -1.501 1.184 ETKDGv3 15
K66 C32 -1.824 -2.795 -0.801 ETKDGv3 16
K66 C34 -1.388 1.374 0.005 ETKDGv3 17
K66 C36 -1.120 1.744 -1.421 ETKDGv3 18
K66 O38 -0.473 2.938 -1.720 ETKDGv3 19
K66 O40 -1.447 0.955 -2.348 ETKDGv3 20
K66 H30 -2.399 -0.719 1.913 ETKDGv3 21
K66 H30A -3.641 -1.187 0.684 ETKDGv3 22
K66 H30B -2.885 -2.440 1.746 ETKDGv3 23
K66 H32 -1.721 -2.379 -1.826 ETKDGv3 24
K66 H32A -2.827 -3.266 -0.712 ETKDGv3 25
K66 H32B -1.052 -3.577 -0.643 ETKDGv3 26
K66 H34 -2.397 0.920 0.069 ETKDGv3 27
K66 H34A -1.426 2.280 0.637 ETKDGv3 28
K66 HO38 -0.268 3.192 -2.679 ETKDGv3 29
#