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 ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 1Z6F
#
_pdbe_chem_comp_drugbank_details.comp_id BO9
_pdbe_chem_comp_drugbank_details.drugbank_id DB04647
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name BOC-GAMMA-D-GLU-L-LYS(CBZ)-D-BOROALA
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id BO9
_pdbe_chem_comp_synonyms.name BOC-GAMMA-D-GLU-L-LYS(CBZ)-D-BOROALA
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id BO9
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04647
_pdbe_chem_comp_drugbank_classification.parent Dipeptides
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
BO9 DB04647 'D-alanyl-D-alanine carboxypeptidase DacA' 'Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)' P0AEB3 unknown 1
BO9 DB04647 'D-alanyl-D-alanine carboxypeptidase DacA' 'Escherichia coli (strain K12)' P0AEB2 unknown 2
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
BO9 O36 O 4.299 7.976 1
BO9 C35 C 5.598 8.726 2
BO9 O37 O 5.598 10.226 3
BO9 C38 C 4.299 10.976 4
BO9 C41 C 3.000 11.726 5
BO9 C40 C 5.049 12.274 6
BO9 C39 C 3.549 9.677 7
BO9 N34 N 6.897 7.976 8
BO9 C30 C 6.897 6.476 9
BO9 C31 C 5.598 5.726 10
BO9 O33 O 4.299 6.476 11
BO9 O32 O 5.598 4.226 12
BO9 C29 C 8.196 5.726 13
BO9 C28 C 8.196 4.226 14
BO9 C26 C 9.495 3.475 15
BO9 O27 O 10.794 4.226 16
BO9 N25 N 9.495 1.976 17
BO9 C9 C 10.794 1.226 18
BO9 C7 C 12.093 1.976 19
BO9 O8 O 12.093 3.475 20
BO9 N6 N 13.392 1.226 21
BO9 C4 C 14.691 1.976 22
BO9 C5 C 14.691 3.475 23
BO9 B1 B 15.990 1.226 24
BO9 O3 O 17.290 1.976 25
BO9 O2 O 15.990 -0.275 26
BO9 C10 C 10.794 -0.275 27
BO9 C11 C 9.495 -1.024 28
BO9 C12 C 9.495 -2.525 29
BO9 C13 C 8.196 -3.275 30
BO9 N14 N 8.196 -4.774 31
BO9 C15 C 6.897 -5.524 32
BO9 O16 O 5.598 -4.774 33
BO9 O17 O 6.897 -7.024 34
BO9 C18 C 5.598 -7.774 35
BO9 C19 C 5.598 -9.274 36
BO9 C24 C 4.299 -10.024 37
BO9 C23 C 4.299 -11.524 38
BO9 C22 C 5.598 -12.274 39
BO9 C21 C 6.897 -11.524 40
BO9 C20 C 6.897 -10.024 41
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
BO9 O36 C35 DOUBLE NONE 1
BO9 C35 O37 SINGLE NONE 2
BO9 C35 N34 SINGLE NONE 3
BO9 O37 C38 SINGLE NONE 4
BO9 C38 C41 SINGLE NONE 5
BO9 C38 C40 SINGLE NONE 6
BO9 C38 C39 SINGLE NONE 7
BO9 N34 C30 SINGLE NONE 8
BO9 C30 C31 SINGLE NONE 9
BO9 C30 C29 SINGLE BEGINWEDGE 10
BO9 C31 O33 DOUBLE NONE 11
BO9 C31 O32 SINGLE NONE 12
BO9 C29 C28 SINGLE NONE 13
BO9 C28 C26 SINGLE NONE 14
BO9 C26 O27 DOUBLE NONE 15
BO9 C26 N25 SINGLE NONE 16
BO9 N25 C9 SINGLE NONE 17
BO9 C9 C7 SINGLE NONE 18
BO9 C9 C10 SINGLE BEGINDASH 19
BO9 C7 O8 DOUBLE NONE 20
BO9 C7 N6 SINGLE NONE 21
BO9 N6 C4 SINGLE NONE 22
BO9 C4 C5 SINGLE BEGINDASH 23
BO9 C4 B1 SINGLE NONE 24
BO9 B1 O3 SINGLE NONE 25
BO9 B1 O2 SINGLE NONE 26
BO9 C10 C11 SINGLE NONE 27
BO9 C11 C12 SINGLE NONE 28
BO9 C12 C13 SINGLE NONE 29
BO9 C13 N14 SINGLE NONE 30
BO9 N14 C15 SINGLE NONE 31
BO9 C15 O16 DOUBLE NONE 32
