data_52O
#
_chem_comp.id 52O
_chem_comp.name "pivalyl-coenzyme A"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C26 H44 N7 O17 P3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-07-16
_chem_comp.pdbx_modified_date 2015-09-04
_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 851.651
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 52O
_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 5CJW
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
52O O3 O1 O 0 1 N N N N N N -208.012 -104.914 -36.615 -7.861 2.648 1.004 O3 52O 1
52O C4 C1 C 0 1 N N R N N N -210.059 -104.819 -35.319 -5.459 2.450 0.600 C4 52O 2
52O C5 C2 C 0 1 N N N N N N -208.426 -104.988 -32.167 -5.156 -0.884 -0.845 C5 52O 3
52O O4 O2 O 0 1 N N N N N N -209.466 -104.067 -31.781 -3.939 -1.469 -0.378 O4 52O 4
52O C6 C3 C 0 1 Y N N N N N -212.004 -103.314 -35.955 -5.008 4.934 0.779 C6 52O 5
52O N1 N1 N 0 1 Y N N N N N -211.202 -103.955 -35.042 -4.881 3.720 0.153 N1 52O 6
52O C7 C4 C 0 1 Y N N N N N -211.714 -103.638 -33.811 -4.119 3.911 -0.961 C7 52O 7
52O C8 C5 C 0 1 Y N N N N N -212.965 -102.649 -35.210 -4.292 5.852 -0.008 C8 52O 8
52O N2 N2 N 0 1 Y N N N N N -212.768 -102.860 -33.854 -3.774 5.163 -1.053 N2 52O 9
52O C9 C6 C 0 1 N N N N N N -209.391 -100.640 -26.025 2.113 -5.214 1.772 C9 52O 10
52O O5 O3 O 0 1 N N N N N N -206.608 -101.692 -35.975 -10.130 -1.328 0.985 O5 52O 11
52O C10 C7 C 0 1 N N R N N N -208.742 -100.692 -24.619 3.400 -6.038 1.697 C10 52O 12
52O O6 O4 O 0 1 N N N N N N -205.793 -103.838 -36.936 -8.656 -1.768 -1.016 O6 52O 13
52O C11 C8 C 0 1 N N N N N N -209.544 -102.041 -26.615 1.598 -4.942 0.357 C11 52O 14
52O C12 C9 C 0 1 Y N N N N N -213.928 -101.913 -35.924 -4.254 7.194 0.407 C12 52O 15
52O N3 N3 N 0 1 Y N N N N N -211.891 -103.326 -37.288 -5.623 5.365 1.875 N3 52O 16
52O C13 C10 C 0 1 N N N N N N -208.517 -99.807 -26.969 1.055 -5.992 2.558 C13 52O 17
52O O7 O5 O 0 1 N N N N N N -210.748 -103.281 -29.691 -1.784 -2.975 -0.424 O7 52O 18
52O C14 C11 C 0 1 N N N N N N -210.779 -99.997 -25.929 2.397 -3.886 2.475 C14 52O 19
52O O8 O6 O 0 1 N N N N N N -210.745 -102.121 -27.396 0.396 -4.173 0.427 O8 52O 20
52O C15 C12 C 0 1 Y N N N N N -212.853 -102.592 -37.855 -5.564 6.633 2.223 C15 52O 21
52O N4 N4 N 0 1 Y N N N N N -213.839 -101.904 -37.272 -4.896 7.531 1.521 N4 52O 22
52O O9 O7 O 0 1 N N N N N N -204.453 -102.687 -35.141 -10.124 0.284 -1.092 O9 52O 23
52O P1 P1 P 0 1 N N N N N N -205.818 -102.968 -35.674 -9.221 -0.687 -0.179 P1 52O 24
52O O2 O8 O 0 1 N N N N N N -206.677 -103.790 -34.582 -8.022 0.161 0.482 O2 52O 25
52O C1 C13 C 0 1 N N S N N N -208.113 -103.834 -34.437 -6.982 0.768 -0.287 C1 52O 26
