data_F6Q # _chem_comp.id F6Q _chem_comp.name "N,N-pyridylbenzimidazole derivative-Pd complex" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H15 Cl2 N3 O3 Pd S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date 2018-06-04 _chem_comp.pdbx_modified_date 2026-07-31 _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 494.689 _chem_comp.one_letter_code ? _chem_comp.three_letter_code F6Q _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details MetalCoord _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6GOB _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI _chem_comp.pdbx_comp_type "metal-containing ligand" _chem_comp.pdbx_pcm Y # 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 F6Q OAU O1 O 0 1 N N N N N N -28.213 -9.674 -30.158 4.390 -0.485 -2.138 OAU F6Q 1 F6Q SAV S1 S 0 1 N N N N N N -27.227 -8.674 -29.536 3.724 -1.753 -2.019 SAV F6Q 2 F6Q OAS O2 O 0 1 N N N N N N -26.157 -9.455 -28.762 4.554 -2.926 -2.006 OAS F6Q 3 F6Q OAT O3 O 0 1 N N N N N N -27.994 -7.741 -28.614 2.678 -1.909 -3.091 OAT F6Q 4 F6Q CAP C1 C 0 1 N N N N N N -26.484 -7.656 -30.826 2.838 -1.748 -0.483 CAP F6Q 5 F6Q CAO C2 C 0 1 N N N N N N -25.475 -6.756 -30.108 1.954 -0.516 -0.275 CAO F6Q 6 F6Q CAN C3 C 0 1 N N N N N N -26.090 -5.431 -30.172 1.031 -0.583 0.934 CAN F6Q 7 F6Q NAM N1 N 0 1 Y N N N N N -25.184 -4.417 -29.461 0.001 0.460 0.918 NAM F6Q 8 F6Q CAB C4 C 0 1 Y N N N N N -24.313 -3.725 -30.209 0.169 1.730 1.450 CAB F6Q 9 F6Q CAC C5 C 0 1 Y N N N N N -23.772 -3.985 -31.434 1.260 2.379 2.024 CAC F6Q 10 F6Q CAD C6 C 0 1 Y N N N N N -22.827 -3.150 -32.053 1.059 3.676 2.442 CAD F6Q 11 F6Q CAE C7 C 0 1 Y N N N N N -22.368 -2.082 -31.320 -0.171 4.317 2.281 CAE F6Q 12 F6Q CAF C8 C 0 1 Y N N N N N -22.898 -1.917 -30.038 -1.242 3.683 1.697 CAF F6Q 13 F6Q CAA C9 C 0 1 Y N N N N N -23.883 -2.680 -29.492 -1.067 2.361 1.291 CAA F6Q 14 F6Q NAL N2 N 0 1 Y N N N N N -24.678 -2.546 -28.401 -1.938 1.492 0.667 NAL F6Q 15 F6Q CAG C10 C 0 1 Y N N N N N -25.518 -3.623 -28.429 -1.340 0.324 0.666 CAG F6Q 16 F6Q CAH C11 C 0 1 Y N N N N N -26.060 -4.008 -27.330 -2.158 -0.614 -0.104 CAH F6Q 17 F6Q NAQ N3 N 0 1 Y N N N N N -25.709 -3.126 -26.426 -1.886 -0.624 -1.387 NAQ F6Q 18 F6Q CAI C12 C 0 1 Y N N N N N -26.585 -2.914 -25.300 -2.550 -1.490 -2.158 CAI F6Q 19 F6Q CAK C13 C 0 1 Y N N N N N -27.463 -3.929 -24.939 -3.531 -2.329 -1.681 CAK F6Q 20 F6Q CAJ C14 C 0 1 Y N N N N N -27.711 -4.930 -25.852 -3.808 -2.305 -0.336 CAJ F6Q 21 F6Q CAR C15 C 0 1 Y N N N N N -27.082 -4.913 -27.100 -3.109 -1.439 0.477 CAR F6Q 22 F6Q CL2 CL2 CL -1 0 N Y N N N N -24.216 -0.760 -24.948 -3.076 1.329 -3.591 CL2 F6Q 23 F6Q PD PD1 PD ? 