data_X1B # _chem_comp.id X1B _chem_comp.name "{(4Z)-2-[(1S)-1-amino-2-(1-methyl-1H-imidazol-5-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetaldehyde" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C18 H19 N5 O4" _chem_comp.mon_nstd_parent_comp_id "HIS, TYR, GLY" _chem_comp.pdbx_synonyms "CHROMOPHORE (N1-METHYLATED HIS-TYR-GLY)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-10-18 _chem_comp.pdbx_modified_date 2024-09-27 _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 369.375 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X1B _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 8UB6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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 X1B C12 C2 C 0 1 Y N N N N N 3.463 27.041 18.450 6.008 -0.542 0.117 C2 X1B 1 X1B C4 C4 C 0 1 Y N N N N N 2.105 28.433 16.989 4.081 -1.907 -0.376 C4 X1B 2 X1B C5 C5 C 0 1 Y N N N N N 1.293 27.355 16.721 3.251 -0.867 -0.046 C5 X1B 3 X1B C7 C7 C 0 1 Y N N N N N 1.553 26.097 17.272 3.796 0.354 0.377 C7 X1B 4 X1B C8 C8 C 0 1 N N N N N N 0.545 25.108 16.883 2.915 1.469 0.731 C8 X1B 5 X1B CA2 C9 C 0 1 N N N Y N N 0.556 23.678 17.078 1.556 1.363 0.533 C9 X1B 6 X1B C10 C10 C 0 1 Y N N N N N 4.687 18.420 21.017 -5.068 -2.946 0.099 C10 X1B 7 X1B C2 C12 C 0 1 N N N Y N N -0.501 22.819 16.522 0.544 2.416 0.726 C12 X1B 8 X1B C1 C14 C 0 1 N N N Y N N 1.090 21.630 17.464 -0.397 0.542 0.046 C14 X1B 9 X1B CA1 C16 C 0 1 N N S Y N N 1.875 20.430 17.884 -1.464 -0.431 -0.382 C16 X1B 10 X1B CA3 C17 C 0 1 N N N Y N N -0.715 20.369 16.183 -1.947 2.490 0.444 C17 X1B 11 X1B C21 C21 C 0 1 Y N N N N N 3.502 19.581 19.574 -3.052 -2.158 0.423 C21 X1B 12 X1B C22 C22 C 0 1 N N N N N N 5.176 20.861 20.938 -4.960 -0.682 1.185 C22 X1B 13 X1B C23 C23 C 0 1 Y N N N N N 3.158 18.264 19.516 -2.968 -3.367 -0.164 C23 X1B 14 X1B C11 C1 C 0 1 Y N N N N N 3.221 28.319 17.850 5.461 -1.752 -0.296 C1 X1B 15 X1B C6 C6 C 0 1 Y N N N N N 2.645 25.946 18.142 5.188 0.504 0.454 C6 X1B 16 X1B O4 O3 O 0 1 N N N N N N 3.984 29.355 18.082 6.277 -2.786 -0.624 O3 X1B 17 X1B N11 N11 N 0 1 Y N N N N N 3.906 17.541 20.422 -4.215 -3.824 -0.352 N11 X1B 18 X1B N3 N13 N 0 1 N N N Y N N -0.121 21.548 16.805 -0.635 1.838 0.407 N13 X1B 19 X1B N2 N15 N 0 1 N N N Y N N 1.504 22.874 17.673 0.867 0.260 0.110 N15 X1B 20 X1B C20 C20 C 0 1 N N N N N N 3.003 20.785 18.831 -1.901 -1.271 0.821 C20 X1B 21 X1B N22 N22 N 0 1 Y N N N N N 4.479 19.654 20.535 -4.384 -1.889 0.587 N22 X1B 22 X1B O2 O25 O 0 1 N N N Y N N -1.495 23.096 15.883 0.731 3.562 1.095 O25 X1B 23 X1B N1 N N 0 1 N N N Y Y N 2.376 19.741 16.686 -0.931 -1.314 -1.428 N X1B 24 X1B C3 C C 0 1 N N N Y N Y -2.131 20.106 16.693 -2.231 3.121 -0.895 C X1B 25 X1B O3 O O 0 1 N N N Y N Y -2.813 19.313 16.037 -1.422 3.035 -1.788 O X1B 26 X1B H1 H1 H 0 1 N N N N N N 4.281 26.921 19.144 7.080 -0.427 0.176 H1 X1B 27 X1B H19 H2 H 0 1 N N N N N N 1.885 29.387 16.532 3.662 -2.849 -0.698 H2 X1B 28 X1B H3 H3 H 0 1 N N N N N N 0.439 27.483 16.073 2.180 -0.989 -0.107 H3 X1B 29 X1B H4 H4 H 0 1 N N N N N N -0.326 25.503 16.381 3.331 2.374 1.148 H4 X1B 30 X1B H5 H5 H 0 1 N N N N N N 5.401 18.178 21.791 -6.144 -3.046 0.080 H5 X1B 31 X1B HA1 H6 H 0 1 N N N Y N N 1.194 19.748 18.415 -2.321 0.118 -0.772 H6 X1B 32 X1B HA31 H7 H 0 1 N N N Y N N -0.088 19.494 16.409 -2.715 1.750 0.667 H7 X1B 33 X1B HA32 H8 H 0 1 N N N Y N N -0.752 20.522 15.094 -1.949 3.260 1.216 H8 X1B 34 X1B H9 H9 H 0 1 N N N N N N 5.904 20.619 21.726 -5.127 0.064 0.409 H9 X1B 35 X1B H10 H10 H 0 1 N N N N N N 5.703 21.287 20.071 -5.909 -0.930 1.662 H10 X1B 36 X1B H11 H11 H 0 1 N N N N N N 4.450 21.593 21.322 -4.273 -0.283 1.931 H11 X1B 37 X1B H12 