data_BO9
# 
_chem_comp.id                                    BO9 
_chem_comp.name                                  "N1-[(1R)-1-(DIHYDROXYBORYL)ETHYL]-N2-[(TERT-BUTOXYCARBONYL)-D-GAMMA-GLUTAMYL]-N6-[(BENZYLOXY)CARBONYL-L-LYSINAMIDE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H41 B N4 O10" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "BOC-GAMMA-D-GLU-L-LYS(CBZ)-D-BOROALA" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2005-04-18 
_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                        580.436 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     BO9 
_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   N 
_chem_comp.pdbx_model_coordinates_db_code        1Z6F 
_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 
BO9 O36  O36  O 0 1 N N N N N N 50.529 7.921  32.892 -5.609 -3.955 0.161  O36  BO9 1  
BO9 C35  C35  C 0 1 N N N N N N 49.619 8.303  33.615 -5.885 -2.901 -0.377 C35  BO9 2  
BO9 O37  O37  O 0 1 N N N N N N 49.866 9.405  34.553 -6.516 -2.897 -1.566 O37  BO9 3  
BO9 C38  C38  C 0 1 N N N N N N 50.682 10.563 34.299 -6.866 -4.152 -2.206 C38  BO9 4  
BO9 C41  C41  C 0 1 N N N N N N 50.261 11.233 32.994 -7.803 -4.946 -1.294 C41  BO9 5  
BO9 C40  C40  C 0 1 N N N N N N 50.465 11.543 35.447 -7.569 -3.868 -3.535 C40  BO9 6  
BO9 C39  C39  C 0 1 N N N N N N 52.161 10.188 34.226 -5.596 -4.965 -2.465 C39  BO9 7  
BO9 N34  N34  N 0 1 N N N N N N 48.424 7.706  33.563 -5.560 -1.736 0.218  N34  BO9 8  
BO9 C30  C30  C 0 1 N N S N N N 47.268 8.083  34.377 -4.873 -1.741 1.512  C30  BO9 9  
BO9 C31  C31  C 0 1 N N N N N N 47.538 7.965  35.884 -5.889 -1.855 2.619  C31  BO9 10 
BO9 O33  O33  O 0 1 N N N N N N 47.805 6.844  36.380 -7.066 -1.926 2.354  O33  BO9 11 
BO9 O32  O32  O 0 1 N N N N N N 47.491 9.009  36.576 -5.487 -1.879 3.899  O32  BO9 12 
BO9 C29  C29  C 0 1 N N N N N N 46.114 7.158  33.958 -4.085 -0.440 1.676  C29  BO9 13 
BO9 C28  C28  C 0 1 N N N N N N 46.109 6.844  32.461 -2.972 -0.382 0.628  C28  BO9 14 
BO9 C26  C26  C 0 1 N N N N N N 44.734 6.794  31.819 -2.195 0.899  0.789  C26  BO9 15 
BO9 O27  O27  O 0 1 N N N N N N 44.362 5.770  31.256 -2.502 1.689  1.657  O27  BO9 16 
BO9 N25  N25  N 0 1 N N N N N N 43.982 7.897  31.870 -1.160 1.168  -0.031 N25  BO9 17 
BO9 C9   C9   C 0 1 N N S N N N 42.666 7.968  31.244 -0.405 2.413  0.126  C9   BO9 18 
BO9 C7   C7   C 0 1 N N N N N N 42.898 8.486  29.847 -1.100 3.520  -0.625 C7   BO9 19 
BO9 O8   O8   O 0 1 N N N N N N 43.567 9.499  29.670 -2.125 3.290  -1.232 O8   BO9 20 
BO9 N6   N6   N 0 1 N N N N N N 42.413 7.770  28.828 -0.583 4.764  -0.623 N6   BO9 21 
