data_SBD
# 
_chem_comp.id                                    SBD 
_chem_comp.name                                  "D-NAPHTHYL-1-ACETAMIDO BORONIC ACID ALANINE" 
_chem_comp.type                                  "D-PEPTIDE LINKING" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C17 H22 B N2 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    -1 
_chem_comp.pdbx_initial_date                     1999-07-08 
_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                        361.177 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     SBD 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   Y 
_chem_comp.pdbx_model_coordinates_db_code        3VSB 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              N 
# 
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 
SBD N    N    N 0  1 N N N N N N 16.854 4.064  26.569 3.846  0.566  1.786  N    SBD 1  
SBD CA   CA   C 0  1 N N S N N N 17.845 3.019  26.288 3.696  0.943  0.374  CA   SBD 2  
SBD CB   CB   C 0  1 N N N N N N 18.296 3.103  24.828 2.212  0.939  0.001  CB   SBD 3  
SBD O3   O3   O 0  1 N N N N N N 17.361 2.526  23.943 1.700  -0.392 0.093  O3   SBD 4  
SBD C    C    C 0  1 N N N N N N 19.056 3.238  27.184 4.264  2.322  0.158  C    SBD 5  
SBD O    O    O 0  1 N N N N N N 19.813 2.307  27.456 4.608  2.720  -1.077 O    SBD 6  
SBD OXT  OXT  O 0  1 N Y N N N N 19.283 4.505  27.532 4.411  3.068  1.097  OXT  SBD 7  
SBD N13  N13  N 0  1 N N N N N N 14.970 2.420  21.506 0.565  -2.731 -0.935 N13  SBD 8  
SBD C12  C12  C 0  1 N N S N N N 15.365 2.779  22.857 -0.259 -1.794 -0.167 C12  SBD 9  
SBD C11  C11  C 0  1 N N N N N N 14.180 3.276  23.707 -1.675 -1.766 -0.747 C11  SBD 10 
SBD C1   C1   C 0  1 Y N N N N N 13.012 2.308  23.599 -2.558 -0.912 0.125  C1   SBD 11 
SBD C10  C10  C 0  1 Y N N N N N 12.037 2.457  22.596 -2.936 0.374  -0.297 C10  SBD 12 
SBD C5   C5   C 0  1 Y N N N N N 10.925 1.578  22.523 -3.771 1.161  0.534  C5   SBD 13 
SBD C2   C2   C 0  1 Y N N N N N 12.877 1.271  24.522 -2.990 -1.379 1.328  C2   SBD 14 
SBD C3   C3   C 0  1 Y N N N N N 11.784 0.411  24.443 -3.808 -0.604 2.148  C3   SBD 15 
SBD C4   C4   C 0  1 Y N N N N N 10.805 0.548  23.458 -4.197 0.644  1.769  C4   SBD 16 
SBD O1   O1   O 0  1 N N N N N N 17.715 3.830  21.994 0.260  0.145  -1.525 O1   SBD 17 
SBD O2   O2   O 0  1 N N N N N N 16.585 4.876  24.077 -0.279 0.501  0.612  O2   SBD 18 
SBD B    B    B -1 1 N N N N N N 16.642 3.609  23.093 0.379  -0.332 -0.250 B    SBD 19 
SBD C14  C14  C 0  1 N N N N N N 15.745 2.198  20.453 1.388  -3.585 -0.295 C14  SBD 20 
SBD O15  O15  O 0  1 N N N N N N 16.735 2.861  20.218 1.521  -3.513 0.908  O15  SBD 21 
SBD C16  C16  C 0  1 N N N N N N 15.261 1.219  19.402 2.145  -4.629 -1.075 C16  SBD 22 
SBD C9   C9   C 0  1 Y N N N N N 12.145 3.517  21.689 -2.514 0.889  -1.535 C9   SBD 23 
SBD C8   C8   C 0  1 Y N N N N N 11.155 3.697  20.740 -2.904 2.137  -1.914 C8   SBD 24 
SBD C7   C7   C 0  1 Y N N N N N 10.066 2.841  20.676 -3.721 2.913  -1.093 C7   SBD 25 
SBD C6   C6   C 0  1 Y N N N N N 9.940  1.781  21.550 -4.153 2.445  0.109  C6   SBD 26 
SBD H    1HN  H 0  1 N N N N N N 16.553 4.008  27.542 4.822  0.682  2.014  H    SBD 27 
SBD H2   2HN  H 0  1 N Y N N N N 16.065 4.026  25.922 3.339  1.252  2.324  H2   SBD 28 
SBD HA   HA   H 0  1 N N N N N N 17.389 2.019  26.478 4.229  0.228  -0.252 HA   SBD 29 
SBD HB2  1HB  H 0  1 N N N N N N 18.527 4.154  24.538 2.093  1.304  -1.020 HB2  SBD 30 
SBD HB3  2HB  H 0  1 N N N N N N 19.307 2.653  24.693 1.664  1.587  0.684  HB3  SBD 31 
SBD HXT  HXT  H 0  1 N Y N N N N 20.038 4.641  28.091 ?      ?      ?      HXT  SBD 32 
SBD HN3  HN3  H 0  1 N N N N N N 13.987 2.305  21.255 0.518  -2.736 -1.904 HN3  SBD 33 
SBD H12  H12  H 0  1 N N N N N N 15.709 1.783  23.222 -0.299 -2.115 0.874  H12  SBD 34 
SBD H111 1H11 H 0  0 N N N N N N 14.474 3.455  24.767 -1.647 -1.350 -1.754 H111 SBD 35 
SBD H112 2H11 H 0  0 N N N N N N 13.883 4.317  23.439 -2.072 -2.781 -0.784 H112 SBD 36 
SBD HC2  H2   H 0  1 N N N N N N 13.633 1.131  25.312 -2.695 -2.366 1.652  HC2  SBD 37 
SBD H3   H3   H 0  1 N N N N N N 11.691 -0.402 25.182 -4.137 -0.999 3.098  H3   SBD 38 
SBD H4   H4   H 0  1 N N N N N N 9.949  -0.147 23.419 -4.831 1.234  2.415  H4   SBD 39 
SBD HO1  HO1  H 0  1 N N N N N N 17.275 4.492  21.474 0.680  -0.503 -2.106 HO1  SBD 40 
SBD HO2  HO2  H 0  1 N N N N N N 16.145 5.538  23.557 -0.170 0.129  1.498  HO2  SBD 41 
SBD H161 1H16 H 0  0 N N N N N N 15.912 1.032  18.516 1.548  -5.539 -1.139 H161 SBD 42 
SBD H162 2H16 H 0  0 N N N N N N 15.024 0.245  19.892 2.347  -4.256 -2.080 H162 SBD 43 
SBD H163 3H16 H 0  0 N N N N N N 14.250 1.531  19.050 3.087  -4.847 -0.572 H163 SBD 44 
SBD H9   H9   H 0  1 N N N N N N 13.005 4.206  21.721 -1.881 0.299  -2.181 H9   SBD 45 
SBD H8   H8   H 0  1 N N N N N N 11.234 4.533  20.025 -2.576 2.531  -2.864 H8   SBD 46 
SBD H7   H7   H 0  1 N N N N N N 9.284  3.006  19.915 -4.017 3.900  -1.418 H7   SBD 47 
SBD H6   H6   H 0  1 N N N N N N 9.068  1.109  21.472 -4.787 3.058  0.734  H6   SBD 48 
# 
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 
SBD N   CA   SING N N 1  
SBD N   H    SING N N 2  
SBD N   H2   SING N N 3  
SBD CA  CB   SING N N 4  
SBD CA  C    SING N N 5  
SBD CA  HA   SING N N 6  
SBD CB  O3   SING N N 7  
SBD CB  HB2  SING N N 8  
SBD CB  HB3  SING N N 9  
SBD O3  B    SING N N 10 
SBD C   O    DOUB N N 11 
SBD C   OXT  SING N N 12 
SBD OXT HXT  SING N N 13 
SBD N13 C12  SING N N 14 
SBD N13 C14  SING N N 15 
SBD N13 HN3  SING N N 16 
SBD C12 C11  SING N N 17 
SBD C12 B    SING N N 18 
