data_R2D # _chem_comp.id R2D _chem_comp.name "[3-(4-chlorophenyl)[1,3]thiazolo[3,2-a]benzimidazol-2-yl]acetic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H11 Cl N2 O2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-01-27 _chem_comp.pdbx_modified_date 2020-05-08 _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 342.799 _chem_comp.one_letter_code ? _chem_comp.three_letter_code R2D _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 6VLM _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 R2D C1 C1 C 0 1 Y N N N N N -2.940 -20.169 -36.320 2.635 0.999 -0.288 C1 R2D 1 R2D C2 C2 C 0 1 Y N N N N N -5.087 -20.287 -36.752 2.154 -1.130 0.024 C2 R2D 2 R2D C3 C3 C 0 1 Y N N N N N -2.689 -20.945 -34.079 0.250 2.011 -0.547 C3 R2D 3 R2D C4 C4 C 0 1 Y N N N N N -5.137 -21.279 -33.670 -0.887 -0.138 -0.260 C4 R2D 4 R2D C6 C5 C 0 1 Y N N N N N -4.407 -19.804 -37.863 3.544 -0.949 0.063 C6 R2D 5 R2D C7 C6 C 0 1 Y N N N N N -6.450 -20.490 -36.729 1.612 -2.394 0.200 C7 R2D 6 R2D C8 C7 C 0 1 N N N N N N -2.128 -21.355 -32.770 -1.003 2.828 -0.728 C8 R2D 7 R2D C9 C8 C 0 1 Y N N N N N -5.948 -20.232 -33.291 -1.707 -0.287 -1.380 C9 R2D 8 R2D C10 C9 C 0 1 Y N N N N N -5.396 -22.561 -33.222 -1.220 -0.783 0.932 C10 R2D 9 R2D C11 C10 C 0 1 Y N N N N N -5.058 -19.469 -39.031 4.375 -2.054 0.276 C11 R2D 10 R2D C15 C11 C 0 1 Y N N N N N -6.465 -22.782 -32.373 -2.356 -1.563 0.997 C15 R2D 11 R2D C16 C12 C 0 1 Y N N N N N -6.429 -19.664 -39.014 3.825 -3.293 0.449 C16 R2D 12 R2D O17 O1 O 0 1 N N N N N N -2.335 -23.642 -33.472 -0.752 3.202 1.585 O17 R2D 13 R2D C18 C13 C 0 1 Y N N N N N -7.269 -21.725 -31.992 -3.165 -1.707 -0.117 C18 R2D 14 R2D N N1 N 0 1 Y N N N N N -4.098 -20.490 -35.807 1.588 0.131 -0.197 N R2D 15 R2D C C14 C 0 1 Y N N N N N -4.014 -20.945 -34.504 0.332 0.695 -0.338 C R2D 16 R2D S S1 S 0 1 Y N N N N N -1.587 -20.398 -35.303 1.922 2.597 -0.568 S R2D 17 R2D N5 N2 N 0 1 Y N N N N N -3.047 -19.731 -37.572 3.779 0.371 -0.137 N5 R2D 18 R2D C12 C15 C 0 1 Y N N N N N -7.097 -20.159 -37.906 2.450 -3.471 0.405 C12 R2D 19 R2D C13 C16 C 0 1 N N N N N N -1.652 -22.807 -32.813 -1.411 3.421 0.596 C13 R2D 20 R2D C14 C17 C 0 1 Y N N N N N -7.023 -20.452 -32.459 -2.840 -1.069 -1.303 C14 R2D 21 R2D O O2 O 0 1 N N N N N N -0.602 -23.017 -32.163 -2.507 4.191 0.677 O R2D 22 R2D CL CL1 CL 0 0 N N N N N N -8.605 -21.979 -30.931 -4.592 -2.691 -0.028 CL R2D 23 R2D H1 H1 H 0 1 N N N N N N -6.970 -20.875 -35.864 0.541 -2.534 0.176 H1 R2D 24 R2D H2 H2 H 0 1 N N N N N N -1.277 -20.704 -32.523 -0.815 3.629 -1.442 H2 R2D 25 R2D H3 H3 H 0 1 N N N N N N -2.904 -21.253 -31.997 -1.803 2.188 -1.102 H3 R2D 26 R2D H4 H4 H 0 1 N N N N N N -5.740 -19.234 -33.648 -1.455 0.211 -2.305 H4 R2D 27 R2D H5 H5 H 0 1 N N N N N N -4.769 -23.383 -33.533 -0.589 -0.672 1.802 H5 R2D 28 R2D