data_KY7
# 
_chem_comp.id                                    KY7 
_chem_comp.name                                  "{(4Z)-2-[(1S)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C14 H14 N4 O6 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "CHROMOPHORE (CYS-TYR-GLY)-3-NO2" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-01-23 
_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                        366.349 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     KY7 
_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        6NQR 
_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 
KY7 N1   N    N 0  1 N N N Y Y N -11.250 -24.660 0.247  2.155  -2.210 -1.206 N    KY7 1  
KY7 SG1  SG1  S 0  1 N N N N N N -11.230 -27.295 0.355  4.198  -3.566 0.721  SG1  KY7 2  
KY7 CB1  CB1  C 0  1 N N N N N N -12.615 -26.590 -0.512 3.059  -2.197 1.070  CB1  KY7 3  
KY7 CA1  CA1  C 0  1 N N S Y N N -12.734 -25.296 -0.023 2.839  -1.381 -0.205 CA1  KY7 4  
KY7 C1   C1   C 0  1 N N N Y N N -13.608 -24.504 -0.693 1.992  -0.175 0.111  C1   KY7 5  
KY7 N2   N2   N 0  1 N N N Y N N -14.851 -24.632 -0.553 0.696  -0.171 0.109  N2   KY7 6  
KY7 N3   N3   N 0  1 N N N Y N N -13.344 -23.501 -1.522 2.492  1.053  0.443  N3   KY7 7  
KY7 C2   C2   C 0  1 N N N Y N N -14.455 -22.960 -1.923 1.454  1.890  0.665  C2   KY7 8  
KY7 O2   O2   O 0  1 N N N Y N N -14.529 -22.040 -2.685 1.507  3.065  0.981  O2   KY7 9  
KY7 CA2  CA2  C 0  1 N N N Y N N -15.509 -23.739 -1.272 0.247  1.078  0.438  CA2  KY7 10 
KY7 CA3  CA3  C 0  1 N N N Y N N -12.049 -23.033 -1.906 3.911  1.402  0.541  CA3  KY7 11 
KY7 CB2  CB2  C 0  1 N N N N N N -16.899 -23.606 -1.349 -1.064 1.490  0.542  CB2  KY7 12 
KY7 CG2  CG2  C 0  1 Y N N N N N -17.816 -24.579 -0.670 -2.149 0.587  0.151  CG2  KY7 13 
KY7 CD1  CD1  C 0  1 Y N N N N N -19.197 -24.394 -0.642 -3.484 0.949  0.381  CD1  KY7 14 
KY7 CD2  CD2  C 0  1 Y N N N N N -17.304 -25.699 -0.052 -1.857 -0.641 -0.460 CD2  KY7 15 
KY7 CE1  CE1  C 0  1 Y N N N N N -20.030 -25.310 -0.013 -4.497 0.095  0.010  CE1  KY7 16 
KY7 CE2  CE2  C 0  1 Y N N N N N -18.137 -26.597 0.560  -2.871 -1.480 -0.824 CE2  KY7 17 
KY7 CZ   CZ   C 0  1 Y N N N N N -19.478 -26.406 0.584  -4.195 -1.123 -0.590 CZ   KY7 18 
KY7 OH   OH   O 0  1 N N N N N N -20.252 -27.309 1.200  -5.196 -1.964 -0.954 OH   KY7 19 
KY7 C3   C    C 0  1 N N N Y N Y -11.921 -22.208 -3.377 4.388  1.944  -0.782 C    KY7 20 
KY7 O3   O    O 0  1 N N N Y N Y -11.033 -21.548 -2.985 3.621  2.030  -1.711 O    KY7 21 
KY7 OB   OB   O 0  1 N N N N N N -22.294 -26.025 0.006  -6.173 1.538  0.776  OB   KY7 22 
KY7 NA   NA   N 1  1 N N N N N N -21.480 -25.107 -0.033 -5.908 0.471  0.250  NA   KY7 23 
KY7 OA   OA   O -1 1 N N N N N N -21.847 -23.979 -0.159 -6.805 -0.285 -0.078 OA   KY7 24 
KY7 H    HN1  H 0  1 N N N Y Y N -10.689 -25.322 0.744  2.682  -3.047 -1.403 HN1  KY7 25 
KY7 H2   HN2  H 0  1 N Y N Y Y N -10.815 -24.445 -0.628 1.217  -2.435 -0.910 HN2  KY7 26 
KY7 HG1  HG1  H 0  1 N N N N N N -11.178 -28.493 -0.147 4.297  -4.187 1.911  HG1  KY7 27 
KY7 HB11 HB11 H 0  0 N N N N N N -13.530 -27.165 -0.308 2.105  -2.597 1.414  HB11 KY7 28 
KY7 HB12 HB12 H 0  0 N N N N N N -12.425 -26.576 -1.595 3.485  -1.558 1.842  HB12 KY7 29 
KY7 HA1  HA1  H 0  1 N N N Y N N -13.146 -25.404 0.991  3.801  -1.055 -0.599 HA1  KY7 30 
KY7 HA31 HA31 H 0  0 N N N Y N N -11.385 -23.908 -1.960 4.047  2.158  1.314  HA31 KY7 31 
KY7 HA32 HA32 H 0  0 N N N Y N N -11.696 -22.354 -1.116 4.487  0.513  0.798  HA32 KY7 32 
KY7 HB2  HB2  H 0  1 N N N N N N -17.321 -22.785 -1.909 -1.291 2.479  0.913  HB2  KY7 33 
KY7 HD1  HD1  H 0  1 N N N N N N -19.626 -23.524 -1.117 -3.716 1.895  0.848  HD1  KY7 34 
KY7 HD2  HD2  H 0  1 N N N N N N -16.238 -25.870 -0.050 -0.831 -0.922 -0.643 HD2  KY7 35 
