data_YDB
# 
_chem_comp.id                                    YDB 
_chem_comp.name                                  "1-[(2R)-2-{2-[(5-amino-1,3,4-thiadiazol-2-yl)sulfanyl]acetamido}-2-boronoethyl]-1H-1,2,3-triazole-4-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H12 B N7 O5 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-25 
_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                        373.176 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YDB 
_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        8FQW 
_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 
YDB N1  N1  N 0 1 N N N N N N -5.946 1.810  -63.373 8.722  -0.426 0.701  N1  YDB 1  
YDB C1  C1  C 0 1 Y N N N N N -5.711 1.476  -64.761 7.346  -0.336 0.521  C1  YDB 2  
YDB N2  N2  N 0 1 Y N N N N N -6.001 0.307  -65.307 6.507  0.152  1.379  N2  YDB 3  
YDB N3  N3  N 0 1 Y N N N N N -5.690 0.187  -66.680 5.185  0.142  0.990  N3  YDB 4  
YDB C2  C2  C 0 1 Y N N N N N -5.134 1.336  -67.182 4.950  -0.354 -0.184 C2  YDB 5  
YDB S1  S1  S 0 1 N N N N N N -4.607 1.585  -68.896 3.361  -0.492 -0.934 S1  YDB 6  
YDB C3  C3  C 0 1 N N N N N N -5.397 0.262  -69.844 2.254  0.206  0.322  C3  YDB 7  
YDB C4  C4  C 0 1 N N N N N N -4.808 0.330  -71.240 0.834  0.159  -0.178 C4  YDB 8  
YDB O1  O1  O 0 1 N N N N N N -4.031 1.187  -71.510 0.592  -0.301 -1.274 O1  YDB 9  
YDB N4  N4  N 0 1 N N N N N N -5.211 -0.669 -72.206 -0.168 0.627  0.592  N4  YDB 10 
YDB C5  C5  C 0 1 N N R N N N -4.694 -0.650 -73.560 -1.549 0.581  0.106  C5  YDB 11 
YDB C6  C6  C 0 1 N N N N N N -3.278 -1.211 -73.665 -2.465 0.067  1.219  C6  YDB 12 
YDB N5  N5  N 0 1 Y N N N N N -3.048 -2.283 -72.719 -3.846 0.021  0.733  N5  YDB 13 
YDB C7  C7  C 0 1 Y N N N N N -3.031 -3.649 -73.008 -4.666 -1.049 0.743  C7  YDB 14 
YDB C8  C8  C 0 1 Y N N N N N -2.767 -4.325 -71.825 -5.852 -0.643 0.198  C8  YDB 15 
YDB C9  C9  C 0 1 N N N N N N -2.649 -5.840 -71.658 -7.046 -1.487 0.008  C9  YDB 16 
YDB O2  O2  O 0 1 N N N N N N -2.432 -6.565 -72.674 -7.027 -2.652 0.350  O2  YDB 17 
YDB O3  O3  O 0 1 N N N N N N -2.756 -6.351 -70.504 -8.159 -0.964 -0.544 O3  YDB 18 
YDB N6  N6  N 0 1 Y N N N N N -2.615 -3.394 -70.817 -5.745 0.655  -0.136 N6  YDB 19 
YDB N7  N7  N 0 1 Y N N N N N -2.789 -2.122 -71.377 -4.571 1.083  0.173  N7  YDB 20 
YDB B1  B1  B 0 1 N N N N N N -5.695 -1.467 -74.459 -2.002 2.022  -0.321 B1  YDB 21 
YDB O5  O4  O 0 1 N N N N N N -6.351 -2.369 -73.693 -2.959 2.188  -1.357 O5  YDB 22 
YDB O6  O5  O 0 1 N N N N N N -5.027 -2.111 -75.443 -1.455 3.160  0.329  O6  YDB 23 
YDB S2  S2  S 0 1 Y N N N N N -5.002 2.602  -65.916 6.470  -0.861 -0.913 S2  YDB 24 
YDB H1  H1  H 0 1 N N N N N N -5.647 2.749  -63.200 9.125  -0.108 1.525  H1  YDB 25 
YDB H2  H2  H 0 1 N N N N N N -6.922 1.729  -63.171 9.278  -0.810 0.006  H2  YDB 26 
YDB H3  H3  H 0 1 N N N N N N -6.485 0.418  -69.882 2.336  -0.375 1.241  H3  YDB 27 
YDB H4  H4  H 0 1 N N N N N N -5.182 -0.715 -69.387 2.536  1.240  0.520  H4  YDB 28 
YDB H5  H5  H 0 1 N N N N N N -5.856 -1.384 -71.935 0.026  0.994  1.469  H5  YDB 29 
YDB H6  H6  H 0 1 N N N N N N -4.682 0.386  -73.929 -1.610 -0.088 -0.752 H6  YDB 30 
YDB H7  H7  H 0 1 N N N N N N -3.123 -1.597 -74.683 -2.150 -0.934 1.515  H7  YDB 31 
YDB H8  H8  H 0 1 N N N N N N -2.560 -0.402 -73.466 -2.404 0.736  2.077  H8  YDB 32 