H6 H6 H 0 1 N N N N N N -4.538 -19.083 -39.895 5.447 -1.927 0.313 H6 R2D 29 R2D H7 H7 H 0 1 N N N N N N -6.671 -23.778 -32.009 -2.614 -2.063 1.919 H7 R2D 30 R2D H8 H8 H 0 1 N N N N N N -6.999 -19.421 -39.898 4.469 -4.144 0.614 H8 R2D 31 R2D H9 H9 H 0 1 N N N N N N -8.167 -20.292 -37.963 2.032 -4.457 0.543 H9 R2D 32 R2D H10 H10 H 0 1 N N N N N N -7.668 -19.634 -32.175 -3.475 -1.185 -2.168 H10 R2D 33 R2D H11 H11 H 0 1 N N N N N N -0.366 -23.935 -32.229 -2.729 4.549 1.548 H11 R2D 34 # 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 R2D C11 C16 DOUB Y N 1 R2D C11 C6 SING Y N 2 R2D C16 C12 SING Y N 3 R2D C12 C7 DOUB Y N 4 R2D C6 N5 SING Y N 5 R2D C6 C2 DOUB Y N 6 R2D N5 C1 DOUB Y N 7 R2D C2 C7 SING Y N 8 R2D C2 N SING Y N 9 R2D C1 N SING Y N 10 R2D C1 S SING Y N 11 R2D N C SING Y N 12 R2D S C3 SING Y N 13 R2D C C3 DOUB Y N 14 R2D C C4 SING N N 15 R2D C3 C8 SING N N 16 R2D C4 C9 DOUB Y N 17 R2D C4 C10 SING Y N 18 R2D O17 C13 DOUB N N 19 R2D C9 C14 SING Y N 20 R2D C10 C15 DOUB Y N 21 R2D C13 C8 SING N N 22 R2D C13 O SING N N 23 R2D C14 C18 DOUB Y N 24 R2D C15 C18 SING Y N 25 R2D C18 CL SING N N 26 R2D C7 H1 SING N N 27 R2D C8 H2 SING N N 28 R2D C8 H3 SING N N 29 R2D C9 H4 SING N N 30 R2D C10 H5 SING N N 31 R2D C11 H6 SING N N 32 R2D C15 H7 SING N N 33 R2D C16 H8 SING N N 34 R2D C12 H9 SING N N 35 R2D C14 H10 SING N N 36 R2D O H11 SING N N 37 # 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 R2D SMILES ACDLabs 12.01 c32n(c1ccccc1n2)c(c(CC(=O)O)s3)c4ccc(cc4)Cl R2D InChI InChI 1.03 InChI=1S/C17H11ClN2O2S/c18-11-7-5-10(6-8-11)16-14(9-15(21)22)23-17-19-12-3-1-2-4-13(12)20(16)17/h1-8H,9H2,(H,21,22) R2D InChIKey InChI 1.03 PUYFLGQZLHVTHX-UHFFFAOYSA-N R2D SMILES_CANONICAL CACTVS 3.385 OC(=O)Cc1sc2nc3ccccc3n2c1c4ccc(Cl)cc4 R2D SMILES CACTVS 3.385 OC(=O)Cc1sc2nc3ccccc3n2c1c4ccc(Cl)cc4 R2D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc2c(c1)nc3n2c(c(s3)CC(=O)O)c4ccc(cc4)Cl R2D SMILES "OpenEye OEToolkits" 2.0.7 c1ccc2c(c1)nc3n2c(c(s3)CC(=O)O)c4ccc(cc4)Cl # 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 R2D "SYSTEMATIC NAME" ACDLabs 12.01 "[3-(4-chlorophenyl)[1,3]thiazolo[3,2-a]benzimidazol-2-yl]acetic acid" R2D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[1-(4-chlorophenyl)-[1,3]thiazolo[3,2-a]benzimidazol-2-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 R2D 'Create component' 2020-01-27 RCSB R2D 'Initial release' 2020-05-13 RCSB # loop_ _software.name _software.version _software.description rdkit 2023.09.6 'Core functionality.' pdbeccdutils 0.8.6 '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 R2D C1 C 8.005 2.278 1 R2D C2 C 5.577 2.278 2 R2D C3 C 8.747 -0.020 3 R2D C4 C 6.376 -1.236 4 R2D C6 C 6.041 3.704 5 R2D C7 C 4.054 1.929 6 R2D C8 C 9.628 -1.233 7 R2D C9 C 4.884 -1.082 8 R2D C10 C 6.988 -2.605 9 R2D