data_XBK
#
_chem_comp.id XBK
_chem_comp.name 4,5-DE-EPOXYPIMARICIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C33 H47 N O12"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-04-12
_chem_comp.pdbx_modified_date 2011-06-04
_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 649.726
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XBK
_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 2xbk
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
XBK N N N 0 1 N N N N N N 21.283 -6.146 3.060 6.852 -3.881 -0.825 N XBK 1
XBK C1 C1 C 0 1 N N S N N N 26.194 -3.376 7.949 3.211 3.709 0.318 C1 XBK 2
XBK O1 O1 O 0 1 N N N N N N 26.095 -4.342 9.014 4.357 4.244 -0.348 O1 XBK 3
XBK C2 C2 C 0 1 N N R N N N 26.416 -4.099 6.603 3.507 2.275 0.791 C2 XBK 4
XBK O2 O2 O 0 1 N N N N N N 25.558 -6.347 6.057 5.850 2.760 1.402 O2 XBK 5
XBK C3 C3 C 0 1 N N N N N N 25.321 -5.077 6.285 4.648 2.290 1.775 C3 XBK 6
XBK O3 O3 O 0 1 N N N N N N 24.166 -4.721 6.220 4.483 1.880 2.899 O3 XBK 7
XBK C4 C4 C 0 1 N N S N N N 26.498 -3.037 5.527 2.250 1.723 1.467 C4 XBK 8
XBK O4 O4 O 0 1 N N N N N N 24.757 -2.816 3.000 2.814 -1.866 0.994 O4 XBK 9
XBK C5 C5 C 0 1 N N N N N N 26.861 -3.719 4.203 2.496 0.317 1.982 C5 XBK 10
XBK O5 O5 O 0 1 N N N N N N 22.076 -3.691 3.552 4.217 -4.140 0.143 O5 XBK 11
XBK C6 C6 C 0 1 N N R N N N 26.182 -3.062 2.982 1.923 -0.750 1.052 C6 XBK 12
XBK O6 O6 O 0 1 N N N N N N 21.511 -6.373 0.151 6.105 -2.754 -3.371 O6 XBK 13
XBK C7 C7 C 0 1 N N R N N N 24.136 -3.891 2.253 3.810 -1.762 -0.026 C7 XBK 14
XBK O7 O7 O 0 1 N N N N N N 23.709 -3.487 0.940 3.196 -1.912 -1.308 O7 XBK 15
XBK C8 C8 C 0 1 N N S N N N 23.076 -4.605 3.097 4.856 -2.862 0.169 C8 XBK 16
XBK O8 O8 O 0 1 N N N N N N 32.180 6.682 2.896 -7.658 -0.285 -0.008 O8 XBK 17
XBK C9 C9 C 0 1 N N S N N N 22.444 -5.770 2.311 5.887 -2.782 -0.962 C9 XBK 18
XBK O9 O9 O 0 1 N N N N N N 32.647 5.062 1.443 -7.376 0.376 -2.117 O9 XBK 19
XBK C10 C10 C 0 1 N N S N N N 22.025 -5.288 0.916 5.163 -2.900 -2.306 C10 XBK 20
XBK O10 O10 O 0 1 N N N N N N 28.540 1.295 5.971 -1.008 4.825 0.541 O10 XBK 21
XBK C11 C11 C 0 1 N N R N N N 23.154 -4.582 0.173 4.104 -1.799 -2.406 C11 XBK 22
XBK O11 O11 O 0 1 N N N N N N 26.582 -0.555 7.012 0.504 3.854 1.189 O11 XBK 23
XBK C12 C12 C 0 1 N N N N N N 22.644 -3.959 -1.110 3.336 -1.947 -3.720 C12 XBK 24
XBK O12 O12 O 0 1 N N N N N N 27.648 -2.180 5.855 1.167 1.729 0.524 O12 XBK 25
XBK C13 C13 C 0 1 N N N N N N 26.892 -1.840 2.448 0.595 -1.193 1.594 C13 XBK 26
XBK C14 C14 C 0 1 N N N N N N 26.852 -0.651 2.952 0.185 -2.461 1.555 C14 XBK 27
XBK C15 C15 C 0 1 N N N N N N 27.640 0.244 2.149 -1.142 -2.787 2.066 C15 XBK 28