0 N N N N N N -24.342 -1.570 -26.917 -2.390 1.436 -1.397 PD F6Q 24 F6Q H1 H1 H 0 1 N N N N N N -25.975 -8.288 -31.569 3.478 -1.799 0.240 H1 F6Q 25 F6Q H2 H2 H 0 1 N N N N N N -27.253 -7.049 -31.327 2.288 -2.545 -0.446 H2 F6Q 26 F6Q H3 H3 H 0 1 N N N N N N -25.337 -7.075 -29.064 1.401 -0.379 -1.085 H3 F6Q 27 F6Q H4 H4 H 0 1 N N N N N N -24.504 -6.764 -30.625 2.533 0.281 -0.185 H4 F6Q 28 F6Q H5 H5 H 0 1 N N N N N N -26.218 -5.136 -31.224 1.564 -0.497 1.751 H5 F6Q 29 F6Q H6 H6 H 0 1 N N N N N N -27.072 -5.457 -29.677 0.589 -1.456 0.956 H6 F6Q 30 F6Q H7 H7 H 0 1 N N N N N N -24.086 -4.878 -31.954 2.089 1.950 2.141 H7 F6Q 31 F6Q H8 H8 H 0 1 N N N N N N -22.478 -3.338 -33.057 1.771 4.142 2.843 H8 F6Q 32 F6Q H9 H9 H 0 1 N N N N N N -21.630 -1.401 -31.717 -0.268 5.204 2.576 H9 F6Q 33 F6Q H10 H10 H 0 1 N N N N N N -22.493 -1.120 -29.432 -2.070 4.116 1.596 H10 F6Q 34 F6Q H11 H11 H 0 1 N N N N N N -26.559 -1.986 -24.749 -2.365 -1.491 -3.084 H11 F6Q 35 F6Q H12 H12 H 0 1 N N N N N N -27.938 -3.933 -23.969 -3.993 -2.911 -2.261 H12 F6Q 36 F6Q H13 H13 H 0 1 N N N N N N -28.393 -5.730 -25.603 -4.467 -2.873 0.028 H13 F6Q 37 F6Q H14 H14 H 0 1 N N N N N N -27.390 -5.598 -27.876 -3.279 -1.402 1.403 H14 F6Q 38 F6Q CL1 CL1 CL -1 0 N Y N N N N ? ? ? -2.748 3.707 -1.466 CL1 F6Q 39 F6Q H16 H16 H 0 1 N N N N N N -28.915 -7.975 -28.620 2.118 -1.239 -3.190 H16 F6Q 40 # 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 _chem_comp_bond.pdbx_metal_coordination_flag _chem_comp_bond.pdbx_metal_pi_flag F6Q OAU SAV DOUB N N 1 N N F6Q SAV OAS DOUB N N 2 N N F6Q SAV OAT SING N N 3 N N F6Q SAV CAP SING N N 4 N N F6Q CAP CAO SING N N 5 N N F6Q CAO CAN SING N N 6 N N F6Q CAN NAM SING N N 7 N N F6Q NAM CAB SING Y N 8 N N F6Q NAM CAG SING Y N 9 N N F6Q CAB CAC DOUB Y N 10 N N F6Q CAB CAA SING Y N 11 N N F6Q CAC CAD SING Y N 12 N N F6Q CAD CAE DOUB Y N 13 N N F6Q CAE CAF SING Y N 14 N N F6Q CAF CAA DOUB Y N 15 N N F6Q CAA NAL SING Y N 16 N N F6Q NAL CAG DOUB Y N 17 N N F6Q NAL PD SING N N 18 Y N F6Q CAG CAH SING N N 19 N N F6Q CAH NAQ DOUB Y N 20 N N F6Q CAH CAR SING Y N 21 N N F6Q NAQ CAI SING Y N 22 N N F6Q NAQ PD SING N N 23 Y N F6Q CAI CAK DOUB Y N 24 N N F6Q CAK CAJ SING Y N 25 N N F6Q CAJ CAR DOUB Y N 26 N N F6Q CL2 PD SING N N 27 Y N F6Q CAP H1 SING N N 28 N N F6Q CAP H2 SING N N 29 N N F6Q CAO H3 SING N N 30 N N F6Q CAO H4 SING N N 31 N N F6Q CAN H5 SING N N 32 N N F6Q CAN H6 SING