data_Y6C # _chem_comp.id Y6C _chem_comp.name "4-oxidanylidene-4-(1,10-phenanthrolin-5-ylamino)but-2-enoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H11 N3 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-12-11 _chem_comp.pdbx_modified_date 2024-12-06 _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 293.277 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y6C _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 8XBJ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 Y6C CAA C1 C 0 1 N N N N N N 1.980 -10.974 22.157 -4.665 0.428 -0.541 CAA Y6C 1 Y6C CAC C2 C 0 1 Y N N N N N -0.667 -7.963 15.902 2.944 -3.377 -0.103 CAC Y6C 2 Y6C CAD C3 C 0 1 Y N N N N N -2.722 -14.244 18.099 2.069 3.489 0.350 CAD Y6C 3 Y6C CAE C4 C 0 1 Y N N N N N -1.123 -8.976 15.036 3.955 -2.534 0.345 CAE Y6C 4 Y6C CAF C5 C 0 1 Y N N N N N -2.713 -13.862 16.743 3.269 2.878 0.694 CAF Y6C 5 Y6C CAG C6 C 0 1 Y N N N N N -0.642 -8.224 17.240 1.735 -2.854 -0.472 CAG Y6C 6 Y6C CAH C7 C 0 1 Y N N N N N -2.305 -13.347 19.030 1.017 2.727 -0.084 CAH Y6C 7 Y6C CAI C8 C 0 1 Y N N N N N -1.040 -9.820 19.096 0.325 -0.874 -0.746 CAI Y6C 8 Y6C CAM C9 C 0 1 N N N N N N 2.919 -12.114 22.524 -4.597 -0.364 0.701 CAM Y6C 9 Y6C CAN C10 C 0 1 Y N N N N N -1.464 -11.037 19.522 0.130 0.467 -0.662 CAN Y6C 10 Y6C CAO C11 C 0 1 Y N N N N N -1.048 -9.485 17.721 1.553 -1.462 -0.378 CAO Y6C 11 Y6C CAP C12 C 0 1 Y N N N N N -1.880 -12.056 18.610 1.198 1.340 -0.178 CAP Y6C 12 Y6C CAQ C13 C 0 1 Y N N N N N -1.484 -10.447 16.778 2.623 -0.667 0.091 CAQ Y6C 13 Y6C CAR C14 C 0 1 Y N N N N N -1.917 -11.757 17.234 2.444 0.786 0.187 CAR Y6C 14 Y6C NAJ N1 N 0 1 Y N N N N N -1.513 -10.185 15.438 3.780 -1.235 0.425 NAJ Y6C 15 Y6C NAK N2 N 0 1 Y N N N N N -2.326 -12.667 16.314 3.427 1.577 0.608 NAK Y6C 16 Y6C NAL N3 N 0 1 N N N N N N -1.366 -11.405 20.874 -1.100 1.013 -1.023 NAL Y6C 17 Y6C OAB O1 O 0 1 N N N N N N 4.093 -12.091 22.101 -3.554 -0.437 1.318 OAB Y6C 18 Y6C OAM O2 O 0 1 N N N N N N 2.488 -12.996 23.268 -5.693 -1.007 1.150 OAM Y6C 19 Y6C CAS C15 C 0 0 N N N N N N -0.208 -11.920 21.335 -2.237 0.330 -0.782 CAA1 Y6C 20 Y6C CAT C16 C 0 0 N N N N N N 0.641 -10.960 22.064 -3.545 0.951 -1.067 CAAB Y6C 21 Y6C OAS O3 O 0 0 N N N N N N 0.202 -13.057 21.073 -2.185 -0.797 -0.329 OAA2 Y6C 22 Y6C HAA H1 H 0 1 N N N N N N 2.464 -10.034 21.938 -5.615 0.585 -1.031 HAA Y6C 23 Y6C HAC H2 H 0 1 N N N N N N -0.346 -7.006 15.517 3.115 -4.441 -0.164 HAC Y6C 24 Y6C HAD H3 H 0 1 N N N N N N -3.053 -15.229 18.392 1.964 4.561 0.430 HAD Y6C 25 Y6C HAE H4 H 0 1 N N N N N N -1.159 -8.759 13.979 