C11 C 5.014 4.881 10 R2D C15 C 6.109 -3.820 11 R2D C16 C 3.483 4.568 12 R2D O17 O 12.002 -2.290 13 R2D C18 C 4.617 -3.666 14 R2D N N 6.791 1.396 15 R2D C C 7.255 -0.021 16 R2D S S 9.209 1.398 17 R2D N5 N 7.541 3.704 18 R2D C12 C 3.000 3.082 19 R2D C13 C 11.120 -1.077 20 R2D C14 C 4.004 -2.297 21 R2D O O 11.730 0.294 22 R2D CL Cl 3.737 -4.881 23 # 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 R2D C11 C16 DOUBLE NONE 1 R2D C11 C6 SINGLE NONE 2 R2D C16 C12 SINGLE NONE 3 R2D C12 C7 DOUBLE NONE 4 R2D C6 N5 SINGLE NONE 5 R2D C6 C2 DOUBLE NONE 6 R2D N5 C1 DOUBLE NONE 7 R2D C2 C7 SINGLE NONE 8 R2D C2 N SINGLE NONE 9 R2D C1 N SINGLE NONE 10 R2D C1 S SINGLE NONE 11 R2D N C SINGLE NONE 12 R2D S C3 SINGLE NONE 13 R2D C C3 DOUBLE NONE 14 R2D C C4 SINGLE NONE 15 R2D C3 C8 SINGLE NONE 16 R2D C4 C9 DOUBLE NONE 17 R2D C4 C10 SINGLE NONE 18 R2D O17 C13 DOUBLE NONE 19 R2D C9 C14 SINGLE NONE 20 R2D C10 C15 DOUBLE NONE 21 R2D C13 C8 SINGLE NONE 22 R2D C13 O SINGLE NONE 23 R2D C14 C18 DOUBLE NONE 24 R2D C15 C18 SINGLE NONE 25 R2D C18 CL SINGLE NONE 26 # 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 R2D MurckoScaffold S1 scaffold c1ccc(-c2csc3nc4ccccc4n23)cc1 InChI=1S/C15H10N2S/c1-2-6-11(7-3-1)14-10-18-15-16-12-8-4-5-9-13(12)17(14)15/h1-10H RCBRAUDXOGLXQO-UHFFFAOYSA-N R2D 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 R2D imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N R2D phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N R2D thiazole F4 fragment c1cscn1 InChI=1S/C3H3NS/c1-2-5-3-4-1/h1-3H FZWLAAWBMGSTSO-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 R2D C1 S1 1 R2D C2 S1 1 R2D C3 S1 1 R2D C4 S1 1 R2D C6 S1 1 R2D C7 S1 1 R2D C9 S1 1 R2D C10 S1 1 R2D C11 S1 1 R2D C15 S1 1 R2D C16 S1 1 R2D C18 S1 1 R2D N S1 1 R2D C S1 1 R2D S S1 1 R2D N5 S1 1 R2D C12 S1 1 R2D C14 S1 1 R2D C2 F1 1 R2D N F1 1 R2D C1 F1 1 R2D N5 F1 1 R2D C6 F1 1 R2D C11 F1 1 R2D C16 F1 1 R2D C12 F1 1 R2D C7 F1 1 R2D C2 F2 1 R2D C6 F2 1 R2D N5 F2 1 R2D C1 F2 1 R2D N F2 1 R2D C2 F3 1 R2D C6 F3 1 R2D C11 F3 1 R2D C16 F3 1 R2D C12 F3 1 R2D C7 F3 1 R2D C4 F3 2 R2D C9 F3 2 R2D C14 F3 2 R2D C18 F3 2 R2D C15 F3 2 R2D C10 F3 2 R2D C3 F4 1 R2D C F4 1 R2D N F4 1 R2D C1 F4 1 R2D S F4 1 # _pdbe_chem_comp_rdkit_properties.comp_id R2D _pdbe_chem_comp_rdkit_properties.exactmw 342.023 _pdbe_chem_comp_rdkit_properties.amw 342.807 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 4 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 1 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3 _pdbe_chem_comp_rdkit_properties.NumHBD 1 _pdbe_chem_comp_rdkit_properties.NumHBA 5 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23 _pdbe_chem_comp_rdkit_properties.NumAtoms 34 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.059 _pdbe_chem_comp_rdkit_properties.NumRings 