N N 33 N N F6Q CAC H7 SING N N 34 N N F6Q CAD H8 SING N N 35 N N F6Q CAE H9 SING N N 36 N N F6Q CAF H10 SING N N 37 N N F6Q CAI H11 SING N N 38 N N F6Q CAK H12 SING N N 39 N N F6Q CAJ H13 SING N N 40 N N F6Q CAR H14 SING N N 41 N N F6Q PD CL1 SING N N 42 Y N F6Q OAT H16 SING N N 43 N N # 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 F6Q InChI InChI 1.03 "InChI=1S/C15H15N3O3S.2ClH.Pd/c19-22(20,21)11-5-10-18-14-8-2-1-6-12(14)17-15(18)13-7-3-4-9-16-13;;;/h1-4,6-9H,5,10-11H2,(H,19,20,21);2*1H;/q;;;+4/p-2" F6Q InChIKey InChI 1.03 DTXSGQZIKSCPLR-UHFFFAOYSA-L F6Q SMILES_CANONICAL CACTVS 3.385 "O[S](=O)(=O)CCCn1c2ccccc2[n+]3c1c4cccc[n+]4[Pd]3(Cl)Cl" F6Q SMILES CACTVS 3.385 "O[S](=O)(=O)CCCn1c2ccccc2[n+]3c1c4cccc[n+]4[Pd]3(Cl)Cl" F6Q SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)n(c-3[n+]2[Pd]([n+]4c3cccc4)(Cl)Cl)CCCS(=O)(=O)O" F6Q SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc2c(c1)n(c-3[n+]2[Pd]([n+]4c3cccc4)(Cl)Cl)CCCS(=O)(=O)O" # loop_ _pdbx_chem_comp_atom_coordination.geometry_id _pdbx_chem_comp_atom_coordination.comp_id _pdbx_chem_comp_atom_coordination.atom_id _pdbx_chem_comp_atom_coordination.number _pdbx_chem_comp_atom_coordination.geometry_calculated _pdbx_chem_comp_atom_coordination.geometry_generic _pdbx_chem_comp_atom_coordination.geometry_abbr _pdbx_chem_comp_atom_coordination.provenance _pdbx_chem_comp_atom_coordination.representative_entry_id 1 F6Q PD 4 "square plane" "square planar" SPL FindGeo 6GOB 1 F6Q PD 4 square-planar "square planar" SPL MetalCoord 6GOB # loop_ _pdbx_chem_comp_atom_coordination_sphere.id _pdbx_chem_comp_atom_coordination_sphere.geometry_id _pdbx_chem_comp_atom_coordination_sphere.comp_id _pdbx_chem_comp_atom_coordination_sphere.atom_id _pdbx_chem_comp_atom_coordination_sphere.descriptor _pdbx_chem_comp_atom_coordination_sphere.provenance _pdbx_chem_comp_atom_coordination_sphere.representative_entry_id 1 1 F6Q PD "@SPL{Pd,Cl,N,Cl,N}" MetalCoord 6GOB 2 1 F6Q PD "@SPL{Pd,Cl,N,N,O}" MetalCoord 6GOB 3 1 F6Q PD "@SPL{Pd,N,N,N,O}" MetalCoord 6GOK # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession _pdbx_chem_comp_pcm.position 1 F6Q ASP None "Metal coordination" "Any position" PD OD1 ? ? "Amino-acid side chain" 2 F6Q HIS None "Metal coordination" "Any position" PD ND1 ? ? "Amino-acid side chain" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site F6Q "Create component" 2018-06-04 EBI F6Q "Initial release" 2018-07-25 RCSB F6Q "Other modification" 2026-07-17 RCSB F6Q "Other modification" 2026-07-31 RCSB #