XBK C16 C16 C 0 1 N N N N N N 27.671 1.521 2.440 -1.803 -3.931 1.837 C16 XBK 29
XBK C17 C17 C 0 1 N N N N N N 28.485 2.405 1.623 -3.178 -4.001 2.171 C17 XBK 30
XBK C18 C18 C 0 1 N N N N N N 28.575 3.706 1.909 -4.083 -3.780 1.207 C18 XBK 31
XBK C19 C19 C 0 1 N N N N N N 29.356 4.732 1.190 -5.500 -3.537 1.461 C19 XBK 32
XBK C20 C20 C 0 1 N N N N N N 29.524 5.948 1.782 -6.227 -2.979 0.481 C20 XBK 33
XBK C21 C21 C 0 1 N N N N N N 30.238 7.243 1.358 -7.673 -2.618 0.665 C21 XBK 34
XBK C22 C22 C 0 1 N N R N N N 31.757 7.439 1.760 -8.064 -1.593 -0.408 C22 XBK 35
XBK C23 C23 C 0 1 N N N N N N 32.225 8.867 2.111 -9.582 -1.616 -0.602 C23 XBK 36
XBK C24 C24 C 0 1 N N N N N N 32.417 5.348 2.595 -7.079 0.498 -0.944 C24 XBK 37
XBK C25 C25 C 0 1 N N N N N N 32.318 4.433 3.736 -6.121 1.466 -0.544 C25 XBK 38
XBK C26 C26 C 0 1 N N N N N N 31.646 3.325 3.593 -5.363 2.117 -1.454 C26 XBK 39
XBK C27 C27 C 0 1 N N N N N N 31.490 2.414 4.738 -4.332 3.063 -1.019 C27 XBK 40
XBK C28 C28 C 0 1 N N N N N N 30.825 1.287 4.540 -3.417 3.496 -1.886 C28 XBK 41
XBK C29 C29 C 0 1 N N N N N N 30.667 0.324 5.670 -2.326 4.436 -1.442 C29 XBK 42
XBK C30 C30 C 0 1 N N S N N N 29.209 0.020 5.895 -1.528 3.799 -0.307 C30 XBK 43
XBK C31 C31 C 0 1 N N N N N N 29.052 -0.854 7.166 -0.369 2.973 -0.877 C31 XBK 44
XBK C32 C32 C 0 1 N N R N N N 27.657 -1.516 7.091 0.824 3.036 0.061 C32 XBK 45
XBK C33 C33 C 0 1 N N N N N N 27.373 -2.449 8.263 2.028 3.654 -0.652 C33 XBK 46
XBK HN HN H 0 1 N N N N N N 21.523 -6.234 4.027 7.338 -3.828 0.058 HN XBK 47
XBK HNA HNA H 0 1 N N N N N N 20.577 -5.446 2.954 6.400 -4.776 -0.937 HNA XBK 48
XBK H1 H1 H 0 1 N N N N N N 25.266 -2.790 7.870 2.958 4.334 1.174 H1 XBK 49
XBK HO1 HO1 H 0 1 N N N N N N 26.073 -5.218 8.647 4.238 5.147 -0.672 HO1 XBK 50
XBK H2 H2 H 0 1 N N N N N N 27.344 -4.687 6.660 3.768 1.653 -0.065 H2 XBK 51
XBK H4 H4 H 0 1 N N N N N N 25.550 -2.483 5.458 1.991 2.390 2.289 H4 XBK 52
XBK H5 H5 H 0 1 N N N N N N 27.951 -3.656 4.069 3.570 0.160 2.081 H5 XBK 53
XBK H5A H5A H 0 1 N N N N N N 26.509 -4.760 4.258 2.034 0.214 2.964 H5A XBK 54
XBK HO5 HO5 H 0 1 N N N N N N 22.225 -3.488 4.468 3.547 -4.259 0.831 HO5 XBK 55
XBK H6 H6 H 0 1 N N N N N N 26.298 -3.911 2.292 1.793 -0.333 0.053 H6 XBK 56
XBK HO6 HO6 H 0 1 N N N N N N 21.397 -6.099 -0.751 5.715 -2.818 -4.253 HO6 XBK 57
XBK H7 H7 H 0 1 N N N N N N 24.902 -4.652 2.043 4.292 -0.786 0.035 H7 XBK 58
XBK H8 H8 H 0 1 N N N N N N 23.575 -5.023 3.984 5.356 -2.724 1.128 H8 XBK 59
XBK H9 H9 H 0 1 N N N N N N 23.144 -6.609 2.182 6.411 -1.828 -0.911 H9 XBK 60
XBK H10 H10 H 0 1 N N N N N N 21.230 -4.541 1.057 4.682 -3.876 -2.377 H10 XBK 61