52O C2 C14 C 0 1 N N R N N N -208.801 -104.076 -35.777 -6.884 2.277 0.030 C2 52O 27
52O N5 N5 N 0 1 N N N N N N -214.923 -101.233 -35.346 -3.564 8.143 -0.326 N5 52O 28
52O O1 O9 O 0 1 N N N N N N -209.726 -105.515 -34.131 -4.709 1.339 0.062 O1 52O 29
52O C3 C15 C 0 1 N N R N N N -208.416 -105.116 -33.670 -5.604 0.207 0.130 C3 52O 30
52O P2 P2 P 0 1 N N N N N N -209.354 -103.185 -30.457 -3.180 -2.655 -1.160 P2 52O 31
52O O12 O10 O 0 1 N N N N N N -209.022 -101.766 -30.719 -2.917 -2.237 -2.555 O12 52O 32
52O O10 O11 O 0 1 N N N N N N -208.292 -103.808 -29.551 -4.102 -3.974 -1.160 O10 52O 33
52O P3 P3 P 0 1 N N N N N N -211.098 -103.478 -28.149 -0.422 -3.704 -0.878 P3 52O 34
52O O14 O12 O 0 1 N N N N N N -210.380 -104.661 -27.615 0.476 -2.678 -1.734 O14 52O 35
52O O13 O13 O 0 1 N N N N N N -212.601 -103.676 -28.036 -0.748 -4.885 -1.708 O13 52O 36
52O O11 O14 O 0 1 N N N N N N -208.324 -99.389 -24.256 3.109 -7.330 1.161 O11 52O 37
52O C16 C16 C 0 1 N N N N N N -209.681 -101.238 -23.555 4.393 -5.337 0.805 C16 52O 38
52O O15 O15 O 0 1 N N N N N N -210.017 -102.420 -23.570 4.698 -5.824 -0.263 O15 52O 39
52O N6 N6 N 0 1 N N N N N N -210.085 -100.375 -22.626 4.942 -4.170 1.196 N6 52O 40
52O C17 C17 C 0 1 N N N N N N -210.880 -100.768 -21.474 5.833 -3.440 0.289 C17 52O 41
52O C18 C18 C 0 1 N N N N N N -210.393 -100.084 -20.221 6.315 -2.158 0.971 C18 52O 42
52O C19 C19 C 0 1 N N N N N N -211.354 -100.227 -19.070 7.231 -1.408 0.039 C19 52O 43
52O O16 O16 O 0 1 N N N N N N -212.400 -100.862 -19.177 7.474 -1.854 -1.062 O16 52O 44
52O N7 N7 N 0 1 N N N N N N -210.994 -99.616 -17.948 7.780 -0.240 0.429 N7 52O 45
52O C20 C20 C 0 1 N N N N N N -211.816 -99.587 -16.749 8.671 0.489 -0.477 C20 52O 46
52O C21 C21 C 0 1 N N N N N N -211.175 -98.651 -15.745 9.153 1.771 0.205 C21 52O 47
52O S1 S1 S 0 1 N N N N N N -212.060 -98.460 -14.176 10.253 2.673 -0.915 S1 52O 48
52O C22 C22 C 0 1 N N N N N N -210.985 -97.362 -13.316 10.636 4.022 0.067 C22 52O 49
52O O17 O17 O 0 1 N N N N N N -209.968 -96.937 -13.792 10.164 4.115 1.181 O17 52O 50
52O C23 C23 C 0 1 N N N N N N -211.473 -97.013 -11.936 11.558 5.095 -0.452 C23 52O 51
52O C24 C24 C 0 1 N N N N N N -210.375 -97.225 -10.922 12.920 4.480 -0.783 C24 52O 52
52O C25 C25 C 0 1 N N N N N N -212.638 -97.886 -11.573 10.958 5.715 -1.716 C25 52O 53
52O C26 C26 C 0 1 N N N N N N -211.905 -95.571 -11.909 11.733 6.178 0.614 C26 52O 54
52O H1 H1 H 0 1 N N N N N N -207.159 -104.517 -36.748 -7.806 3.572 1.285 H1 52O 55
52O H2 H2 H 0 1 N N N N N N -210.335 -105.539 -36.104 -5.476 2.404 1.689 H2 52O 56
52O H3 H3 H 0 1 N N N N N N -208.618 -105.972 -31.714 -4.996 -0.448 -1.830 H3 52O 57
52O H4 H4 H 0 1 N N N N N N -207.452 -104.610 -31.823 -5.927 -1.652 -0.908 H4 52O 58