BO9 C15 O17 SINGLE NONE 33
BO9 O17 C18 SINGLE NONE 34
BO9 C18 C19 SINGLE NONE 35
BO9 C19 C24 DOUBLE NONE 36
BO9 C19 C20 SINGLE NONE 37
BO9 C24 C23 SINGLE NONE 38
BO9 C23 C22 DOUBLE NONE 39
BO9 C22 C21 SINGLE NONE 40
BO9 C21 C20 DOUBLE NONE 41
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
BO9 MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
BO9 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
BO9 peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
BO9 phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
BO9 C19 S1 1
BO9 C24 S1 1
BO9 C23 S1 1
BO9 C22 S1 1
BO9 C21 S1 1
BO9 C20 S1 1
BO9 N25 F1 1
BO9 C26 F1 1
BO9 O27 F1 1
BO9 C28 F1 1
BO9 N6 F1 2
BO9 C7 F1 2
BO9 O8 F1 2
BO9 C9 F1 2
BO9 O33 F2 1
BO9 C31 F2 1
BO9 C30 F2 1
BO9 N34 F2 1
BO9 O8 F2 2
BO9 C7 F2 2
BO9 C9 F2 2
BO9 N25 F2 2
BO9 C19 F3 1
BO9 C24 F3 1
BO9 C23 F3 1
BO9 C22 F3 1
BO9 C21 F3 1
BO9 C20 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id BO9
_pdbe_chem_comp_rdkit_properties.exactmw 580.292
_pdbe_chem_comp_rdkit_properties.amw 580.444
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 14
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 19
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 41
_pdbe_chem_comp_rdkit_properties.NumAtoms 82
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 15
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 4
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.577
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 297.336
_pdbe_chem_comp_rdkit_properties.tpsa 212.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.788
_pdbe_chem_comp_rdkit_properties.CrippenMR 147.969
_pdbe_chem_comp_rdkit_properties.chi0v 19.449
_pdbe_chem_comp_rdkit_properties.chi1v 9.590
_pdbe_chem_comp_rdkit_properties.chi2v 2.973
_pdbe_chem_comp_rdkit_properties.chi3v 2.973
_pdbe_chem_comp_rdkit_properties.chi4v 1.567
_pdbe_chem_comp_rdkit_properties.chi0n 60.449
_pdbe_chem_comp_rdkit_properties.chi1n 29.604
_pdbe_chem_comp_rdkit_properties.chi2n 2.973
_pdbe_chem_comp_rdkit_properties.chi3n 2.973
_pdbe_chem_comp_rdkit_properties.chi4n 1.567
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.845
_pdbe_chem_comp_rdkit_properties.kappa1 7.951
_pdbe_chem_comp_rdkit_properties.kappa2 17.763
_pdbe_chem_comp_rdkit_properties.kappa3 16.118
_pdbe_chem_comp_rdkit_properties.Phi 3.445
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
BO9 UniChem DrugBank DB04647
BO9 UniChem PDBe BO9
BO9 UniChem ZINC ZINC000169748488
BO9 UniChem PubChem 5287824
BO9 UniChem 'Probes And Drugs' PD005934
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
BO9 O36 8.015 -1.195 -1.408 ETKDGv3 1
BO9 C35 7.626 -0.028 -1.129 ETKDGv3 2
BO9 O37 8.535 0.960 -0.723 ETKDGv3 3
BO9 C38 9.955 0.801 -0.578 ETKDGv3 4
BO9 C41 10.276 -0.262 0.490 ETKDGv3 5
BO9 C40 10.518 2.154 -0.116 ETKDGv3 6
BO9 C39 10.599 0.429 -1.927 ETKDGv3 7
BO9 N34 6.237 0.306 -1.224 ETKDGv3 8