XBK HO10 HO10 H 0 0 N N N N N N 28.393 1.522 6.882 -1.686 5.382 0.946 HO10 XBK 62
XBK H11 H11 H 0 1 N N N N N N 23.914 -5.355 -0.013 4.590 -0.824 -2.376 H11 XBK 63
XBK H12 H12 H 0 1 N N N N N N 22.520 -2.875 -0.968 2.581 -1.163 -3.791 H12 XBK 64
XBK H12A H12A H 0 0 N N N N N N 23.366 -4.143 -1.919 4.028 -1.860 -4.558 H12A XBK 65
XBK H12B H12B H 0 0 N N N N N N 21.675 -4.407 -1.375 2.850 -2.922 -3.750 H12B XBK 66
XBK H13 H13 H 0 1 N N N N N N 27.491 -1.973 1.559 -0.050 -0.448 2.063 H13 XBK 67
XBK H14 H14 H 0 1 N N N N N N 26.308 -0.372 3.842 0.822 -3.239 1.163 H14 XBK 68
XBK H15 H15 H 0 1 N N N N N N 28.204 -0.135 1.309 -1.636 -2.039 2.694 H15 XBK 69
XBK H16 H16 H 0 1 N N N N N N 27.102 1.910 3.272 -1.325 -4.792 1.391 H16 XBK 70
XBK H17 H17 H 0 1 N N N N N N 29.023 2.006 0.776 -3.483 -4.234 3.181 H17 XBK 71
XBK H18 H18 H 0 1 N N N N N N 28.012 4.047 2.765 -3.740 -3.793 0.169 H18 XBK 72
XBK H19 H19 H 0 1 N N N N N N 29.783 4.524 0.220 -5.935 -3.788 2.411 H19 XBK 73
XBK H20 H20 H 0 1 N N N N N N 29.058 6.017 2.754 -5.734 -2.773 -0.466 H20 XBK 74
XBK H21 H21 H 0 1 N N N N N N 30.198 7.277 0.259 -8.289 -3.512 0.559 H21 XBK 75
XBK H21A H21A H 0 0 N N N N N N 29.707 8.038 1.901 -7.819 -2.186 1.655 H21A XBK 76
XBK H22 H22 H 0 1 N N N N N N 32.201 7.103 0.811 -7.578 -1.851 -1.349 H22 XBK 77
XBK H23 H23 H 0 1 N N N N N N 32.336 8.959 3.201 -9.860 -0.897 -1.372 H23 XBK 78
XBK H23A H23A H 0 0 N N N N N N 33.192 9.065 1.626 -9.894 -2.615 -0.907 H23A XBK 79
XBK H23B H23B H 0 0 N N N N N N 31.480 9.594 1.756 -10.072 -1.352 0.336 H23B XBK 80
XBK H25 H25 H 0 1 N N N N N N 32.792 4.672 4.676 -5.990 1.686 0.507 H25 XBK 81
XBK H26 H26 H 0 1 N N N N N N 31.206 3.077 2.638 -5.514 1.951 -2.513 H26 XBK 82
XBK H27 H27 H 0 1 N N N N N N 31.904 2.656 5.706 -4.335 3.414 0.006 H27 XBK 83
XBK H28 H28 H 0 1 N N N N N N 30.401 1.066 3.571 -3.462 3.168 -2.915 H28 XBK 84
XBK H29 H29 H 0 1 N N N N N N 31.198 -0.608 5.428 -1.661 4.643 -2.281 H29 XBK 85
XBK H29A H29A H 0 0 N N N N N N 31.086 0.771 6.584 -2.770 5.369 -1.094 H29A XBK 86
XBK H30 H30 H 0 1 N N N N N N 28.756 -0.567 5.082 -2.182 3.148 0.273 H30 XBK 87
XBK H31 H31 H 0 1 N N N N N N 29.838 -1.623 7.200 -0.686 1.936 -0.991 H31 XBK 88
XBK H31A H31A H 0 0 N N N N N N 29.146 -0.242 8.075 -0.085 3.372 -1.851 H31A XBK 89
XBK H33 H33 H 0 1 N N N N N N 27.128 -1.846 9.150 1.778 4.663 -0.981 H33 XBK 90
XBK H33A H33A H 0 0 N N N N N N 28.266 -3.064 8.448 2.293 3.043 -1.516 H33A XBK 91
XBK HO2 HO2 H 0 1 N N N N N N 24.741 -6.794 5.870 6.551 2.750 2.068 HO2 XBK 92
XBK HO11 HO11 H 0 0 N N N N N N 26.280 -0.344 7.888 -0.238 3.526 1.715 HO11 XBK 93