SBD C12 H12  SING N N 19 
SBD C11 C1   SING N N 20 
SBD C11 H111 SING N N 21 
SBD C11 H112 SING N N 22 
SBD C1  C10  DOUB Y N 23 
SBD C1  C2   SING Y N 24 
SBD C10 C5   SING Y N 25 
SBD C10 C9   SING Y N 26 
SBD C5  C4   DOUB Y N 27 
SBD C5  C6   SING Y N 28 
SBD C2  C3   DOUB Y N 29 
SBD C2  HC2  SING N N 30 
SBD C3  C4   SING Y N 31 
SBD C3  H3   SING N N 32 
SBD C4  H4   SING N N 33 
SBD O1  B    SING N N 34 
SBD O1  HO1  SING N N 35 
SBD O2  B    SING N N 36 
SBD O2  HO2  SING N N 37 
SBD C14 O15  DOUB N N 38 
SBD C14 C16  SING N N 39 
SBD C16 H161 SING N N 40 
SBD C16 H162 SING N N 41 
SBD C16 H163 SING N N 42 
SBD C9  C8   DOUB Y N 43 
SBD C9  H9   SING N N 44 
SBD C8  C7   SING Y N 45 
SBD C8  H8   SING N N 46 
SBD C7  C6   DOUB Y N 47 
SBD C7  H7   SING N N 48 
SBD C6  H6   SING N N 49 
# 
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 
SBD SMILES           ACDLabs              10.04 "O=C(O)C(N)CO[B-](O)(O)C(NC(=O)C)Cc2cccc1ccccc12"                                                                                                                        
SBD SMILES_CANONICAL CACTVS               3.341 "CC(=O)N[C@H](Cc1cccc2ccccc12)[B-](O)(O)OC[C@H](N)C(O)=O"                                                                                                                
SBD SMILES           CACTVS               3.341 "CC(=O)N[CH](Cc1cccc2ccccc12)[B-](O)(O)OC[CH](N)C(O)=O"                                                                                                                  
SBD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[B-]([C@@H](Cc1cccc2c1cccc2)NC(=O)C)(O)(O)OC[C@@H](C(=O)O)N"                                                                                                            
SBD SMILES           "OpenEye OEToolkits" 1.5.0 "[B-](C(Cc1cccc2c1cccc2)NC(=O)C)(O)(O)OCC(C(=O)O)N"                                                                                                                      
SBD InChI            InChI                1.03  "InChI=1S/C17H22BN2O6/c1-11(21)20-16(18(24,25)26-10-15(19)17(22)23)9-13-7-4-6-12-5-2-3-8-14(12)13/h2-8,15-16,24-25H,9-10,19H2,1H3,(H,20,21)(H,22,23)/q-1/t15-,16+/m0/s1" 
SBD InChIKey         InChI                1.03  KJSNEFAXFLDDDR-JKSUJKDBSA-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 
SBD "SYSTEMATIC NAME" ACDLabs              10.04 "[(1S)-1-(acetylamino)-2-naphthalen-1-ylethyl](dihydroxy)(L-serinato-kappaO~3~)borate(1-)"          
SBD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1S)-1-acetamido-2-naphthalen-1-yl-ethyl]-[(2S)-2-amino-3-hydroxy-3-oxo-propoxy]-dihydroxy-boron" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
SBD "Create component"  1999-07-08 RCSB 
SBD "Modify descriptor" 2011-06-04 RCSB 
SBD "Modify PCM"        2024-09-27 PDBE 
# 
