data_CIV # _chem_comp.id CIV _chem_comp.name "2-[2-[(1~{S})-1,5-bis(azanyl)pentyl]-4-[(4-hydroxyphenyl)methyl]-5-oxidanylidene-imidazol-1-yl]ethanamide" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C17 H23 N4 O4" _chem_comp.mon_nstd_parent_comp_id "LYS, TYR, GLY" _chem_comp.pdbx_synonyms "CHROMOPHORE (LYS-TYR-GLY)" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2021-11-22 _chem_comp.pdbx_modified_date 2024-06-28 _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 347.389 _chem_comp.one_letter_code KYG _chem_comp.three_letter_code CIV _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 7SWU _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_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 CIV N1 N1 N 0 1 N N N Y Y N 5.767 10.876 39.079 1.151 0.934 -2.451 N1 CIV 1 CIV CA1 CA1 C 0 1 N N S N Y N 6.006 12.272 39.546 1.626 0.505 -1.129 CA1 CIV 2 CIV CB1 CB1 C 0 1 N N N N N N 4.708 13.081 39.574 1.449 1.648 -0.127 CB1 CIV 3 CIV CG1 CG1 C 0 1 N N N N N N 4.199 13.295 38.146 2.353 2.818 -0.523 CG1 CIV 4 CIV C1 C1 C 0 1 N N N N Y N 6.681 12.188 40.891 0.830 -0.690 -0.673 C1 CIV 5 CIV N2 N2 N 0 1 N N N N Y N 6.120 12.526 42.033 -0.499 -0.657 -0.384 N2 CIV 6 CIV N3 N3 N 1 1 N N N N Y N 7.967 11.764 41.093 1.330 -1.885 -0.511 N3 CIV 7 CIV C2 C2 C 0 1 N N N N Y N 8.276 11.846 42.431 0.326 -2.716 -0.092 C2 CIV 8 CIV O2 O2 O 0 1 N N N N Y N 9.385 11.515 42.915 0.404 -3.895 0.162 O2 CIV 9 CIV CA2 CA2 C 0 1 N N N N Y N 7.076 12.325 43.021 -0.896 -1.842 -0.020 CA2 CIV 10 CIV CA3 CA3 C 0 1 N N N N Y N 8.819 11.063 40.150 2.724 -2.270 -0.740 CA3 CIV 11 CIV C3 C3 C 0 1 N N N N Y Y 9.690 11.939 39.266 3.356 -2.672 0.568 C3 CIV 12 CIV O3 O3 O 0 1 N N N N Y Y 10.481 11.388 38.494 2.707 -2.639 1.587 O3 CIV 13 CIV CB2 CB2 C 0 1 N N N N N N 6.714 12.607 44.448 -2.289 -2.252 0.387 CB2 CIV 14 CIV CG2 CG2 C 0 1 Y N N N N N 7.481 11.812 45.481 -3.205 -1.058 0.313 CG2 CIV 15 CIV CD1 CD1 C 0 1 Y N N N N N 7.873 12.399 46.676 -3.880 -0.778 -0.861 CD1 CIV 16 CIV CD2 CD2 C 0 1 Y N N N N N 7.835 10.488 45.256 -3.375 -0.249 1.421 CD2 CIV 17 CIV CE1 CE1 C 0 1 Y N N N N N 8.642 11.710 47.596 -4.721 0.316 -0.932 CE1 CIV 18 CIV CE2 CE2 C 0 1 Y N N N N N 8.628 9.799 46.152 -4.216 0.846 1.356 CE2 CIV 19 CIV CZ CZ C 0 1 Y N N N N N 9.058 10.421 47.316 -4.889 1.133 0.177 CZ CIV 20 CIV OH OH O 0 1 N N N N N N 9.821 9.762 48.228 -5.717 2.209 0.110 OH CIV 21 CIV CD CD C 