4 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 4 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2 _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 155.679 _pdbe_chem_comp_rdkit_properties.tpsa 54.600 _pdbe_chem_comp_rdkit_properties.CrippenClogP 3.419 _pdbe_chem_comp_rdkit_properties.CrippenMR 87.464 _pdbe_chem_comp_rdkit_properties.chi0v 12.570 _pdbe_chem_comp_rdkit_properties.chi1v 7.318 _pdbe_chem_comp_rdkit_properties.chi2v 4.095 _pdbe_chem_comp_rdkit_properties.chi3v 4.095 _pdbe_chem_comp_rdkit_properties.chi4v 3.231 _pdbe_chem_comp_rdkit_properties.chi0n 21.997 _pdbe_chem_comp_rdkit_properties.chi1n 11.532 _pdbe_chem_comp_rdkit_properties.chi2n 2.950 _pdbe_chem_comp_rdkit_properties.chi3n 2.950 _pdbe_chem_comp_rdkit_properties.chi4n 2.119 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.370 _pdbe_chem_comp_rdkit_properties.kappa1 6.629 _pdbe_chem_comp_rdkit_properties.kappa2 5.367 _pdbe_chem_comp_rdkit_properties.kappa3 2.380 _pdbe_chem_comp_rdkit_properties.Phi 1.547 # 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 R2D UniChem ChEMBL CHEMBL2104737 R2D UniChem 'PubChem DOTF' 12012845 R2D UniChem ZINC ZINC000000002172 R2D UniChem fdasrs 651G60U372 R2D UniChem SureChEMBL SCHEMBL441312 R2D UniChem 'PubChem TPHARMA' 14924989 R2D UniChem PubChem 42747 R2D UniChem ACTor 58433-11-7 R2D UniChem 'EPA CompTox Dashboard' DTXSID40207137 R2D UniChem 'Probes And Drugs' PD068314 R2D UniChem Nikkaji J22.806K # 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 R2D C1 2.083 -1.781 -0.887 ETKDGv3 1 R2D C2 2.228 0.207 0.026 ETKDGv3 2 R2D C3 -0.436 -1.994 -1.072 ETKDGv3 3 R2D C4 -0.951 0.422 -0.682 ETKDGv3 4 R2D C6 3.290 -0.515 0.334 ETKDGv3 5 R2D C7 2.002 1.541 0.608 ETKDGv3 6 R2D C8 -1.856 -2.464 -1.225 ETKDGv3 7 R2D C9 -0.881 1.460 -1.532 ETKDGv3 8 R2D C10 -1.922 0.459 0.438 ETKDGv3 9 R2D C11 4.293 -0.023 1.292 ETKDGv3 10 R2D C15 -2.741 1.507 0.585 ETKDGv3 11 R2D C16 4.115 1.198 1.829 ETKDGv3 12 R2D O17 -1.797 -3.973 0.632 ETKDGv3 13 R2D C18 -2.675 2.638 -0.365 ETKDGv3 14 R2D N 1.389 -0.550 -0.828 ETKDGv3 15 R2D C -0.036 -0.723 -0.835 ETKDGv3 16 R2D S 0.972 -3.125 -1.173 ETKDGv3 17 R2D N5 3.180 -1.837 -0.195 ETKDGv3 18 R2D C12 2.918 2.016 1.471 ETKDGv3 19 R2D C13 -2.383 -3.013 0.063 ETKDGv3 20 R2D C14 -1.788 2.616 -1.369 ETKDGv3 21 R2D O -3.543 -2.482 0.619 ETKDGv3 22 R2D CL -3.752 4.008 -0.167 ETKDGv3 23 R2D H1 1.129 2.126 0.354 ETKDGv3 24 R2D H2 -2.506 -1.638 -1.582 ETKDGv3 25 R2D H3 -1.889 -3.264 -1.994 ETKDGv3 26 R2D H4 -0.167 1.460 -2.346 ETKDGv3 27 R2D H5 -1.956 -0.351 1.155 ETKDGv3 28 R2D H6 5.147 -0.631 1.562 ETKDGv3 29 R2D H7 -3.444 1.533 1.407 ETKDGv3 30 R2D H8 4.837 1.587 2.536 ETKDGv3 31 R2D H9 2.785 2.993 1.917 ETKDGv3 32 R2D H10 -1.728 3.442 -2.066 ETKDGv3 33 R2D H11 -3.917 -2.845 1.487 ETKDGv3 34 #