#
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
XBK N C9 SING N N 1
XBK C1 O1 SING N N 2
XBK C1 C2 SING N N 3
XBK C1 C33 SING N N 4
XBK C2 C3 SING N N 5
XBK C2 C4 SING N N 6
XBK O2 C3 SING N N 7
XBK C3 O3 DOUB N N 8
XBK C4 C5 SING N N 9
XBK C4 O12 SING N N 10
XBK O4 C6 SING N N 11
XBK O4 C7 SING N N 12
XBK C5 C6 SING N N 13
XBK O5 C8 SING N N 14
XBK C6 C13 SING N N 15
XBK O6 C10 SING N N 16
XBK C7 O7 SING N N 17
XBK C7 C8 SING N N 18
XBK O7 C11 SING N N 19
XBK C8 C9 SING N N 20
XBK O8 C22 SING N N 21
XBK O8 C24 SING N N 22
XBK C9 C10 SING N N 23
XBK O9 C24 DOUB N N 24
XBK C10 C11 SING N N 25
XBK O10 C30 SING N N 26
XBK C11 C12 SING N N 27
XBK O11 C32 SING N N 28
XBK O12 C32 SING N N 29
XBK C13 C14 DOUB N N 30
XBK C14 C15 SING N N 31
XBK C15 C16 DOUB N N 32
XBK C16 C17 SING N N 33
XBK C17 C18 DOUB N N 34
XBK C18 C19 SING N N 35
XBK C19 C20 DOUB N N 36
XBK C20 C21 SING N N 37
XBK C21 C22 SING N N 38
XBK C22 C23 SING N N 39
XBK C24 C25 SING N N 40
XBK C25 C26 DOUB N N 41
XBK C26 C27 SING N N 42
XBK C27 C28 DOUB N N 43
XBK C28 C29 SING N N 44
XBK C29 C30 SING N N 45
XBK C30 C31 SING N N 46
XBK C31 C32 SING N N 47
XBK C32 C33 SING N N 48
XBK N HN SING N N 49
XBK N HNA SING N N 50
XBK C1 H1 SING N N 51
XBK O1 HO1 SING N E 52
XBK C2 H2 SING N N 53
XBK C4 H4 SING N N 54
XBK C5 H5 SING N N 55
XBK C5 H5A SING N E 56
XBK O5 HO5 SING N N 57
XBK C6 H6 SING N N 58
XBK O6 HO6 SING N N 59
XBK C7 H7 SING N E 60
XBK C8 H8 SING N N 61
XBK C9 H9 SING N N 62
XBK C10 H10 SING N N 63
XBK O10 HO10 SING N E 64
XBK C11 H11 SING N N 65
XBK C12 H12 SING N N 66
XBK C12 H12A SING N N 67
XBK C12 H12B SING N N 68
XBK C13 H13 SING N N 69
XBK C14 H14 SING N N 70
XBK C15 H15 SING N N 71
XBK C16 H16 SING N N 72
XBK C17 H17 SING N N 73
XBK C18 H18 SING N N 74
XBK C19 H19 SING N N 75
XBK C20 H20 SING N N 76
XBK C21 H21 SING N E 77
XBK C21 H21A SING N N 78
XBK C22 H22 SING N N 79
XBK C23 H23 SING N N 80
XBK C23 H23A SING N E 81
XBK C23 H23B SING N N 82
XBK C25 H25 SING N N 83
XBK C26 H26 SING N N 84
XBK C27 H27 SING N N 85
XBK C28 H28 SING N N 86
XBK C29 H29 SING N N 87
XBK C29 H29A SING N N 88
XBK C30 H30 SING N N 89
XBK C31 H31 SING N N 90
XBK C31 H31A SING N N 91
XBK C33 H33 SING N N 92
XBK C33 H33A SING N N 93
XBK O2 HO2 SING N N 94
XBK O11 HO11 SING N N 95
#
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
XBK SMILES ACDLabs 10.04 O=C(O)C1C(O)CC3(O)OC1CC(OC2OC(C)C(O)C(N)C2O)C=CC=CC=CC=CCC(OC(=O)C=CC=CCC(O)C3)C
XBK SMILES_CANONICAL CACTVS 3.352 C[C@@H]1C/C=C/C=C/C=C/C=C/[C@@H](C[C@@H]2O[C@](O)(C[C@@H](O)C/C=C/C=C/C(=O)O1)C[C@H](O)[C@H]2C(O)=O)O[C@@H]3O[C@H](C)[C@@H](O)[C@H](N)[C@@H]3O