4.906 -2.957 0.633 HAE Y6C 26 Y6C HAF H5 H 0 1 N N N N N N -3.040 -14.584 16.009 4.090 3.488 1.039 HAF Y6C 27 Y6C HAG H6 H 0 1 N N N N N N -0.311 -7.464 17.932 0.941 -3.493 -0.826 HAG Y6C 28 Y6C HAH H7 H 0 1 N N N N N N -2.296 -13.611 20.077 0.076 3.184 -0.356 HAH Y6C 29 Y6C HAI H8 H 0 1 N N N N N N -0.691 -9.096 19.818 -0.477 -1.504 -1.101 HAI Y6C 30 Y6C HNAL H9 H 0 0 N N N N N N -2.146 -11.286 21.488 -1.139 1.884 -1.449 HNAL Y6C 31 Y6C H1 H10 H 0 1 N N N N N N 3.179 -13.622 23.450 -5.599 -1.514 1.969 H1 Y6C 32 Y6C HAAB H11 H 0 0 N N N N N N 0.131 -10.159 22.579 -3.602 1.825 -1.699 HAAB Y6C 33 # 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 Y6C CAA CAM SING N N 1 Y6C CAA CAT DOUB N Z 2 Y6C CAM OAB DOUB N N 3 Y6C CAM OAM SING N N 4 Y6C NAL CAN SING N N 5 Y6C NAL CAS SING N N 6 Y6C CAN CAP DOUB Y N 7 Y6C CAN CAI SING Y N 8 Y6C CAP CAH SING Y N 9 Y6C CAP CAR SING Y N 10 Y6C CAH CAD DOUB Y N 11 Y6C CAD CAF SING Y N 12 Y6C CAF NAK DOUB Y N 13 Y6C NAK CAR SING Y N 14 Y6C CAR CAQ DOUB Y N 15 Y6C CAQ NAJ SING Y N 16 Y6C CAQ CAO SING Y N 17 Y6C NAJ CAE DOUB Y N 18 Y6C CAE CAC SING Y N 19 Y6C CAC CAG DOUB Y N 20 Y6C CAG CAO SING Y N 21 Y6C CAO CAI DOUB Y N 22 Y6C CAT CAS SING N N 23 Y6C CAS OAS DOUB N N 24 Y6C CAA HAA SING N N 25 Y6C CAC HAC SING N N 26 Y6C CAD HAD SING N N 27 Y6C CAE HAE SING N N 28 Y6C CAF HAF SING N N 29 Y6C CAG HAG SING N N 30 Y6C CAH HAH SING N N 31 Y6C CAI HAI SING N N 32 Y6C NAL HNAL SING N N 33 Y6C OAM H1 SING N N 34 Y6C CAT HAAB SING N N 35 # 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 Y6C InChI InChI 1.06 "InChI=1S/C16H11N3O3/c20-13(5-6-14(21)22)19-12-9-10-3-1-7-17-15(10)16-11(12)4-2-8-18-16/h1-9H,(H,19,20)(H,21,22)/b6-5-" Y6C InChIKey InChI 1.06 TVPGTODVJPAAAB-WAYWQWQTSA-N Y6C SMILES_CANONICAL CACTVS 3.385 "OC(=O)\C=C/C(=O)Nc1cc2cccnc2c3ncccc13" Y6C SMILES CACTVS 3.385 "OC(=O)C=CC(=O)Nc1cc2cccnc2c3ncccc13" Y6C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2cc(c3cccnc3c2nc1)NC(=O)C=CC(=O)O" Y6C SMILES "OpenEye OEToolkits" 2.0.7 "c1cc2cc(c3cccnc3c2nc1)NC(=O)C=CC(=O)O" # _pdbx_chem_comp_identifier.comp_id Y6C _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "4-oxidanylidene-4-(1,10-phenanthrolin-5-ylamino)but-2-enoic 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 Y6C "Create component" 2023-12-11 PDBC Y6C "Modify atom id" 2023-12-13 PDBC Y6C "Modify PCM" 2024-09-27 PDBE Y6C "Initial release" 2024-12-11 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id Y6C _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom CAT _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #