data_A1D9A
# 
_chem_comp.id                                    A1D9A 
_chem_comp.name                                  "(2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H26 Cl2 N4 O3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         JR14a 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-06-17 
_chem_comp.pdbx_modified_date                    2025-04-18 
_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                        533.470 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D9A 
_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        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_chem_comp.pdbx_pcm                              ? 
# 
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 
A1D9A N1  N1  N  0 1 N N N N N N ? ? ? 2.801  1.573  0.284  N1  A1D9A 1  
A1D9A N3  N2  N  0 1 N N N N N N ? ? ? 3.769  -3.344 -2.458 N3  A1D9A 2  
A1D9A C4  C1  C  0 1 Y N N N N N ? ? ? -1.533 0.745  1.676  C4  A1D9A 3  
A1D9A C5  C2  C  0 1 Y N N N N N ? ? ? -1.173 1.347  2.815  C5  A1D9A 4  
A1D9A C6  C3  C  0 1 N N N N N N ? ? ? -2.906 0.186  1.403  C6  A1D9A 5  
A1D9A C7  C4  C  0 1 Y N N N N N ? ? ? -3.503 0.883  0.207  C7  A1D9A 6  
A1D9A C8  C5  C  0 1 Y N N N N N ? ? ? -2.865 0.825  -1.017 C8  A1D9A 7  
A1D9A C10 C6  C  0 1 Y N N N N N ? ? ? -4.600 2.162  -1.985 C10 A1D9A 8  
A1D9A C13 C7  C  0 1 Y N N N N N ? ? ? -2.800 -1.291 1.122  C13 A1D9A 9  
A1D9A C15 C8  C  0 1 Y N N N N N ? ? ? -3.500 -3.539 1.555  C15 A1D9A 10 
A1D9A C17 C9  C  0 1 Y N N N N N ? ? ? -1.814 -3.105 -0.090 C17 A1D9A 11 
A1D9A C20 C10 C  0 1 N N S N N N ? ? ? 4.201  1.927  0.039  C20 A1D9A 12 
A1D9A C21 C11 C  0 1 N N N N N N ? ? ? 4.790  0.982  -1.011 C21 A1D9A 13 
A1D9A C22 C12 C  0 1 N N N N N N ? ? ? 4.824  -0.442 -0.453 C22 A1D9A 14 
A1D9A C24 C13 C  0 1 N N N N N N ? ? ? 4.695  -3.676 -1.498 C24 A1D9A 15 
A1D9A CL1 CL1 CL 0 0 N N N N N N ? ? ? -5.288 2.965  -3.362 CL1 A1D9A 16 
A1D9A CL2 CL2 CL 0 0 N N N N N N ? ? ? -2.485 -5.701 0.281  CL2 A1D9A 17 
A1D9A C1  C14 C  0 1 N N N N N N ? ? ? 0.729  2.491  4.045  C1  A1D9A 18 
A1D9A O1  O1  O  0 1 N N N N N N ? ? ? 2.865  2.459  2.321  O1  A1D9A 19 
A1D9A S1  S1  S  0 1 Y N N N N N ? ? ? -0.234 0.702  0.571  S1  A1D9A 20 
A1D9A C2  C15 C  0 1 Y N N N N N ? ? ? 0.128  1.790  2.854  C2  A1D9A 21 
A1D9A N2  N3  N  0 1 N N N N N N ? ? ? 5.445  -2.750 -0.969 N2  A1D9A 22 
A1D9A O2  O2  O  0 1 N N N N N N ? ? ? 3.271  3.996  -0.600 O2  A1D9A 23 
A1D9A C3  C16 C  0 1 Y N N N N N ? ? ? 0.822  1.530  1.706  C3  A1D9A 24 
A1D9A O3  O3  O  0 1 N N N N N N ? ? ? 5.473  3.889  -0.754 O3  A1D9A 25 
A1D9A N4  N4  N  0 1 N N N N N N ? ? ? 4.829  -4.983 -1.095 N4  A1D9A 26 
A1D9A C9  C17 C  0 1 Y N N N N N ? ? ? -3.412 1.464  -2.114 C9  A1D9A 27 
A1D9A C11 C18 C  0 1 Y N N N N N ? ? ? -5.242 2.215  -0.761 C11 A1D9A 28 
A1D9A C12 C19 C  0 1 Y N N N N N ? ? ? -4.693 1.576  0.335  C12 A1D9A 29 
A1D9A C14 C20 C  0 1 Y N N N N N ? ? ? -3.596 -2.184 1.813  C14 A1D9A 30 
A1D9A C16 C21 C  0 1 Y N N N N N ? ? ? -2.606 -4.000 0.605  C16 A1D9A 31 
A1D9A C18 C22 C  0 1 Y N N N N N ? ? ? -1.911 -1.751 0.169  C18 A1D9A 32 