BO9 C4   C4   C 0 1 N N S N N N 42.623 8.205  27.449 -1.258 5.840  -1.353 C4   BO9 22 
BO9 C5   C5   C 0 1 N N N N N N 41.289 8.666  26.864 -0.226 6.645  -2.145 C5   BO9 23 
BO9 B1   B1   B 0 1 N N N N N N 43.248 6.996  26.598 -1.990 6.785  -0.335 B1   BO9 24 
BO9 O3   O3   O 0 1 N N N N N N 44.660 6.651  27.108 -3.333 6.519  0.041  O3   BO9 25 
BO9 O2   O2   O 0 1 N N N N N N 42.369 5.746  26.675 -1.308 7.905  0.210  O2   BO9 26 
BO9 C10  C10  C 0 1 N N N N N N 41.912 8.996  32.081 1.007  2.227  -0.432 C10  BO9 27 
BO9 C11  C11  C 0 1 N N N N N N 40.411 8.779  32.182 1.756  1.192  0.410  C11  BO9 28 
BO9 C12  C12  C 0 1 N N N N N N 39.855 9.729  33.247 3.168  1.006  -0.147 C12  BO9 29 
BO9 C13  C13  C 0 1 N N N N N N 39.370 8.994  34.499 3.917  -0.030 0.695  C13  BO9 30 
BO9 N14  N14  N 0 1 N N N N N N 40.218 9.385  35.619 5.269  -0.208 0.161  N14  BO9 31 
BO9 C15  C15  C 0 1 N N N N N N 39.993 10.274 36.596 6.116  -1.077 0.747  C15  BO9 32 
BO9 O16  O16  O 0 1 N N N N N N 40.819 10.473 37.477 5.757  -1.714 1.718  O16  BO9 33 
BO9 O17  O17  O 0 1 N N N N N N 38.754 11.048 36.648 7.359  -1.241 0.256  O17  BO9 34 
BO9 C18  C18  C 0 1 N N N N N N 38.581 12.208 35.828 8.271  -2.178 0.888  C18  BO9 35 
BO9 C19  C19  C 0 1 Y N N N N N 37.876 13.322 36.569 9.586  -2.172 0.152  C19  BO9 36 
BO9 C24  C24  C 0 1 Y N N N N N 38.168 14.650 36.255 10.587 -1.298 0.532  C24  BO9 37 
BO9 C23  C23  C 0 1 Y N N N N N 37.529 15.692 36.928 11.793 -1.293 -0.143 C23  BO9 38 
BO9 C22  C22  C 0 1 Y N N N N N 36.587 15.405 37.917 11.999 -2.162 -1.198 C22  BO9 39 
BO9 C21  C21  C 0 1 Y N N N N N 36.290 14.078 38.233 10.998 -3.037 -1.578 C21  BO9 40 
BO9 C20  C20  C 0 1 Y N N N N N 36.934 13.037 37.560 9.793  -3.045 -0.900 C20  BO9 41 
BO9 H411 1H41 H 0 0 N N N N N N 50.893 12.130 32.797 -8.708 -4.367 -1.110 H411 BO9 42 
BO9 H412 2H41 H 0 0 N N N N N N 50.274 10.519 32.137 -8.067 -5.888 -1.775 H412 BO9 43 
BO9 H413 3H41 H 0 0 N N N N N N 49.173 11.480 32.985 -7.303 -5.148 -0.347 H413 BO9 44 
BO9 H401 1H40 H 0 0 N N N N N N 51.097 12.440 35.250 -6.901 -3.302 -4.186 H401 BO9 45 
BO9 H402 2H40 H 0 0 N N N N N N 49.390 11.795 35.603 -7.832 -4.810 -4.016 H402 BO9 46 
BO9 H403 3H40 H 0 0 N N N N N N 50.656 11.088 36.447 -8.474 -3.288 -3.352 H403 BO9 47 
BO9 H391 1H39 H 0 0 N N N N N N 52.793 11.085 34.029 -5.096 -5.168 -1.518 H391 BO9 48 
BO9 H392 2H39 H 0 0 N N N N N N 52.492 9.644  35.141 -5.859 -5.907 -2.945 H392 BO9 49 
BO9 H393 3H39 H 0 0 N N N N N N 52.344 9.383  33.475 -4.929 -4.400 -3.115 H393 BO9 50 
BO9 H34  H34  H 0 1 N N N N N N 48.393 6.944  32.885 -5.780 -0.895 -0.211 H34  BO9 51 
