data_653 # _chem_comp.id 653 _chem_comp.name "5-(2-AMINOETHYL)-3-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}-1,1'-BIPHENYL-2-OLATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C22 H22 N5 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms CRA_23653 _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2003-03-14 _chem_comp.pdbx_modified_date 2020-06-17 _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 372.443 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 653 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1O38 _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.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 653 C1 C1 C 0 1 Y N N 44.022 -3.031 26.234 5.337 0.361 0.073 C1 653 1 653 C2 C2 C 0 1 Y N N 44.333 -1.625 26.242 5.072 1.547 -0.623 C2 653 2 653 C3 C3 C 0 1 Y N N 44.231 -0.821 27.373 3.794 1.872 -0.976 C3 653 3 653 C4 C4 C 0 1 Y N N 43.817 -1.434 28.514 2.742 1.026 -0.647 C4 653 4 653 C5 C5 C 0 1 Y N N 43.517 -2.750 28.575 2.990 -0.171 0.052 C5 653 5 653 C6 C6 C 0 1 Y N N 43.591 -3.604 27.467 4.298 -0.502 0.406 C6 653 6 653 C7 C7 C 0 1 N N N 44.153 -3.791 25.043 6.726 0.022 0.450 C7 653 7 653 N1 N1 N 0 1 N N N 43.929 -5.095 25.062 6.980 -1.106 1.111 N1 653 8 653 N2 N2 N 1 1 N N N 44.495 -3.164 23.927 7.723 0.845 0.127 N2 653 9 653 N3 N3 N 0 1 Y N N 43.652 -0.951 29.699 1.380 1.073 -0.857 N3 653 10 653 N4 N4 N 0 1 Y N N 43.150 -3.116 29.790 1.794 -0.785 0.232 N4 653 11 653 C8 C8 C 0 1 Y N N 43.256 -1.952 30.426 0.843 -0.058 -0.301 C8 653 12 653 "C1'" "C1'" C 0 1 Y N N 43.009 -1.840 31.818 -0.594 -0.405 -0.301 "C1'" 653 13 653 "C2'" "C2'" C 0 1 Y N N 42.656 -2.971 32.593 -0.995 -1.726 -0.510 "C2'" 653 14 653 "C3'" "C3'" C 0 1 Y N N 42.406 -2.887 33.964 -2.336 -2.051 -0.510 "C3'" 653 15 653 "CV'" "C31'" C 0 1 N N N 42.043 -4.149 34.816 -2.760 -3.479 -0.737 "CV'" 653 16 653 "CW'" "C32'" C 0 1 N N N 40.537 -4.558 34.655 -2.845 -4.205 0.607 "CW'" 653 17 653 "NX'" "N33'" N 1 1 N N N 40.338 -5.959 35.203 -3.259 -5.597 0.386 "NX'" 653 18 653 "C4'" "C4'" C 0 1 Y N N 42.506 -1.643 34.575 -3.293 -1.075 -0.303 "C4'" 653 19 653 "C5'" "C5'" C 0 1 Y N N 42.849 -0.484 33.872 -2.911 0.248 -0.092 "C5'" 653 20 653 "C6'" "C6'" C 0 1 Y N N 43.094 -0.605 32.498 -1.556 0.588 -0.086 "C6'" 653 21 653 "O6'" "O6'" O -1 1 N N N 43.433 0.529 31.809 -1.175 1.874 0.119 "O6'" 653 22 653 C1B "C1''" C 0 1 Y N N 42.928 0.728 34.573 -3.940 1.293 0.130 C1B 653 23 653 C2B "C2''" C 0 1 Y N N 44.121 1.467 34.685 -3.831 2.164 1.212 C2B 653 24 653 C3B "C3''" C 0 1 Y N N 44.173 2.663 35.421 -4.791 3.134 1.414 C3B 653 25 653 C4B "C4''" C 0 1 Y N N 43.042 3.158 36.062 -5.862 3.242 0.544 C4B 653 26 653 C5B "C5''" C 0 1 Y N N 41.845 2.445 35.966 -5.976 2.380 -0.531 C5B 653 27 653 C6B "C6''" C 0 1 Y N N 41.792 1.251 35.228 -5.018 1.410 -0.747 C6B 653 28 653 HC2 HC2 H 0 1 N N N 44.676 -1.150 25.346 5.885 2.210 -0.881 HC2 653 29 653 HC3 HC3 H 0 1 N N N 44.461 0.230 27.361 3.600 2.789 -1.512 HC3 653 30 653 HC6 HC6 H 0 1 N N N 43.334 -4.653 27.553 4.503 -1.420 0.937 HC6 653 31 653 HH11 HH11 H 0 0 N N N 43.688 -5.517 25.952 7.891 -1.328 1.359 HH11 653 32 653 HH12 HH12 H 0 0 N N N 43.979 -5.719 24.287 6.254 -1.704 1.346 HH12 653 33 653 HH21 HH21 H 0 0 N N N 44.641 -2.164 23.931 7.538 1.666 -0.355 HH21 653 34 653 HH22 HH22 H 0 0 N N N 44.650 -3.632 23.060 8.634 0.624 0.378 HH22 653 35 653 HN3 HN3 H 0 1 N N N 43.757 -0.029 30.023 0.892 1.776 -1.314 HN3 653 36 653 "HC2'" "HC2'" H 0 0 N N N 42.574 -3.936 32.111 -0.254 -2.495 -0.672 "HC2'" 653 37 653 H31A H31A H 0 0 N N N 42.276 -3.950 35.863 -3.737 -3.495 -1.221 H31A 653 38 653 H31B H31B H 0 0 N N N 42.697 -4.958 34.521 -2.030 -3.978 -1.374 H31B 653 39 653 H32A H32A H 0 0 N N N 40.227 -4.506 33.620 -1.869 -4.189 1.091 H32A 653 40 653 H32B H32B H 0 0 N N N 39.912 -3.859 35.199 -3.575 -3.706 1.245 H32B 653 41 653 H33A H33A H 0 0 N N N 40.281 -6.682 34.451 -4.163 -5.613 -0.062 H33A 653 42 653 H33B H33B H 0 0 N N N 39.473 -6.037 35.783 -2.583 -6.059 -0.204 H33B 653 43 653 H33C H33C H 0 0 N N N 41.148 -6.192 35.806 -3.315 -6.076 1.272 H33C 653 44 653 "HC4'" "HC4'" H 0 0 N N N 42.312 -1.567 35.637 -4.340 -1.339 -0.305 "HC4'" 653 45 653 H2B "H2''" H 0 1 N N N 45.017 1.109 34.195 -2.996 2.080 1.892 H2B 653 46 653 H3B "H3''" H 0 1 N N N 45.101 3.214 35.499 -4.708 3.810 2.252 H3B 653 47 653 H4B "H4''" H 0 1 N N N 43.088 4.080 36.632 -6.611 4.003 0.706 H4B 653 48 653 H5B "H5''" H 0 1 N N N 40.955 2.814 36.458 -6.814 2.469 -1.207 H5B 653 49 653 H6B "H6''" H 0 1 N N N 40.852 0.718 35.170 -5.107 0.738 -1.587 H6B 653 50 # # 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 653 C1 C2 DOUB Y N 1 653 C1 C6 SING Y N 2 653 C1 C7 SING N N 3 653 C2 C3 SING Y N 4 653 C2 HC2 SING N N 5 653 C3 C4 DOUB Y N 6 653 C3 HC3 SING N N 7 653 C4 C5 SING Y N 8 653 C4 N3 SING Y N 9 653 C5 C6 DOUB Y N 10 653 C5 N4 SING Y N 11 653 C6 HC6 SING N N 12 653 C7 N1 SING N N 13 653 C7 N2 DOUB N N 14 653 N1 HH11 SING N N 15 653 N1 HH12 SING N N 16 653 N2 HH21 SING N N 17 653 N2 HH22 SING N N 18 653 N3 C8 SING Y N 19 653 N3 HN3 SING N N 20 653 N4 C8 DOUB Y N 21 653 C8 "C1'" SING Y N 22 653 "C1'" "C2'" DOUB Y N 23 653 "C1'" "C6'" SING Y N 24 653 "C2'" "C3'" SING Y N 25 653 "C2'" "HC2'" SING N N 26 653 "C3'" "CV'" SING N N 27 653 "C3'" "C4'" DOUB Y N 28 653 "CV'" "CW'" SING N N 29 653 "CV'" H31A SING N N 30 653 "CV'" H31B SING N N 31 653 "CW'" "NX'" SING N N 32 653 "CW'" H32A SING N N 33 653 "CW'" H32B SING N N 34 653 "NX'" H33A SING N N 35 653 "NX'" H33B SING N N 36 653 "NX'" H33C SING N N 37 653 "C4'" "C5'" SING Y N 38 653 "C4'" "HC4'" SING N N 39 653 "C5'" "C6'" DOUB Y N 40 653 "C5'" C1B SING Y N 41 653 "C6'" "O6'" SING N N 42 653 C1B C2B DOUB Y N 43 653 C1B C6B SING Y N 44 653 C2B C3B SING Y N 45 653 C2B H2B SING N N 46 653 C3B C4B DOUB Y N 47 653 C3B H3B SING N N 48 653 C4B C5B SING Y N 49 653 C4B H4B SING N N 50 653 C5B C6B DOUB Y N 51 653 C5B H5B SING N N 52 653 C6B H6B SING N N 53 # # 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 653 SMILES ACDLabs 10.04 "[O-]c4c(c1ccccc1)cc(cc4c3nc2cc(ccc2n3)\C(=[NH2+])N)CC[NH3+]" 653 SMILES_CANONICAL CACTVS 3.341 "NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3cc(CC[NH3+])cc(c3[O-])c4ccccc4" 653 SMILES CACTVS 3.341 "NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3cc(CC[NH3+])cc(c3[O-])c4ccccc4" 653 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)c2cc(cc(c2[O-])c3[nH]c4ccc(cc4n3)C(=[NH2+])N)CC[NH3+]" 653 SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)c2cc(cc(c2[O-])c3[nH]c4ccc(cc4n3)C(=[NH2+])N)CC[NH3+]" 653 InChI InChI 1.03 "InChI=1S/C22H21N5O/c23-9-8-13-10-16(14-4-2-1-3-5-14)20(28)17(11-13)22-26-18-7-6-15(21(24)25)12-19(18)27-22/h1-7,10-12,28H,8-9,23H2,(H3,24,25)(H,26,27)/p+1" 653 InChIKey InChI 1.03 YYUZFCLHOQHMPT-UHFFFAOYSA-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 653 "SYSTEMATIC NAME" ACDLabs 10.04 "3-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-5-(2-ammonioethyl)biphenyl-2-olate" 653 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[5-(amino-azaniumylidene-methyl)-1H-benzimidazol-2-yl]-4-(2-azaniumylethyl)-6-phenyl-phenolate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 653 "Create component" 2003-03-14 RCSB 653 "Modify aromatic_flag" 2011-06-04 RCSB 653 "Modify descriptor" 2011-06-04 RCSB 653 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 653 _pdbx_chem_comp_synonyms.name CRA_23653 _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##