A1D9A C19 C23 C  0 1 N N N N N N ? ? ? 2.224  1.884  1.461  C19 A1D9A 33 
A1D9A C23 C24 C  0 1 N N N N N N ? ? ? 5.413  -1.387 -1.503 C23 A1D9A 34 
A1D9A C25 C25 C  0 1 N N N N N N ? ? ? 4.281  3.346  -0.462 C25 A1D9A 35 
A1D9A H1  H1  H  0 1 N N N N N N ? ? ? 2.289  1.119  -0.403 H1  A1D9A 36 
A1D9A H2  H2  H  0 1 N N N N N N ? ? ? 3.287  -4.042 -2.929 H2  A1D9A 37 
A1D9A H3  H3  H  0 1 N N N N N N ? ? ? 3.598  -2.412 -2.665 H3  A1D9A 38 
A1D9A H4  H4  H  0 1 N N N N N N ? ? ? -1.854 1.476  3.643  H4  A1D9A 39 
A1D9A H5  H5  H  0 1 N N N N N N ? ? ? -3.543 0.346  2.272  H5  A1D9A 40 
A1D9A H6  H6  H  0 1 N N N N N N ? ? ? -1.938 0.281  -1.117 H6  A1D9A 41 
A1D9A H7  H7  H  0 1 N N N N N N ? ? ? -4.122 -4.237 2.096  H7  A1D9A 42 
A1D9A H8  H8  H  0 1 N N N N N N ? ? ? -1.119 -3.464 -0.835 H8  A1D9A 43 
A1D9A H9  H9  H  0 1 N N N N N N ? ? ? 4.767  1.837  0.967  H9  A1D9A 44 
A1D9A H10 H10 H  0 1 N N N N N N ? ? ? 4.172  1.006  -1.908 H10 A1D9A 45 
A1D9A H11 H11 H  0 1 N N N N N N ? ? ? 5.803  1.300  -1.258 H11 A1D9A 46 
A1D9A H12 H12 H  0 1 N N N N N N ? ? ? 5.442  -0.466 0.445  H12 A1D9A 47 
A1D9A H13 H13 H  0 1 N N N N N N ? ? ? 3.811  -0.760 -0.206 H13 A1D9A 48 
A1D9A H14 H14 H  0 1 N N N N N N ? ? ? 1.170  1.755  4.716  H14 A1D9A 49 
A1D9A H15 H15 H  0 1 N N N N N N ? ? ? 1.500  3.184  3.708  H15 A1D9A 50 
A1D9A H16 H16 H  0 1 N N N N N N ? ? ? -0.049 3.043  4.573  H16 A1D9A 51 
A1D9A H18 H18 H  0 1 N N N N N N ? ? ? 5.473  4.802  -1.072 H18 A1D9A 52 
A1D9A H19 H19 H  0 1 N N N N N N ? ? ? 4.271  -5.672 -1.489 H19 A1D9A 53 
A1D9A H20 H20 H  0 1 N N N N N N ? ? ? 5.483  -5.218 -0.418 H20 A1D9A 54 
A1D9A H21 H21 H  0 1 N N N N N N ? ? ? -2.913 1.419  -3.070 H21 A1D9A 55 
A1D9A H22 H22 H  0 1 N N N N N N ? ? ? -6.169 2.760  -0.660 H22 A1D9A 56 
A1D9A H23 H23 H  0 1 N N N N N N ? ? ? -5.194 1.617  1.291  H23 A1D9A 57 
A1D9A H24 H24 H  0 1 N N N N N N ? ? ? -4.294 -1.824 2.555  H24 A1D9A 58 
A1D9A H25 H25 H  0 1 N N N N N N ? ? ? -1.291 -1.052 -0.374 H25 A1D9A 59 
A1D9A H26 H26 H  0 1 N N N N N N ? ? ? 4.795  -1.363 -2.400 H26 A1D9A 60 
A1D9A H27 H27 H  0 1 N N N N N N ? ? ? 6.426  -1.069 -1.750 H27 A1D9A 61 
# 
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 
A1D9A CL1 C10 SING N N 1  
A1D9A C10 C9  DOUB Y N 2  
A1D9A C10 C11 SING Y N 3  
A1D9A C9  C8  SING Y N 4  
A1D9A C11 C12 DOUB Y N 5  
A1D9A C17 C18 DOUB Y N 6  
A1D9A C17 C16 SING Y N 7  
A1D9A CL2 C16 SING N N 8  
A1D9A C18 C13 SING Y N 9  
A1D9A C8  C7  DOUB Y N 10 
A1D9A C12 C7  SING Y N 11 
A1D9A C16 C15 DOUB Y N 12 
A1D9A C7  C6  SING N N 13 
A1D9A C13 C6  SING N N 14 
A1D9A C13 C14 DOUB Y N 15 
A1D9A C15 C14 SING Y N 16 
A1D9A C6  C4  SING N N 17 
A1D9A C4  S1  SING Y N 18 
A1D9A C4  C5  DOUB Y N 19 
A1D9A S1  C3  SING Y N 20 
A1D9A O2  C25 DOUB N N 21 
A1D9A C5  C2  SING Y N 22 
A1D9A C25 O3  SING N N 23 
A1D9A C25 C20 SING N N 24 
A1D9A C3  C2  DOUB Y N 25 
A1D9A C3  C19 SING N N 26 
A1D9A N1  C19 SING N N 27 
A1D9A N1  C20 SING N N 28 
A1D9A C2  C1  SING N N 29 
A1D9A C19 O1  DOUB N N 30 
A1D9A C20 C21 SING N N 31 
A1D9A C22 C23 SING N N 32 