YDB H9  H9  H 0 1 N N N N N N -3.194 -4.098 -73.977 -4.431 -2.036 1.111  H9  YDB 33 
YDB H10 H10 H 0 1 N N N N N N -2.649 -7.293 -70.563 -8.916 -1.556 -0.648 H10 YDB 34 
YDB H11 H11 H 0 1 N N N N N N -6.820 -1.917 -73.002 -3.273 1.357  -1.738 H11 YDB 35 
YDB H12 H12 H 0 1 N N N N N N -4.566 -1.478 -75.981 -0.812 2.947  1.020  H12 YDB 36 
# 
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 
YDB O6 B1  SING N N 1  
YDB B1 O5  SING N N 2  
YDB B1 C5  SING N N 3  
YDB C6 C5  SING N N 4  
YDB C6 N5  SING N N 5  
YDB C5 N4  SING N N 6  
YDB C7 N5  SING Y N 7  
YDB C7 C8  DOUB Y N 8  
YDB N5 N7  SING Y N 9  
YDB O2 C9  DOUB N N 10 
YDB N4 C4  SING N N 11 
YDB C8 C9  SING N N 12 
YDB C8 N6  SING Y N 13 
YDB C9 O3  SING N N 14 
YDB O1 C4  DOUB N N 15 
YDB N7 N6  DOUB Y N 16 
YDB C4 C3  SING N N 17 
YDB C3 S1  SING N N 18 
YDB S1 C2  SING N N 19 
YDB C2 N3  DOUB Y N 20 
YDB C2 S2  SING Y N 21 
YDB N3 N2  SING Y N 22 
YDB S2 C1  SING Y N 23 
YDB N2 C1  DOUB Y N 24 
YDB C1 N1  SING N N 25 
YDB N1 H1  SING N N 26 
YDB N1 H2  SING N N 27 
YDB C3 H3  SING N N 28 
YDB C3 H4  SING N N 29 
YDB N4 H5  SING N N 30 
YDB C5 H6  SING N N 31 
YDB C6 H7  SING N N 32 
YDB C6 H8  SING N N 33 
YDB C7 H9  SING N N 34 
YDB O3 H10 SING N N 35 
YDB O5 H11 SING N N 36 
YDB O6 H12 SING N N 37 
# 
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 
YDB SMILES           ACDLabs              12.01 "O=C(CSc1nnc(N)s1)NC(Cn1cc(nn1)C(=O)O)B(O)O"                                                                                                          
YDB InChI            InChI                1.06  "InChI=1S/C9H12BN7O5S2/c11-8-14-15-9(24-8)23-3-6(18)12-5(10(21)22)2-17-1-4(7(19)20)13-16-17/h1,5,21-22H,2-3H2,(H2,11,14)(H,12,18)(H,19,20)/t5-/m0/s1" 
YDB InChIKey         InChI                1.06  JADCONPWNUDUNV-YFKPBYRVSA-N                                                                                                                           
YDB SMILES_CANONICAL CACTVS               3.385 "Nc1sc(SCC(=O)N[C@@H](Cn2cc(nn2)C(O)=O)B(O)O)nn1"                                                                                                     
YDB SMILES           CACTVS               3.385 "Nc1sc(SCC(=O)N[CH](Cn2cc(nn2)C(O)=O)B(O)O)nn1"                                                                                                       
YDB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "B([C@H](Cn1cc(nn1)C(=O)O)NC(=O)CSc2nnc(s2)N)(O)O"                                                                                                    
YDB SMILES           "OpenEye OEToolkits" 2.0.7 "B(C(Cn1cc(nn1)C(=O)O)NC(=O)CSc2nnc(s2)N)(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 
YDB "SYSTEMATIC NAME" ACDLabs              12.01 "1-[(2R)-2-{2-[(5-amino-1,3,4-thiadiazol-2-yl)sulfanyl]acetamido}-2-boronoethyl]-1H-1,2,3-triazole-4-carboxylic acid"                  
YDB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[(2~{R})-2-[2-[(5-azanyl-1,3,4-thiadiazol-2-yl)sulfanyl]ethanoylamino]-2-(dihydroxyboranyl)ethyl]-1,2,3-triazole-4-carboxylic 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 
YDB "Create component" 2023-01-25 RCSB 
YDB "Initial release"  2023-07-05 RCSB 
YDB "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YDB 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               B1 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