52O H5 H5 H 0 1 N N N N N N -211.287 -103.998 -32.887 -3.842 3.139 -1.662 H5 52O 59
52O H6 H6 H 0 1 N N N N N N -206.912 -101.712 -36.875 -10.873 -1.854 0.659 H6 52O 60
52O H7 H7 H 0 1 N N N N N N -207.867 -101.356 -24.677 3.822 -6.145 2.696 H7 52O 61
52O H8 H8 H 0 1 N N N N N N -209.592 -102.776 -25.798 2.351 -4.388 -0.203 H8 52O 62
52O H9 H9 H 0 1 N N N N N N -208.678 -102.262 -27.256 1.396 -5.889 -0.144 H9 52O 63
52O H10 H10 H 0 1 N N N N N N -208.396 -98.793 -26.559 0.120 -5.433 2.560 H10 52O 64
52O H11 H11 H 0 1 N N N N N N -207.530 -100.282 -27.069 0.897 -6.964 2.091 H11 52O 65
52O H12 H12 H 0 1 N N N N N N -208.997 -99.748 -27.957 1.396 -6.133 3.584 H12 52O 66
52O H13 H13 H 0 1 N N N N N N -211.412 -100.590 -25.253 3.063 -3.283 1.858 H13 52O 67
52O H14 H14 H 0 1 N N N N N N -210.683 -98.973 -25.538 1.461 -3.349 2.631 H14 52O 68
52O H15 H15 H 0 1 N N N N N N -211.238 -99.966 -26.928 2.870 -4.079 3.439 H15 52O 69
52O H16 H16 H 0 1 N N N N N N -212.830 -102.549 -38.934 -6.076 6.951 3.120 H16 52O 70
52O H17 H17 H 0 1 N N N N N N -203.804 -103.108 -35.693 -10.527 1.017 -0.607 H17 52O 71
52O H18 H18 H 0 1 N N N N N N -208.520 -102.949 -33.926 -7.153 0.609 -1.351 H18 52O 72
52O H19 H19 H 0 1 N N N N N N -209.063 -103.124 -36.261 -7.007 2.869 -0.877 H19 52O 73
52O H20 H20 H 0 1 N N N N N N -215.482 -100.796 -36.051 -3.099 7.885 -1.138 H20 52O 74
52O H21 H21 H 0 1 N N N N N N -215.490 -101.861 -34.813 -3.546 9.066 -0.030 H21 52O 75
52O H22 H22 H 0 1 N N N N N N -207.676 -105.878 -33.955 -5.644 -0.184 1.146 H22 52O 76
52O H23 H23 H 0 1 N N N N N N -207.634 -103.157 -29.340 -4.315 -4.305 -0.276 H23 52O 77
52O H24 H24 H 0 1 N N N N N N -211.010 -105.303 -27.310 0.727 -1.878 -1.251 H24 52O 78
52O H25 H25 H 0 1 N N N N N N -207.925 -99.413 -23.394 2.730 -7.311 0.272 H25 52O 79
52O H26 H26 H 0 1 N N N N N N -209.830 -99.413 -22.725 4.748 -3.813 2.076 H26 52O 80
52O H27 H27 H 0 1 N N N N N N -211.930 -100.491 -21.650 6.691 -4.065 0.042 H27 52O 81
52O H28 H28 H 0 1 N N N N N N -210.806 -101.857 -21.341 5.293 -3.185 -0.623 H28 52O 82
52O H29 H29 H 0 1 N N N N N N -209.428 -100.526 -19.931 5.457 -1.533 1.219 H29 52O 83
52O H30 H30 H 0 1 N N N N N N -210.257 -99.014 -20.435 6.855 -2.413 1.884 H30 52O 84
52O H31 H31 H 0 1 N N N N N N -210.109 -99.150 -17.926 7.586 0.117 1.310 H31 52O 85
52O H32 H32 H 0 1 N N N N N N -212.825 -99.227 -17.000 9.529 -0.135 -0.725 H32 52O 86
52O H33 H33 H 0 1 N N N N N N -211.884 -100.598 -16.322 8.131 0.744 -1.389 H33 52O 87
52O H34 H34 H 0 1 N N N N N N -210.168 -99.033 -15.521 8.295 2.396 0.453 H34 52O 88
52O H35 H35 H 0 1 N N N N N N -211.095 -97.658 -16.211 9.693 1.517 1.117 H35 52O 89
