data_SD0
# 
_chem_comp.id                                    SD0 
_chem_comp.name                                  "(S)-5-amino-2-(4-(2-amino-2-carboxyethyl)phenyl)-2-hydroxy-5-(hydroxymethyl)-1,3,2-dioxaborinan-2-uide" 
_chem_comp.type                                  peptide-like 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C13 H20 B N2 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "(2~{S})-2-azanyl-3-[4-[5-azanyl-5-(hydroxymethyl)-2-$l^{3}-oxidanyl-1,3,2$l^{4}-dioxaborinan-2-yl]phenyl]propanal" 
_chem_comp.pdbx_formal_charge                    -1 
_chem_comp.pdbx_initial_date                     2023-08-30 
_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                        311.119 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     SD0 
_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        8QDH 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
SD0 N   N   N 0  1 N N N Y Y N -6.233  9.856  -21.320 -3.989 1.044  1.417  N   SD0 1  
SD0 CA  CA  C 0  1 N N S Y N N -7.173  10.251 -20.254 -4.358 0.642  0.053  CA  SD0 2  
SD0 C   C   C 0  1 N N N Y N Y -8.585  10.277 -20.929 -5.857 0.693  -0.097 C   SD0 3  
SD0 O   O   O 0  1 N N N Y N Y -9.578  9.814  -20.360 -6.563 0.669  0.883  O   SD0 4  
SD0 CB  CB  C 0  1 N N N N N N -6.940  11.598 -19.569 -3.867 -0.783 -0.209 CB  SD0 5  
SD0 CG  CG  C 0  1 Y N N N N N -7.982  11.775 -18.464 -2.361 -0.809 -0.180 CG  SD0 6  
SD0 CD1 CD1 C 0  1 Y N N N N N -9.197  12.408 -18.709 -1.643 -0.590 -1.341 CD1 SD0 7  
SD0 CD2 CD2 C 0  1 Y N N N N N -7.795  11.196 -17.220 -1.696 -1.046 1.008  CD2 SD0 8  
SD0 CE1 CE1 C 0  1 Y N N N N N -10.168 12.513 -17.711 -0.262 -0.614 -1.315 CE1 SD0 9  
SD0 CE2 CE2 C 0  1 Y N N N N N -8.770  11.286 -16.226 -0.314 -1.070 1.035  CE2 SD0 10 
SD0 CZ  CZ  C 0  1 Y N N N N N -9.966  11.960 -16.451 0.403  -0.856 -0.127 CZ  SD0 11 
SD0 B1  B1  B -1 1 N N N N N N -11.157 12.067 -15.307 1.959  -0.883 -0.097 B1  SD0 12 
SD0 C1  C1  C 0  1 N N N N N N -10.979 9.761  -14.222 3.819  -0.517 1.284  C1  SD0 13 
SD0 C2  C2  C 0  1 N N N N N N -12.329 9.350  -14.784 4.451  0.370  0.204  C2  SD0 14 
SD0 C3  C3  C 0  1 N N N N N N -12.385 7.826  -14.980 4.122  1.837  0.483  C3  SD0 15 
SD0 C4  C4  C 0  1 N N N N N N -12.480 10.060 -16.121 3.874  -0.038 -1.156 C4  SD0 16 
SD0 N2  N2  N 0  1 N N N N N N -13.442 9.794  -13.880 5.908  0.182  0.200  N2  SD0 17 
SD0 O1  O1  O 0  1 N N N N N N -10.858 11.204 -14.145 2.396  -0.478 1.132  O1  SD0 18 
SD0 O2  O2  O 0  1 N N N N N N -12.351 11.503 -15.957 2.445  -0.047 -1.062 O2  SD0 19 
SD0 O3  O3  O 0  1 N N N N N N -12.331 7.090  -13.769 4.713  2.659  -0.525 O3  SD0 20 
SD0 O5  O5  O 0  1 N N N N N N -11.418 13.422 -14.917 2.395  -2.156 -0.337 O5  SD0 21 
SD0 H   H1  H 0  1 N N N Y Y N -5.305  9.820  -20.950 -4.245 2.004  1.593  H1  SD0 22 
SD0 H2  H2  H 0  1 N Y N Y Y N -6.487  8.955  -21.671 -4.403 0.428  2.100  H2  SD0 23 
SD0 HA  HA  H 0  1 N N N Y N N -7.184  9.469  -19.481 -3.898 1.322  -0.663 HA  SD0 24 
SD0 HB2 HB2 H 0  1 N N N N N N -5.931  11.621 -19.133 -4.257 -1.449 0.561  HB2 SD0 25 
SD0 HB1 HB1 H 0  1 N N N N N N -7.040  12.409 -20.305 -4.218 -1.114 -1.187 HB1 SD0 26 
SD0 HD1 HD1 H 0  1 N N N N N N -9.392  12.824 -19.686 -2.162 -0.400 -2.269 HD1 SD0 27 
SD0 HD2 HD2 H 0  1 N N N N N N -6.877  10.665 -17.015 -2.257 -1.213 1.917  HD2 SD0 28 
SD0 HE1 HE1 H 0  1 N N N N N N -11.091 13.032 -17.921 0.299  -0.443 -2.222 HE1 SD0 29 
SD0 HE2 HE2 H 0  1 N N N N N N -8.593  10.825 -15.266 0.205  -1.255 1.964  HE2 SD0 30 
SD0 H11 H11 H 0  1 N N N N N N -10.867 9.338  -13.213 4.171  -1.542 1.168  H11 SD0 31 
SD0 H12 H12 H 0  1 N N N N N N -10.185 9.369  -14.874 4.092  -0.146 2.272  H12 SD0 32 
SD0 H31 H31 H 0  1 N N N N N N -13.324 7.577  -15.495 3.041  1.975  0.476  H31 SD0 33 
SD0 H32 H32 H 0  1 N N N N N N -11.532 7.526  -15.607 4.517  2.119  1.459  H32 SD0 34 
SD0 H41 H41 H 0  1 N N N N N N -13.471 9.832  -16.541 4.186  0.678  -1.915 H41 SD0 35 
