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      ? 
# 