BO9 C30 5.229 -0.655 -1.680 ETKDGv3 9
BO9 C31 5.294 -0.777 -3.175 ETKDGv3 10
BO9 O33 5.322 -1.915 -3.715 ETKDGv3 11
BO9 O32 5.297 0.368 -3.968 ETKDGv3 12
BO9 C29 3.815 -0.215 -1.256 ETKDGv3 13
BO9 C28 3.646 -0.239 0.269 ETKDGv3 14
BO9 C26 2.254 0.168 0.646 ETKDGv3 15
BO9 O27 2.020 1.368 0.956 ETKDGv3 16
BO9 N25 1.189 -0.793 0.611 ETKDGv3 17
BO9 C9 -0.191 -0.438 0.956 ETKDGv3 18
BO9 C7 -0.301 -0.212 2.443 ETKDGv3 19
BO9 O8 0.216 -1.043 3.239 ETKDGv3 20
BO9 N6 -1.031 0.916 2.947 ETKDGv3 21
BO9 C4 -1.331 1.082 4.370 ETKDGv3 22
BO9 C5 -2.653 0.387 4.701 ETKDGv3 23
BO9 B1 -1.364 2.643 4.739 ETKDGv3 24
BO9 O3 -0.168 3.456 4.538 ETKDGv3 25
BO9 O2 -2.578 3.265 5.266 ETKDGv3 26
BO9 C10 -1.159 -1.548 0.501 ETKDGv3 27
BO9 C11 -2.632 -1.150 0.687 ETKDGv3 28
BO9 C12 -3.569 -2.241 0.151 ETKDGv3 29
BO9 C13 -5.046 -1.884 0.369 ETKDGv3 30
BO9 N14 -5.467 -0.777 -0.491 ETKDGv3 31
BO9 C15 -6.789 -0.236 -0.421 ETKDGv3 32
BO9 O16 -7.623 -0.701 0.404 ETKDGv3 33
BO9 O17 -7.143 0.816 -1.273 ETKDGv3 34
BO9 C18 -8.446 1.394 -1.305 ETKDGv3 35
BO9 C19 -9.428 0.445 -1.936 ETKDGv3 36
BO9 C24 -9.342 0.148 -3.245 ETKDGv3 37
BO9 C23 -10.296 -0.801 -3.857 ETKDGv3 38
BO9 C22 -11.246 -1.374 -3.109 ETKDGv3 39
BO9 C21 -11.343 -1.058 -1.669 ETKDGv3 40
BO9 C20 -10.483 -0.197 -1.111 ETKDGv3 41
BO9 H411 11.368 -0.293 0.694 ETKDGv3 42
BO9 H412 9.745 -0.026 1.437 ETKDGv3 43
BO9 H413 9.967 -1.274 0.159 ETKDGv3 44
BO9 H401 10.288 2.943 -0.865 ETKDGv3 45
BO9 H402 10.058 2.453 0.851 ETKDGv3 46
BO9 H403 11.620 2.103 0.017 ETKDGv3 47
BO9 H391 11.708 0.432 -1.844 ETKDGv3 48
BO9 H392 10.300 1.159 -2.709 ETKDGv3 49
BO9 H393 10.290 -0.583 -2.258 ETKDGv3 50
BO9 H34 5.958 1.293 -1.019 ETKDGv3 51
BO9 H30 5.435 -1.650 -1.224 ETKDGv3 52
BO9 H32 5.332 0.300 -4.978 ETKDGv3 53
BO9 H291 3.608 0.809 -1.639 ETKDGv3 54
BO9 H292 3.070 -0.908 -1.707 ETKDGv3 55
BO9 H281 4.372 0.454 0.746 ETKDGv3 56
BO9 H282 3.845 -1.261 0.656 ETKDGv3 57
BO9 H25 1.415 -1.774 0.328 ETKDGv3 58
BO9 H9 -0.458 0.495 0.412 ETKDGv3 59
BO9 HN6 -1.517 1.536 2.258 ETKDGv3 60
BO9 H4 -0.525 0.626 4.986 ETKDGv3 61
BO9 H51 -2.576 -0.696 4.468 ETKDGv3 62
BO9 H52 -3.484 0.818 4.102 ETKDGv3 63
BO9 H53 -2.887 0.492 5.783 ETKDGv3 64
BO9 HO3 0.325 3.394 5.395 ETKDGv3 65
BO9 HO2 -3.069 3.575 4.464 ETKDGv3 66
BO9 H101 -0.951 -2.484 1.065 ETKDGv3 67
BO9 H102 -0.979 -1.752 -0.578 ETKDGv3 68
BO9 H111 -2.841 -0.995 1.767 ETKDGv3 69
BO9 H112 -2.823 -0.194 0.152 ETKDGv3 70
BO9 H121 -3.357 -3.193 0.683 ETKDGv3 71
BO9 H122 -3.383 -2.406 -0.933 ETKDGv3 72
BO9 H131 -5.667 -2.776 0.136 ETKDGv3 73
BO9 H132 -5.213 -1.616 1.435 ETKDGv3 74
BO9 H14 -4.808 -0.372 -1.193 ETKDGv3 75
BO9 H181 -8.407 2.329 -1.904 ETKDGv3 76
BO9 H182 -8.762 1.675 -0.277 ETKDGv3 77
BO9 H24 -8.574 0.597 -3.863 ETKDGv3 78
BO9 H23 -10.222 -1.032 -4.912 ETKDGv3 79
BO9 H22 -11.944 -2.070 -3.556 ETKDGv3 80
BO9 H21 -12.111 -1.526 -1.067 ETKDGv3 81
BO9 H20 -10.559 0.027 -0.054 ETKDGv3 82
#