0 1 N N N N N N 2.907 14.111 38.107 2.176 3.961 0.479 CD CIV 22 CIV CE CE C 0 1 N N N N N N 2.476 14.428 36.684 3.080 5.130 0.083 CE CIV 23 CIV NZ NZ N 0 1 N N N N N N 3.211 15.567 36.114 2.910 6.227 1.045 NZ CIV 24 CIV H H1 H 0 1 N N N Y Y N 6.632 10.374 39.072 1.343 0.232 -3.150 H CIV 25 CIV H2 HN11 H 0 1 N Y N Y Y N 5.124 10.423 39.697 0.168 1.161 -2.426 H2 CIV 26 CIV HA1 HA1 H 0 1 N N N N Y N 6.697 12.761 38.843 2.681 0.237 -1.191 HA1 CIV 27 CIV HB11 HB11 H 0 0 N N N N N N 4.896 14.057 40.045 0.409 1.976 -0.131 HB11 CIV 28 CIV HB12 HB12 H 0 0 N N N N N N 3.950 12.535 40.154 1.718 1.302 0.871 HB12 CIV 29 CIV HG12 HG12 H 0 0 N N N N N N 4.011 12.313 37.686 3.393 2.490 -0.520 HG12 CIV 30 CIV HG11 HG11 H 0 0 N N N N N N 4.971 13.827 37.571 2.084 3.164 -1.521 HG11 CIV 31 CIV HA32 HA32 H 0 0 N N N N Y N 8.173 10.460 39.495 2.760 -3.110 -1.434 HA32 CIV 32 CIV HA31 HA31 H 0 0 N N N N Y N 9.482 10.398 40.724 3.270 -1.427 -1.163 HA31 CIV 33 CIV HB2 HB2 H 0 1 N N N N N N 6.894 13.675 44.639 -2.649 -3.029 -0.286 HB2 CIV 34 CIV H5 H5 H 0 1 N N N N N N 5.644 12.387 44.576 -2.271 -2.634 1.408 H5 CIV 35 CIV HD1 HD1 H 0 1 N N N N N N 7.572 13.413 46.892 -3.749 -1.414 -1.724 HD1 CIV 36 CIV HD2 HD2 H 0 1 N N N N N N 7.484 9.989 44.365 -2.851 -0.472 2.338 HD2 CIV 37 CIV HE1 HE1 H 0 1 N N N N N N 8.917 12.177 48.530 -5.247 0.535 -1.849 HE1 CIV 38 CIV HE2 HE2 H 0 1 N N N N N N 8.913 8.778 45.947 -4.348 1.478 2.221 HE2 CIV 39 CIV HOH HOH H 0 1 N N N N N N 10.018 10.342 48.954 -5.280 3.024 -0.172 HOH CIV 40 CIV HD2A HD2A H 0 0 N N N N N N 3.067 15.055 38.648 1.136 4.288 0.476 HD2A CIV 41 CIV HD1A HD1A H 0 0 N N N N N N 2.109 13.536 38.600 2.445 3.614 1.477 HD1A CIV 42 CIV HE2A HE2A H 0 0 N N N N N N 1.402 14.666 36.685 4.120 4.802 0.087 HE2A CIV 43 CIV HE1A HE1A H 0 0 N N N N N N 2.655 13.543 36.056 2.812 5.476 -0.914 HE1A CIV 44 CIV OXT OXT O 0 1 N Y N N Y Y 9.392 13.252 39.105 4.639 -3.066 0.602 O1 CIV 45 CIV HXT HXT H 0 1 N Y N N Y Y 9.871 13.597 38.360 4.999 -3.313 1.464 H1 CIV 46 CIV H3 H3 H 0 1 N N N N N N 2.893 15.736 35.181 3.091 5.914 1.987 H3 CIV 47 CIV H4 H4 H 0 1 N N N N N N 3.051 16.380 36.673 3.497 7.012 0.806 H4 CIV 48 # 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 CIV NZ CE SING N N 1 CIV CE CD SING N N 2 CIV CD CG1 SING N N 3 CIV CG1 CB1 SING N N 4 CIV O3 C3 DOUB N N 5 CIV N1 CA1 SING N N 6 CIV C3 CA3 SING N N 7 CIV CA1 CB1 SING N N 8 CIV CA1 