XBK SMILES CACTVS 3.352 C[CH]1CC=CC=CC=CC=C[CH](C[CH]2O[C](O)(C[CH](O)CC=CC=CC(=O)O1)C[CH](O)[CH]2C(O)=O)O[CH]3O[CH](C)[CH](O)[CH](N)[CH]3O
XBK SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 C[C@@H]1C\C=C\C=C\C=C\C=C\[C@@H](C[C@H]2[C@@H]([C@H](C[C@](O2)(C[C@H](C\C=C\C=C\C(=O)O1)O)O)O)C(=O)O)O[C@H]3[C@H]([C@H]([C@@H]([C@H](O3)C)O)N)O
XBK SMILES "OpenEye OEToolkits" 1.6.1 CC1CC=CC=CC=CC=CC(CC2C(C(CC(O2)(CC(CC=CC=CC(=O)O1)O)O)O)C(=O)O)OC3C(C(C(C(O3)C)O)N)O
XBK InChI InChI 1.03 InChI=1S/C33H47NO12/c1-20-13-9-6-4-3-5-7-11-15-23(45-32-30(39)28(34)29(38)21(2)44-32)17-25-27(31(40)41)24(36)19-33(42,46-25)18-22(35)14-10-8-12-16-26(37)43-20/h3-12,15-16,20-25,27-30,32,35-36,38-39,42H,13-14,17-19,34H2,1-2H3,(H,40,41)/b4-3+,7-5+,9-6+,10-8+,15-11+,16-12+/t20-,21-,22+,23+,24+,25+,27-,28+,29-,30+,32+,33-/m1/s1
XBK InChIKey InChI 1.03 SQKHCBHOKICFHY-FNNGFRNWSA-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
XBK "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,3S,5E,7E,11R,13E,15E,17E,19E,21R,23S,24R,25S)-21-[(3-amino-3,6-dideoxy-beta-D-mannopyranosyl)oxy]-1,3,25-trihydroxy-11-methyl-9-oxo-10,27-dioxabicyclo[21.3.1]heptacosa-5,7,13,15,17,19-hexaene-24-carboxylic acid"
XBK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "(1S,3R,4E,6E,8E,10E,13R,16E,18E,21S,23R,25S,26R)-3-[(2R,3S,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyl-oxan-2-yl]oxy-21,23,25-trihydroxy-13-methyl-15-oxo-14,27-dioxabicyclo[21.3.1]heptacosa-4,6,8,10,16,18-hexaene-26-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
XBK 'Create component' 2010-04-12 EBI
XBK 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
XBK N N 6.404 -6.766 1
XBK C1 C 7.030 3.993 2
XBK O1 O 5.969 5.054 3
XBK C2 C 6.642 2.544 4
XBK O2 O 4.132 3.217 5
XBK C3 C 5.193 2.156 6
XBK O3 O 4.805 0.707 7
XBK C4 C 7.702 1.484 8
XBK O4 O 9.002 -2.267 9
XBK C5 C 7.702 -0.017 10
XBK O5 O 9.002 -5.266 11
XBK C6 C 9.002 -0.766 12
XBK O6 O 3.805 -5.266 13
XBK C7 C 7.702 -3.017 14
XBK O7 O 6.404 -2.267 15
XBK C8 C 7.702 -4.516 16
XBK O8 O 20.693 4.484 17
XBK C9 C 6.404 -5.266 18
XBK O9 O 20.331 7.231 19
XBK C10 C 5.104 -4.516 20
XBK O10 O 11.583 5.790 21
XBK C11 C 5.104 -3.017 22
XBK O11 O 9.928 4.769 23
XBK C12 C 3.805 -2.267 24
XBK O12 O 9.151 1.872 25
XBK C13 C 10.301 -0.017 26
XBK C14 C 11.600 -0.766 27
XBK C15 C 12.899 -0.017 28
XBK C16 C 12.899 1.484 29
XBK C17 C 14.198 2.233 30
XBK C18 C 15.497 1.484 31
XBK C19 C 16.796 2.233 32
XBK C20 C 18.095 1.484 33
XBK C21 C 19.394 2.233 34
XBK C22 C 19.394 3.733 35
XBK C23 C 18.095 2.984 36
XBK C24 C 19.943 5.782 37
XBK C25 C 18.644 5.032 38
XBK C26 C 17.345 5.782 39
XBK C27 C 16.046 5.032 40
XBK C28 C 14.597 5.421 41
XBK C29 C 13.536 4.360 42
XBK C30 C 12.036 4.360 43
XBK C31 C 10.989 2.933 44
XBK C32 C 9.540 3.321 45
XBK C33 C 8.479 4.381 46
#
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
XBK C9 N SINGLE BEGINWEDGE 1
XBK C1 O1 SINGLE BEGINWEDGE 2
XBK C1 C2 SINGLE NONE 3
XBK C1 C33 SINGLE NONE 4
XBK C2 C3 SINGLE BEGINDASH 5
XBK C2 C4 SINGLE NONE 6
XBK O2 C3 SINGLE NONE 7
XBK C3 O3 DOUBLE NONE 8
XBK C4 C5 SINGLE NONE 9
XBK C4 O12 SINGLE NONE 10
XBK C6 O4 SINGLE BEGINDASH 11
XBK C7 O4 SINGLE BEGINWEDGE 12
XBK C5 C6 SINGLE NONE 13
XBK C8 O5 SINGLE BEGINWEDGE 14
XBK C6 C13 SINGLE ENDUPRIGHT 15
XBK C10 O6 SINGLE BEGINDASH 16
XBK C7 O7 SINGLE NONE 17
XBK C7 C8 SINGLE NONE 18
XBK O7 C11 SINGLE NONE 19
XBK C8 C9 SINGLE NONE 20
XBK O8 C22 SINGLE NONE 21
XBK O8 C24 SINGLE NONE 22
XBK C9 C10 SINGLE NONE 23
XBK O9 C24 DOUBLE NONE 24
XBK C10 C11 SINGLE NONE 25
XBK C30 O10 SINGLE BEGINWEDGE 26
XBK C11 C12 SINGLE BEGINWEDGE 27
XBK C32 O11 SINGLE BEGINDASH 28
XBK O12 C32 SINGLE NONE 29
XBK C13 C14 DOUBLE NONE 30
XBK C14 C15 SINGLE ENDUPRIGHT 31
XBK C15 C16 DOUBLE NONE 32
XBK C16 C17 SINGLE ENDUPRIGHT 33
XBK C17 C18 DOUBLE NONE 34
XBK C18 C19 SINGLE ENDUPRIGHT 35
XBK C19 C20 DOUBLE NONE 36
XBK C20 C21 SINGLE ENDUPRIGHT 37
XBK C21 C22 SINGLE NONE 38
XBK C22 C23 SINGLE BEGINWEDGE 39
XBK C24 C25 SINGLE ENDUPRIGHT 40
XBK C25 C26 DOUBLE NONE 41
XBK C26 C27 SINGLE ENDUPRIGHT 42
XBK C27 C28 DOUBLE NONE 43
XBK C28 C29 SINGLE ENDUPRIGHT 44
XBK C29 C30 SINGLE NONE 45
XBK C30 C31 SINGLE NONE 46
XBK C31 C32 SINGLE NONE 47
XBK C32 C33 SINGLE NONE 48
#
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
XBK MurckoScaffold S1 scaffold 'O=C1/C=C/C=C/CCCC2CCC[C@H](C[C@@H](O[C@H]3CCCCO3)/C=C/C=C/C=C/C=C/CCO1)O2' InChI=1S/C30H42O5/c31-29-21-12-8-5-7-10-17-26-19-16-20-27(34-26)25-28(35-30-22-13-15-24-33-30)18-11-6-3-1-2-4-9-14-23-32-29/h1-6,8-9,11-12,18,21,26-28,30H,7,10,13-17,19-20,22-25H2/b2-1+,6-3+,8-5+,9-4+,18-11+,21-12+/t26-,27-,28+,30+/m1/s1 MNUPNNGMLFVYHU-RONVVXEESA-N
XBK pyranose F1 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-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
XBK C1 S1 1
XBK C2 S1 1
XBK C4 S1 1
XBK O4 S1 1
XBK C5 S1 1
XBK C6 S1 1
XBK C7 S1 1
XBK O7 S1 1
XBK C8 S1 1
XBK O8 S1 1
XBK C9 S1 1
XBK O9 S1 1
XBK C10 S1 1
XBK C11 S1 1
XBK O12 S1 1
XBK C13 S1 1
XBK C14 S1 1
XBK C15 S1 1
XBK C16 S1 1
XBK C17 S1 1
XBK C18 S1 1
XBK C19 S1 1
XBK C20 S1 1
XBK C21 S1 1
XBK C22 S1 1
XBK C24 S1 1
XBK C25 S1 1
XBK C26 S1 1
XBK C27 S1 1
XBK C28 S1 1
XBK C29 S1 1
XBK C30 S1 1
XBK C31 S1 1
XBK C32 S1 1
XBK C33 S1 1
XBK C2 F1 1
XBK C4 F1 1
XBK O12 F1 1
XBK C32 F1 1
XBK C33 F1 1
XBK C1 F1 1
XBK O11 F1 1
XBK C10 F1 2