BO9 H30  H30  H 0 1 N N N N N N 47.021 9.156  34.202 -4.189 -2.588 1.558  H30  BO9 52 
BO9 H32  H32  H 0 1 N N N N N N 47.658 8.936  37.508 -6.139 -1.953 4.610  H32  BO9 53 
BO9 H291 1H29 H 0 0 N N N N N N 46.118 6.219  34.560 -3.647 -0.404 2.673  H291 BO9 54 
BO9 H292 2H29 H 0 0 N N N N N N 45.132 7.577  34.279 -4.754 0.410  1.542  H292 BO9 55 
BO9 H281 1H28 H 0 0 N N N N N N 46.762 7.563  31.914 -3.410 -0.419 -0.370 H281 BO9 56 
BO9 H282 2H28 H 0 0 N N N N N N 46.659 5.894  32.265 -2.302 -1.232 0.762  H282 BO9 57 
BO9 H25  H25  H 0 1 N N N N N N 44.405 8.672  32.378 -0.915 0.536  -0.725 H25  BO9 58 
BO9 H9   H9   H 0 1 N N N N N N 42.107 7.004  31.192 -0.348 2.672  1.183  H9   BO9 59 
BO9 HN6  HN6  H 0 1 N N N N N N 41.903 6.926  29.091 0.237  4.948  -0.138 HN6  BO9 60 
BO9 H4   H4   H 0 1 N N N N N N 43.338 9.059  27.414 -1.988 5.410  -2.039 H4   BO9 61 
BO9 H51  1H5  H 0 1 N N N N N N 41.449 8.997  25.811 0.504  7.074  -1.459 H51  BO9 62 
BO9 H52  2H5  H 0 1 N N N N N N 40.496 7.885  26.947 0.282  5.989  -2.852 H52  BO9 63 
BO9 H53  3H5  H 0 1 N N N N N N 40.800 9.451  27.487 -0.729 7.445  -2.688 H53  BO9 64 
BO9 HO3  HO3  H 0 1 N N N N N N 45.029 5.935  26.604 -3.605 5.723  -0.436 HO3  BO9 65 
BO9 HO2  HO2  H 0 1 N N N N N N 42.738 5.030  26.171 -1.928 8.347  0.805  HO2  BO9 66 
BO9 H101 1H10 H 0 0 N N N N N N 42.358 9.060  33.100 0.948  1.882  -1.464 H101 BO9 67 
BO9 H102 2H10 H 0 0 N N N N N N 42.125 10.024 31.707 1.540  3.178  -0.396 H102 BO9 68 
BO9 H111 1H11 H 0 0 N N N N N N 39.895 8.888  31.199 1.815  1.537  1.442  H111 BO9 69 
BO9 H112 2H11 H 0 0 N N N N N N 40.144 7.714  32.376 1.223  0.241  0.375  H112 BO9 70 
BO9 H121 1H12 H 0 0 N N N N N N 40.599 10.516 33.508 3.109  0.661  -1.179 H121 BO9 71 
BO9 H122 2H12 H 0 0 N N N N N N 39.050 10.375 32.825 3.701  1.956  -0.112 H122 BO9 72 
BO9 H131 1H13 H 0 0 N N N N N N 38.286 9.162  34.702 3.976  0.316  1.727  H131 BO9 73 
BO9 H132 2H13 H 0 0 N N N N N N 39.328 7.888  34.358 3.384  -0.980 0.659  H132 BO9 74 
BO9 H14  H14  H 0 1 N N N N N N 41.136 8.958  35.741 5.555  0.300  -0.614 H14  BO9 75 
BO9 H181 1H18 H 0 0 N N N N N N 39.552 12.554 35.405 8.434  -1.884 1.925  H181 BO9 76 
BO9 H182 2H18 H 0 0 N N N N N N 38.055 11.957 34.877 7.842  -3.179 0.857  H182 BO9 77 
BO9 H24  H24  H 0 1 N N N N N N 38.908 14.877 35.469 10.427 -0.619 1.356  H24  BO9 78 
BO9 H23  H23  H 0 1 N N N N N N 37.767 16.739 36.678 12.575 -0.610 0.154  H23  BO9 79 
BO9 H22  H22  H 0 1 N N N N N N 36.077 16.226 38.448 12.941 -2.157 -1.726 H22  BO9 80 
BO9 H21  H21  H 0 1 N N N N N N 35.545 13.851 39.015 11.158 -3.715 -2.403 H21  BO9 81 