A1D9A C22 C21 SING N N 33 
A1D9A C23 N2  SING N N 34 
A1D9A N2  C24 DOUB N N 35 
A1D9A C24 N3  SING N N 36 
A1D9A C24 N4  SING N N 37 
A1D9A N1  H1  SING N N 38 
A1D9A N3  H2  SING N N 39 
A1D9A N3  H3  SING N N 40 
A1D9A C5  H4  SING N N 41 
A1D9A C6  H5  SING N N 42 
A1D9A C8  H6  SING N N 43 
A1D9A C15 H7  SING N N 44 
A1D9A C17 H8  SING N N 45 
A1D9A C20 H9  SING N N 46 
A1D9A C21 H10 SING N N 47 
A1D9A C21 H11 SING N N 48 
A1D9A C22 H12 SING N N 49 
A1D9A C22 H13 SING N N 50 
A1D9A C1  H14 SING N N 51 
A1D9A C1  H15 SING N N 52 
A1D9A C1  H16 SING N N 53 
A1D9A O3  H18 SING N N 54 
A1D9A N4  H19 SING N N 55 
A1D9A N4  H20 SING N N 56 
A1D9A C9  H21 SING N N 57 
A1D9A C11 H22 SING N N 58 
A1D9A C12 H23 SING N N 59 
A1D9A C14 H24 SING N N 60 
A1D9A C18 H25 SING N N 61 
A1D9A C23 H26 SING N N 62 
A1D9A C23 H27 SING N N 63 
# 
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 
A1D9A InChI            InChI                1.06  "InChI=1S/C25H26Cl2N4O3S/c1-14-13-20(21(15-4-8-17(26)9-5-15)16-6-10-18(27)11-7-16)35-22(14)23(32)31-19(24(33)34)3-2-12-30-25(28)29/h4-11,13,19,21H,2-3,12H2,1H3,(H,31,32)(H,33,34)(H4,28,29,30)/t19-/m0/s1" 
A1D9A InChIKey         InChI                1.06  OHRIKWUZKGNQKQ-IBGZPJMESA-N                                                                                                                                                                                 
A1D9A SMILES_CANONICAL CACTVS               3.385 "Cc1cc(sc1C(=O)N[C@@H](CCCN=C(N)N)C(O)=O)C(c2ccc(Cl)cc2)c3ccc(Cl)cc3"                                                                                                                                       
A1D9A SMILES           CACTVS               3.385 "Cc1cc(sc1C(=O)N[CH](CCCN=C(N)N)C(O)=O)C(c2ccc(Cl)cc2)c3ccc(Cl)cc3"                                                                                                                                         
A1D9A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc(sc1C(=O)N[C@@H](CCCN=C(N)N)C(=O)O)C(c2ccc(cc2)Cl)c3ccc(cc3)Cl"                                                                                                                                       
A1D9A SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1cc(sc1C(=O)NC(CCCN=C(N)N)C(=O)O)C(c2ccc(cc2)Cl)c3ccc(cc3)Cl"                                                                                                                                            
# 
_pdbx_chem_comp_identifier.comp_id           A1D9A 
_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        "(2~{S})-5-[bis(azanyl)methylideneamino]-2-[[5-[bis(4-chlorophenyl)methyl]-3-methyl-thiophen-2-yl]carbonylamino]pentanoic 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 
A1D9A "Create component"   2024-06-17 PDBC 
A1D9A "Modify synonyms"    2024-07-19 PDBC 
A1D9A "Modify coordinates" 2025-04-14 RCSB 
A1D9A "Initial release"    2025-04-23 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1D9A 
_pdbx_chem_comp_synonyms.name         JR14a 
_pdbx_chem_comp_synonyms.provenance   PUBCHEM 
_pdbx_chem_comp_synonyms.type         ? 
# 