H12 H 0 1 N N N N N N 2.410 17.847 18.858 -2.057 -3.879 -0.436 H12 X1B 38 X1B H13 H13 H 0 1 N N N N N N 2.856 24.980 18.576 5.614 1.442 0.779 H13 X1B 39 X1B H14 H14 H 0 1 N N N N N N 4.682 29.108 18.677 6.531 -2.806 -1.557 H14 X1B 40 X1B H15 H15 H 0 1 N N N N N N 3.833 21.216 18.252 -1.067 -1.887 1.156 H15 X1B 41 X1B H16 H16 H 0 1 N N N N N N 2.639 21.527 19.557 -2.214 -0.611 1.630 H16 X1B 42 X1B H H17 H 0 1 N N N Y Y N 2.903 18.936 16.960 -0.135 -1.835 -1.090 H17 X1B 43 X1B H2 H18 H 0 1 N Y N Y Y N 1.604 19.457 16.118 -1.646 -1.934 -1.777 H18 X1B 44 X1B OXT OXT O 0 1 N Y N Y N Y -2.449 20.509 17.933 -3.384 3.779 -1.095 OXT X1B 45 X1B HXT HXT H 0 1 N Y N Y N Y -3.259 20.092 18.204 -3.522 4.167 -1.971 HXT X1B 46 # 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 X1B O2 C2 DOUB N N 1 X1B O3 C3 DOUB N N 2 X1B CA3 C3 SING N N 3 X1B CA3 N3 SING N N 4 X1B C2 N3 SING N N 5 X1B C2 CA2 SING N N 6 X1B N1 CA1 SING N N 7 X1B C5 C4 DOUB Y N 8 X1B C5 C7 SING Y N 9 X1B N3 C1 SING N N 10 X1B C8 CA2 DOUB N Z 11 X1B C8 C7 SING N N 12 X1B C4 C11 SING Y N 13 X1B CA2 N2 SING N N 14 X1B C7 C6 DOUB Y N 15 X1B C1 N2 DOUB N N 16 X1B C1 CA1 SING N N 17 X1B C11 O4 SING N N 18 X1B C11 C12 DOUB Y N 19 X1B CA1 C20 SING N N 20 X1B C6 C12 SING Y N 21 X1B C20 C21 SING N N 22 X1B C23 C21 DOUB Y N 23 X1B C23 N11 SING Y N 24 X1B C21 N22 SING Y N 25 X1B N11 C10 DOUB Y N 26 X1B N22 C22 SING N N 27 X1B N22 C10 SING Y N 28 X1B C12 H1 SING N N 29 X1B C4 H19 SING N N 30 X1B C5 H3 SING N N 31 X1B C8 H4 SING N N 32 X1B C10 H5 SING N N 33 X1B CA1 HA1 SING N N 34 X1B CA3 HA31 SING N N 35 X1B CA3 HA32 SING N N 36 X1B C22 H9 SING N N 37 X1B C22 H10 SING N N 38 X1B C22 H11 SING N N 39 X1B C23 H12 SING N N 40 X1B C6 H13 SING N N 41 X1B O4 H14 SING N N 42 X1B C20 H15 SING N N 43 X1B C20 H16 SING N N 44 X1B N1 H SING N N 45 X1B N1 H2 SING N N 46 X1B C3 OXT SING N N 47 X1B OXT HXT SING N N 48 # 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 X1B SMILES ACDLabs 12.01 "O=C1C(/N=C(C(N)Cc2cncn2C)N1CC(O)=O)=C/c1ccc(O)cc1" X1B InChI InChI 1.06 "InChI=1S/C18H19N5O4/c1-22-10-20-8-12(22)7-14(19)17-21-15(18(27)23(17)9-16(25)26)6-11-2-4-13(24)5-3-11/h2-6,8,10,14,24H,7,9,19H2,1H3,(H,25,26)/b15-6-/t14-/m0/s1" X1B InChIKey InChI 1.06 XLAWDXOKBRPKIJ-WACFDSSMSA-N X1B SMILES_CANONICAL CACTVS 3.385 "Cn1cncc1C[C@H](N)C2=NC(=C/c3ccc(O)cc3)\C(=O)N2CC(O)=O" X1B SMILES CACTVS 3.385 "Cn1cncc1C[CH](N)C2=NC(=Cc3ccc(O)cc3)C(=O)N2CC(O)=O" X1B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cn1cncc1C[C@@H](C2=N/C(=C\c3ccc(cc3)O)/C(=O)N2CC(=O)O)N" X1B SMILES "OpenEye OEToolkits" 2.0.7 "Cn1cncc1CC(C2=NC(=Cc3ccc(cc3)O)C(=O)N2CC(=O)O)N" # 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 X1B "SYSTEMATIC NAME" ACDLabs 12.01 "{(4Z)-2-[(1S)-1-amino-2-(1-methyl-1H-imidazol-5-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid" X1B "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[(4~{Z})-2-[(1~{S})-1-azanyl-2-(3-methylimidazol-4-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id X1B _pdbx_chem_comp_synonyms.name "CHROMOPHORE (N1-METHYLATED HIS-TYR-GLY)" _pdbx_chem_comp_synonyms.provenance AUTHOR _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 X1B "Create component" 2023-10-18 RCSB X1B "Modify backbone" 2023-11-03 PDBE X1B "Initial release" 2023-11-29 RCSB X1B "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id X1B _pdbx_chem_comp_pcm.modified_residue_id "HIS, TYR, GLY" _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category Chromophore/chromophore-like _pdbx_chem_comp_pcm.position "Amino-acid side chain and backbone" _pdbx_chem_comp_pcm.polypeptide_position "Any 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 ? #