BO9 H20  H20  H 0 1 N N N N N N 36.698 11.989 37.811 9.011  -3.728 -1.197 H20  BO9 82 
# 
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 
BO9 O36 C35  DOUB N N 1  
BO9 C35 O37  SING N N 2  
BO9 C35 N34  SING N N 3  
BO9 O37 C38  SING N N 4  
BO9 C38 C41  SING N N 5  
BO9 C38 C40  SING N N 6  
BO9 C38 C39  SING N N 7  
BO9 C41 H411 SING N N 8  
BO9 C41 H412 SING N N 9  
BO9 C41 H413 SING N N 10 
BO9 C40 H401 SING N N 11 
BO9 C40 H402 SING N N 12 
BO9 C40 H403 SING N N 13 
BO9 C39 H391 SING N N 14 
BO9 C39 H392 SING N N 15 
BO9 C39 H393 SING N N 16 
BO9 N34 C30  SING N N 17 
BO9 N34 H34  SING N N 18 
BO9 C30 C31  SING N N 19 
BO9 C30 C29  SING N N 20 
BO9 C30 H30  SING N N 21 
BO9 C31 O33  DOUB N N 22 
BO9 C31 O32  SING N N 23 
BO9 O32 H32  SING N N 24 
BO9 C29 C28  SING N N 25 
BO9 C29 H291 SING N N 26 
BO9 C29 H292 SING N N 27 
BO9 C28 C26  SING N N 28 
BO9 C28 H281 SING N N 29 
BO9 C28 H282 SING N N 30 
BO9 C26 O27  DOUB N N 31 
BO9 C26 N25  SING N N 32 
BO9 N25 C9   SING N N 33 
BO9 N25 H25  SING N N 34 
BO9 C9  C7   SING N N 35 
BO9 C9  C10  SING N N 36 
BO9 C9  H9   SING N N 37 
BO9 C7  O8   DOUB N N 38 
BO9 C7  N6   SING N N 39 
BO9 N6  C4   SING N N 40 
BO9 N6  HN6  SING N N 41 
BO9 C4  C5   SING N N 42 
BO9 C4  B1   SING N N 43 
BO9 C4  H4   SING N N 44 
BO9 C5  H51  SING N N 45 
BO9 C5  H52  SING N N 46 
BO9 C5  H53  SING N N 47 
BO9 B1  O3   SING N N 48 
BO9 B1  O2   SING N N 49 
BO9 O3  HO3  SING N N 50 
BO9 O2  HO2  SING N N 51 
BO9 C10 C11  SING N N 52 
BO9 C10 H101 SING N N 53 
BO9 C10 H102 SING N N 54 
BO9 C11 C12  SING N N 55 
BO9 C11 H111 SING N N 56 
BO9 C11 H112 SING N N 57 
BO9 C12 C13  SING N N 58 
BO9 C12 H121 SING N N 59 
BO9 C12 H122 SING N N 60 
BO9 C13 N14  SING N N 61 
BO9 C13 H131 SING N N 62 
BO9 C13 H132 SING N N 63 
BO9 N14 C15  SING N N 64 
BO9 N14 H14  SING N N 65 
BO9 C15 O16  DOUB N N 66 
BO9 C15 O17  SING N N 67 
BO9 O17 C18  SING N N 68 
BO9 C18 C19  SING N N 69 
BO9 C18 H181 SING N N 70 
BO9 C18 H182 SING N N 71 
BO9 C19 C24  DOUB Y N 72 
BO9 C19 C20  SING Y N 73 
BO9 C24 C23  SING Y N 74 
BO9 C24 H24  SING N N 75 
BO9 C23 C22  DOUB Y N 76 
BO9 C23 H23  SING N N 77 
BO9 C22 C21  SING Y N 78 
BO9 C22 H22  SING N N 79 
BO9 C21 C20  DOUB Y N 80 
BO9 C21 H21  SING N N 81 
BO9 C20 H20  SING N N 82 
# 
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 
BO9 SMILES           ACDLabs              10.04 "O=C(OC(C)(C)C)NC(C(=O)O)CCC(=O)NC(C(=O)NC(B(O)O)C)CCCCNC(=O)OCc1ccccc1"                                                                                                                                                                                    