KY7 HE1  HE1  H 0  1 N N N N N N -17.718 -27.473 1.032  -2.644 -2.425 -1.294 HE1  KY7 36 
KY7 H1   H1   H 0  1 N N N N N N -21.163 -27.147 0.983  -5.519 -1.824 -1.855 H1   KY7 37 
KY7 OXT  OXT  O 0  1 N Y N Y N Y -11.780 -22.770 -5.469 5.665  2.332  -0.927 OXT  KY7 38 
KY7 HXT  HXT  H 0  1 N Y N Y N Y -10.987 -22.405 -5.843 5.924  2.673  -1.794 HXT  KY7 39 
# 
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 
KY7 C3  O3   DOUB N N 1  
KY7 C3  CA3  SING N N 2  
KY7 O2  C2   DOUB N N 3  
KY7 C2  N3   SING N N 4  
KY7 C2  CA2  SING N N 5  
KY7 CA3 N3   SING N N 6  
KY7 N3  C1   SING N N 7  
KY7 CB2 CA2  DOUB N Z 8  
KY7 CB2 CG2  SING N N 9  
KY7 CA2 N2   SING N N 10 
KY7 C1  N2   DOUB N N 11 
KY7 C1  CA1  SING N N 12 
KY7 CG2 CD1  DOUB Y N 13 
KY7 CG2 CD2  SING Y N 14 
KY7 CD1 CE1  SING Y N 15 
KY7 CB1 CA1  SING N N 16 
KY7 CB1 SG1  SING N N 17 
KY7 OA  NA   SING N N 18 
KY7 CD2 CE2  DOUB Y N 19 
KY7 NA  CE1  SING N N 20 
KY7 NA  OB   DOUB N N 21 
KY7 CA1 N1   SING N N 22 
KY7 CE1 CZ   DOUB Y N 23 
KY7 CE2 CZ   SING Y N 24 
KY7 CZ  OH   SING N N 25 
KY7 N1  H    SING N N 26 
KY7 N1  H2   SING N N 27 
KY7 SG1 HG1  SING N N 28 
KY7 CB1 HB11 SING N N 29 
KY7 CB1 HB12 SING N N 30 
KY7 CA1 HA1  SING N N 31 
KY7 CA3 HA31 SING N N 32 
KY7 CA3 HA32 SING N N 33 
KY7 CB2 HB2  SING N N 34 
KY7 CD1 HD1  SING N N 35 
KY7 CD2 HD2  SING N N 36 
KY7 CE2 HE1  SING N N 37 
KY7 OH  H1   SING N N 38 
KY7 C3  OXT  SING N N 39 
KY7 OXT HXT  SING N N 40 
# 
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 
KY7 SMILES           ACDLabs              12.01 "NC(CS)C1=N/C(C(N1CC(=O)O)=O)=C\c2cc(c(cc2)O)[N+](=O)[O-]"                                                                                      
KY7 InChI            InChI                1.03  "InChI=1S/C14H14N4O6S/c15-8(6-25)13-16-9(14(22)17(13)5-12(20)21)3-7-1-2-11(19)10(4-7)18(23)24/h1-4,8,19,25H,5-6,15H2,(H,20,21)/b9-3-/t8-/m1/s1" 
KY7 InChIKey         InChI                1.03  KQMHCDZTMFZTFX-MMEMACFNSA-N                                                                                                                     
KY7 SMILES_CANONICAL CACTVS               3.385 "N[C@H](CS)C1=N\C(=C/c2ccc(O)c(c2)[N+]([O-])=O)C(=O)N1CC(O)=O"                                                                                  
KY7 SMILES           CACTVS               3.385 "N[CH](CS)C1=NC(=Cc2ccc(O)c(c2)[N+]([O-])=O)C(=O)N1CC(O)=O"                                                                                     
KY7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1/C=C\2/C(=O)N(C(=N2)[C@@H](CS)N)CC(=O)O)[N+](=O)[O-])O"                                                                              
KY7 SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C=C2C(=O)N(C(=N2)C(CS)N)CC(=O)O)[N+](=O)[O-])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 
KY7 "SYSTEMATIC NAME" ACDLabs              12.01 "{(4Z)-2-[(1S)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid"          
KY7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[(4~{Z})-2-[(1~{S})-1-azanyl-2-sulfanyl-ethyl]-4-[(3-nitro-4-oxidanyl-phenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic 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 
KY7 "Create component" 2019-01-23 RCSB 
KY7 "Initial release"  2019-06-12 RCSB 
KY7 "Modify synonyms"  2021-03-01 PDBE 
KY7 "Modify backbone"  2023-11-03 PDBE 
KY7 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      KY7 
_pdbx_chem_comp_synonyms.name         "CHROMOPHORE (CYS-TYR-GLY)-3-NO2" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            KY7 
_pdbx_chem_comp_pcm.modified_residue_id                "CYS, 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      ? 
# 