XBK C11 F1 2
XBK O7 F1 2
XBK C7 F1 2
XBK C8 F1 2
XBK C9 F1 2
XBK O4 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id XBK
_pdbe_chem_comp_rdkit_properties.exactmw 649.310
_pdbe_chem_comp_rdkit_properties.amw 649.734
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 13
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 13
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 46
_pdbe_chem_comp_rdkit_properties.NumAtoms 93
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 13
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.576
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 12
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 334.815
_pdbe_chem_comp_rdkit_properties.tpsa 218.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.909
_pdbe_chem_comp_rdkit_properties.CrippenMR 165.638
_pdbe_chem_comp_rdkit_properties.chi0v 21.846
_pdbe_chem_comp_rdkit_properties.chi1v 11.240
_pdbe_chem_comp_rdkit_properties.chi2v 4.286
_pdbe_chem_comp_rdkit_properties.chi3v 4.286
_pdbe_chem_comp_rdkit_properties.chi4v 2.562
_pdbe_chem_comp_rdkit_properties.chi0n 68.846
_pdbe_chem_comp_rdkit_properties.chi1n 34.084
_pdbe_chem_comp_rdkit_properties.chi2n 4.286
_pdbe_chem_comp_rdkit_properties.chi3n 4.286
_pdbe_chem_comp_rdkit_properties.chi4n 2.562
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.980
_pdbe_chem_comp_rdkit_properties.kappa1 8.971
_pdbe_chem_comp_rdkit_properties.kappa2 17.803
_pdbe_chem_comp_rdkit_properties.kappa3 11.368
_pdbe_chem_comp_rdkit_properties.Phi 3.472
#
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
XBK UniChem ZINC ZINC000098209606
XBK UniChem PubChem 49867845
#
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
XBK N -7.478 1.595 0.463 ETKDGv3 1
XBK C1 -2.690 -4.677 -0.471 ETKDGv3 2
XBK O1 -3.288 -4.938 -1.717 ETKDGv3 3
XBK C2 -3.445 -3.553 0.287 ETKDGv3 4
XBK O2 -4.868 -4.928 1.826 ETKDGv3 5
XBK C3 -3.837 -4.005 1.678 ETKDGv3 6
XBK O3 -3.236 -3.576 2.700 ETKDGv3 7
XBK C4 -2.655 -2.211 0.305 ETKDGv3 8
XBK O4 -3.258 0.632 0.068 ETKDGv3 9
XBK C5 -2.711 -1.462 -1.056 ETKDGv3 10
XBK O5 -5.706 -0.324 -0.386 ETKDGv3 11
XBK C6 -2.479 0.066 -0.979 ETKDGv3 12
XBK O6 -5.876 3.723 -2.068 ETKDGv3 13
XBK C7 -4.173 1.612 -0.394 ETKDGv3 14
XBK O7 -4.500 2.457 0.692 ETKDGv3 15
XBK C8 -5.475 0.952 -0.936 ETKDGv3 16
XBK O8 7.922 1.582 -0.013 ETKDGv3 17
XBK C9 -6.716 1.881 -0.759 ETKDGv3 18
XBK O9 6.369 1.337 -1.706 ETKDGv3 19
XBK C10 -6.298 3.369 -0.774 ETKDGv3 20
XBK O10 1.771 -4.784 -1.302 ETKDGv3 21
XBK C11 -5.133 3.645 0.232 ETKDGv3 22
XBK O11 -0.694 -4.347 1.693 ETKDGv3 23
XBK C12 -5.629 4.427 1.450 ETKDGv3 24
XBK O12 -1.313 -2.317 0.771 ETKDGv3 25