BO9 SMILES_CANONICAL CACTVS               3.341 "C[C@@H](NC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(=O)CC[C@H](NC(=O)OC(C)(C)C)C(O)=O)B(O)O"                                                                                                                                                                       
BO9 SMILES           CACTVS               3.341 "C[CH](NC(=O)[CH](CCCCNC(=O)OCc1ccccc1)NC(=O)CC[CH](NC(=O)OC(C)(C)C)C(O)=O)B(O)O"                                                                                                                                                                           
BO9 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "B([C@@H](C)NC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(=O)CC[C@@H](C(=O)O)NC(=O)OC(C)(C)C)(O)O"                                                                                                                                                                    
BO9 SMILES           "OpenEye OEToolkits" 1.5.0 "B(C(C)NC(=O)C(CCCCNC(=O)OCc1ccccc1)NC(=O)CCC(C(=O)O)NC(=O)OC(C)(C)C)(O)O"                                                                                                                                                                                  
BO9 InChI            InChI                1.03  "InChI=1S/C26H41BN4O10/c1-17(27(38)39)29-22(33)19(12-8-9-15-28-24(36)40-16-18-10-6-5-7-11-18)30-21(32)14-13-20(23(34)35)31-25(37)41-26(2,3)4/h5-7,10-11,17,19-20,38-39H,8-9,12-16H2,1-4H3,(H,28,36)(H,29,33)(H,30,32)(H,31,37)(H,34,35)/t17-,19+,20+/m1/s1" 
BO9 InChIKey         InChI                1.03  OTTYWVUOPWENAJ-HOJAQTOUSA-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 
BO9 "SYSTEMATIC NAME" ACDLabs              10.04 "N-(tert-butoxycarbonyl)-L-gamma-glutamyl-N~6~-[(benzyloxy)carbonyl]-N-[(1S)-1-(dihydroxyboranyl)ethyl]-L-lysinamide"                                                         
BO9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-5-[[(2S)-1-[[(1S)-1-(dihydroxyboranyl)ethyl]amino]-1-oxo-6-phenylmethoxycarbonylamino-hexan-2-yl]amino]-2-[(2-methylpropan-2-yl)oxycarbonylamino]-5-oxo-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 
BO9 "Create component"  2005-04-18 RCSB 
BO9 "Modify descriptor" 2011-06-04 RCSB 
BO9 "Modify synonyms"   2021-03-01 PDBE 
BO9 "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      BO9 
_pdbx_chem_comp_synonyms.name         "BOC-GAMMA-D-GLU-L-LYS(CBZ)-D-BOROALA" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            BO9 
_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      ? 
# 