C1 SING N N 9 CIV CA3 N3 SING N N 10 CIV C1 N3 DOUB N N 11 CIV C1 N2 SING N N 12 CIV N3 C2 SING N N 13 CIV N2 CA2 DOUB N N 14 CIV C2 O2 DOUB N N 15 CIV C2 CA2 SING N N 16 CIV CA2 CB2 SING N N 17 CIV CB2 CG2 SING N N 18 CIV CD2 CG2 DOUB Y N 19 CIV CD2 CE2 SING Y N 20 CIV CG2 CD1 SING Y N 21 CIV CE2 CZ DOUB Y N 22 CIV CD1 CE1 DOUB Y N 23 CIV CZ CE1 SING Y N 24 CIV CZ OH SING N N 25 CIV N1 H SING N N 26 CIV N1 H2 SING N N 27 CIV CA1 HA1 SING N N 28 CIV CB1 HB11 SING N N 29 CIV CB1 HB12 SING N N 30 CIV CG1 HG12 SING N N 31 CIV CG1 HG11 SING N N 32 CIV CA3 HA32 SING N N 33 CIV CA3 HA31 SING N N 34 CIV CB2 HB2 SING N N 35 CIV CB2 H5 SING N N 36 CIV CD1 HD1 SING N N 37 CIV CD2 HD2 SING N N 38 CIV CE1 HE1 SING N N 39 CIV CE2 HE2 SING N N 40 CIV OH HOH SING N N 41 CIV CD HD2A SING N N 42 CIV CD HD1A SING N N 43 CIV CE HE2A SING N N 44 CIV CE HE1A SING N N 45 CIV C3 OXT SING N N 46 CIV OXT HXT SING N N 47 CIV NZ H3 SING N N 48 CIV NZ H4 SING N N 49 # 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 CIV SMILES ACDLabs 12.01 "NCCCCC(N)C=1N=C(Cc2ccc(O)cc2)C(=O)[N+]=1CC(N)=O" CIV InChI InChI 1.06 "InChI=1S/C17H22N4O4/c18-8-2-1-3-13(19)16-20-14(17(25)21(16)10-15(23)24)9-11-4-6-12(22)7-5-11/h4-7,13H,1-3,8-10,18-19H2,(H-,22,23,24)/p+1/t13-/m0/s1" CIV InChIKey InChI 1.06 UNAYNKWNLZGKRW-ZDUSSCGKSA-O CIV SMILES_CANONICAL CACTVS 3.385 "NCCCC[C@H](N)C1=[N+](CC(O)=O)C(=O)C(=N1)Cc2ccc(O)cc2" CIV SMILES CACTVS 3.385 "NCCCC[CH](N)C1=[N+](CC(O)=O)C(=O)C(=N1)Cc2ccc(O)cc2" CIV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CC2=NC(=[N+](C2=O)CC(=O)O)[C@H](CCCCN)N)O" CIV SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CC2=NC(=[N+](C2=O)CC(=O)O)C(CCCCN)N)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 CIV "SYSTEMATIC NAME" ACDLabs 12.01 "3-(2-amino-2-oxoethyl)-2-[(1S)-1,5-diaminopentyl]-5-[(4-hydroxyphenyl)methyl]-4-oxo-4H-imidazol-3-ium" CIV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[2-[(1~{S})-1,5-bis(azanyl)pentyl]-4-[(4-hydroxyphenyl)methyl]-5-oxidanylidene-imidazol-1-ium-1-yl]ethanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id CIV _pdbx_chem_comp_synonyms.name "CHROMOPHORE (LYS-TYR-GLY)" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site CIV "Create component" 2021-11-22 RCSB CIV "Initial release" 2022-04-20 RCSB CIV "Modify backbone" 2023-11-03 PDBE CIV "Modify synonyms" 2024-05-06 PDBE CIV "Other modification" 2024-06-28 PDBE #