XBK C13 -1.028 0.409 -0.754 ETKDGv3 26
XBK C14 -0.595 1.665 -0.899 ETKDGv3 27
XBK C15 0.823 2.018 -0.717 ETKDGv3 28
XBK C16 1.262 3.242 -1.036 ETKDGv3 29
XBK C17 2.670 3.673 -0.914 ETKDGv3 30
XBK C18 3.531 3.159 -0.028 ETKDGv3 31
XBK C19 4.918 3.648 0.043 ETKDGv3 32
XBK C20 5.750 3.215 0.993 ETKDGv3 33
XBK C21 7.188 3.650 1.043 ETKDGv3 34
XBK C22 8.027 3.006 -0.079 ETKDGv3 35
XBK C23 9.496 3.399 0.066 ETKDGv3 36
XBK C24 6.934 0.855 -0.686 ETKDGv3 37
XBK C25 6.530 -0.455 -0.154 ETKDGv3 38
XBK C26 5.462 -1.109 -0.618 ETKDGv3 39
XBK C27 4.979 -2.331 0.043 ETKDGv3 40
XBK C28 3.821 -2.887 -0.316 ETKDGv3 41
XBK C29 3.255 -4.050 0.453 ETKDGv3 42
XBK C30 1.806 -4.389 0.046 ETKDGv3 43
XBK C31 0.855 -3.183 0.260 ETKDGv3 44
XBK C32 -0.627 -3.552 0.533 ETKDGv3 45
XBK C33 -1.196 -4.370 -0.652 ETKDGv3 46
XBK HN -7.942 0.663 0.367 ETKDGv3 47
XBK HNA -6.840 1.552 1.290 ETKDGv3 48
XBK H1 -2.758 -5.622 0.114 ETKDGv3 49
XBK HO1 -3.259 -4.100 -2.248 ETKDGv3 50
XBK H2 -4.414 -3.369 -0.228 ETKDGv3 51
XBK H4 -3.190 -1.569 1.037 ETKDGv3 52
XBK H5 -3.713 -1.612 -1.511 ETKDGv3 53
XBK H5A -1.987 -1.890 -1.775 ETKDGv3 54
XBK HO5 -5.586 -0.264 0.597 ETKDGv3 55
XBK H6 -2.745 0.452 -1.994 ETKDGv3 56
XBK HO6 -6.692 3.818 -2.626 ETKDGv3 57
XBK H7 -3.704 2.231 -1.201 ETKDGv3 58
XBK H8 -5.324 0.806 -2.029 ETKDGv3 59
XBK H9 -7.400 1.708 -1.621 ETKDGv3 60
XBK H10 -7.188 3.990 -0.511 ETKDGv3 61
XBK HO10 2.134 -5.708 -1.340 ETKDGv3 62
XBK H11 -4.367 4.292 -0.255 ETKDGv3 63
XBK H12 -6.411 3.855 1.992 ETKDGv3 64
XBK H12A -4.784 4.618 2.145 ETKDGv3 65
XBK H12B -6.049 5.406 1.134 ETKDGv3 66
XBK H13 -0.318 -0.371 -0.516 ETKDGv3 67
XBK H14 -1.297 2.443 -1.177 ETKDGv3 68
XBK H15 1.510 1.263 -0.356 ETKDGv3 69
XBK H16 0.571 3.954 -1.473 ETKDGv3 70
XBK H17 2.987 4.495 -1.544 ETKDGv3 71
XBK H18 3.211 2.389 0.664 ETKDGv3 72
XBK H19 5.274 4.354 -0.699 ETKDGv3 73
XBK H20 5.396 2.525 1.750 ETKDGv3 74
XBK H21 7.244 4.758 0.976 ETKDGv3 75
XBK H21A 7.607 3.349 2.029 ETKDGv3 76
XBK H22 7.678 3.380 -1.068 ETKDGv3 77
XBK H23 9.608 4.503 0.010 ETKDGv3 78
XBK H23A 9.901 3.040 1.037 ETKDGv3 79
XBK H23B 10.088 2.944 -0.756 ETKDGv3 80
XBK H25 7.076 -0.847 0.696 ETKDGv3 81
XBK H26 4.894 -0.702 -1.447 ETKDGv3 82
XBK H27 5.538 -2.746 0.875 ETKDGv3 83
XBK H28 3.256 -2.462 -1.138 ETKDGv3 84
XBK H29 3.276 -3.817 1.540 ETKDGv3 85
XBK H29A 3.902 -4.940 0.290 ETKDGv3 86
XBK H30 1.473 -5.233 0.694 ETKDGv3 87
XBK H31 1.214 -2.580 1.125 ETKDGv3 88
XBK H31A 0.903 -2.514 -0.627 ETKDGv3 89
XBK H33 -1.009 -3.837 -1.607 ETKDGv3 90
XBK H33A -0.663 -5.342 -0.732 ETKDGv3 91
XBK HO2 -5.145 -5.254 2.744 ETKDGv3 92
XBK HO11 -0.419 -3.781 2.461 ETKDGv3 93
#