SD0 H42 H42 H 0  1 N N N N N N -11.699 9.704  -16.809 4.229  -1.034 -1.421 H42 SD0 36 
SD0 H21 H21 H 0  1 N N N N N N -13.357 9.335  -12.995 6.345  0.757  -0.505 H21 SD0 37 
SD0 H23 H23 H 0  1 N N N N N N -13.390 10.784 -13.748 6.299  0.367  1.111  H23 SD0 38 
SD0 HO3 HO3 H 0  1 N N N N N N -12.370 6.160  -13.961 4.545  3.604  -0.411 HO3 SD0 39 
SD0 H4  H4  H 0  1 N N N N N N -12.106 13.437 -14.262 3.357  -2.249 -0.334 H4  SD0 40 
SD0 OXT O4  O 0  1 N Y N Y N Y -8.658  10.821 -22.146 -6.407 0.764  -1.319 O4  SD0 41 
SD0 HXT H3  H 0  1 N Y N Y N Y -9.555  10.782 -22.458 -7.372 0.794  -1.365 H3  SD0 42 
# 
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 
SD0 N   CA  SING N N 1  
SD0 C   O   DOUB N N 2  
SD0 C   CA  SING N N 3  
SD0 CA  CB  SING N N 4  
SD0 CB  CG  SING N N 5  
SD0 CD1 CG  DOUB Y N 6  
SD0 CD1 CE1 SING Y N 7  
SD0 CG  CD2 SING Y N 8  
SD0 CE1 CZ  DOUB Y N 9  
SD0 CD2 CE2 DOUB Y N 10 
SD0 CZ  CE2 SING Y N 11 
SD0 CZ  B1  SING N N 12 
SD0 C4  O2  SING N N 13 
SD0 C4  C2  SING N N 14 
SD0 O2  B1  SING N N 15 
SD0 B1  O5  SING N N 16 
SD0 B1  O1  SING N N 17 
SD0 C3  C2  SING N N 18 
SD0 C3  O3  SING N N 19 
SD0 C2  C1  SING N N 20 
SD0 C2  N2  SING N N 21 
SD0 C1  O1  SING N N 22 
SD0 N   H   SING N N 23 
SD0 N   H2  SING N N 24 
SD0 CA  HA  SING N N 25 
SD0 CB  HB2 SING N N 26 
SD0 CB  HB1 SING N N 27 
SD0 CD1 HD1 SING N N 28 
SD0 CD2 HD2 SING N N 29 
SD0 CE1 HE1 SING N N 30 
SD0 CE2 HE2 SING N N 31 
SD0 C1  H11 SING N N 32 
SD0 C1  H12 SING N N 33 
SD0 C3  H31 SING N N 34 
SD0 C3  H32 SING N N 35 
SD0 C4  H41 SING N N 36 
SD0 C4  H42 SING N N 37 
SD0 N2  H21 SING N N 38 
SD0 N2  H23 SING N N 39 
SD0 O3  HO3 SING N N 40 
SD0 O5  H4  SING N N 41 
SD0 C   OXT SING N N 42 
SD0 OXT HXT SING N N 43 
# 
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 
SD0 InChI            InChI                1.06  "InChI=1S/C13H20BN2O6/c15-11(12(18)19)5-9-1-3-10(4-2-9)14(20)21-7-13(16,6-17)8-22-14/h1-4,11,17,20H,5-8,15-16H2,(H,18,19)/q-1/t11-,13-,14+/m0/s1" 
SD0 InChIKey         InChI                1.06  ODSWUTOGRMJOFF-FPMFFAJLSA-N                                                                                                                       
SD0 SMILES_CANONICAL CACTVS               3.385 "N[C@@H](Cc1ccc(cc1)[B-]2(O)OCC(N)(CO)CO2)C(O)=O"                                                                                                 
SD0 SMILES           CACTVS               3.385 "N[CH](Cc1ccc(cc1)[B-]2(O)OCC(N)(CO)CO2)C(O)=O"                                                                                                   
SD0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[B-]1(OCC(CO1)(CO)N)(c2ccc(cc2)C[C@@H](C(=O)O)N)O"                                                                                               
SD0 SMILES           "OpenEye OEToolkits" 2.0.7 "[B-]1(OCC(CO1)(CO)N)(c2ccc(cc2)CC(C(=O)O)N)O"                                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           SD0 
_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})-2-azanyl-3-[4-[5-azanyl-5-(hydroxymethyl)-2-oxidanyl-1,3-dioxa-2-boranuidacyclohex-2-yl]phenyl]propanoic acid" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      SD0 
_pdbx_chem_comp_synonyms.name         "(2~{S})-2-azanyl-3-[4-[5-azanyl-5-(hydroxymethyl)-2-$l^{3}-oxidanyl-1,3,2$l^{4}-dioxaborinan-2-yl]phenyl]propanal" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_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 
SD0 "Create component" 2023-08-30 PDBE 
SD0 "Modify backbone"  2023-11-03 PDBE 
SD0 "Initial release"  2024-05-01 RCSB 
SD0 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            SD0 
_pdbx_chem_comp_pcm.modified_residue_id                PHE 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_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               ? 
_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      ? 
# 