52O H36 H36 H 0 1 N N N N N N -210.746 -96.966 -9.919 12.795 3.709 -1.543 H36 52O 90
52O H37 H37 H 0 1 N N N N N N -210.062 -98.279 -10.936 13.587 5.256 -1.159 H37 52O 91
52O H38 H38 H 0 1 N N N N N N -209.517 -96.584 -11.172 13.347 4.038 0.117 H38 52O 92
52O H39 H39 H 0 1 N N N N N N -212.991 -97.627 -10.564 9.988 6.153 -1.480 H39 52O 93
52O H40 H40 H 0 1 N N N N N N -213.452 -97.731 -12.297 11.625 6.491 -2.092 H40 52O 94
52O H41 H41 H 0 1 N N N N N N -212.326 -98.941 -11.593 10.834 4.944 -2.476 H41 52O 95
52O H42 H42 H 0 1 N N N N N N -212.262 -95.314 -10.901 12.160 5.736 1.514 H42 52O 96
52O H43 H43 H 0 1 N N N N N N -211.052 -94.928 -12.171 12.400 6.954 0.238 H43 52O 97
52O H44 H44 H 0 1 N N N N N N -212.716 -95.418 -12.636 10.763 6.616 0.850 H44 52O 98
#
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
52O C15 N3 DOUB Y N 1
52O C15 N4 SING Y N 2
52O N3 C6 SING Y N 3
52O N4 C12 DOUB Y N 4
52O O6 P1 DOUB N N 5
52O O3 C2 SING N N 6
52O O5 P1 SING N N 7
52O C6 C8 DOUB Y N 8
52O C6 N1 SING Y N 9
52O C12 N5 SING N N 10
52O C12 C8 SING Y N 11
52O C2 C4 SING N N 12
52O C2 C1 SING N N 13
52O P1 O9 SING N N 14
52O P1 O2 SING N N 15
52O C4 N1 SING N N 16
52O C4 O1 SING N N 17
52O C8 N2 SING Y N 18
52O N1 C7 SING Y N 19
52O O2 C1 SING N N 20
52O C1 C3 SING N N 21
52O O1 C3 SING N N 22
52O N2 C7 DOUB Y N 23
52O C3 C5 SING N N 24
52O C5 O4 SING N N 25
52O O4 P2 SING N N 26
52O O12 P2 DOUB N N 27
52O P2 O7 SING N N 28
52O P2 O10 SING N N 29
52O O7 P3 SING N N 30
52O P3 O13 DOUB N N 31
52O P3 O14 SING N N 32
52O P3 O8 SING N N 33
52O O8 C11 SING N N 34
52O C13 C9 SING N N 35
52O C11 C9 SING N N 36
52O C9 C14 SING N N 37
52O C9 C10 SING N N 38
52O C10 O11 SING N N 39
52O C10 C16 SING N N 40
52O O15 C16 DOUB N N 41
52O C16 N6 SING N N 42
52O N6 C17 SING N N 43
52O C17 C18 SING N N 44
52O C18 C19 SING N N 45
52O O16 C19 DOUB N N 46
52O C19 N7 SING N N 47
52O N7 C20 SING N N 48
52O C20 C21 SING N N 49
52O C21 S1 SING N N 50
52O S1 C22 SING N N 51
52O O17 C22 DOUB N N 52
52O C22 C23 SING N N 53
52O C23 C26 SING N N 54
52O C23 C25 SING N N 55
52O C23 C24 SING N N 56
52O O3 H1 SING N N 57
52O C4 H2 SING N N 58
52O C5 H3 SING N N 59
52O C5 H4 SING N N 60
52O C7 H5 SING N N 61
52O O5 H6 SING N N 62
52O C10 H7 SING N N 63
52O C11 H8 SING N N 64
52O C11 H9 SING N N 65
52O C13 H10 SING N N 66
52O C13 H11 SING N N 67
52O C13 H12 SING N N 68
52O C14 H13 SING N N 69
52O C14 H14 SING N N 70
52O C14 H15 SING N N 71
52O C15 H16 SING N N 72
52O O9 H17 SING N N 73
52O C1 H18 SING N N 74
52O C2 H19 SING N N 75
52O N5 H20 SING N N 76
52O N5 H21 SING N N 77
52O C3 H22 SING N N 78
52O O10 H23 SING N N 79
52O O14 H24 SING N N 80
52O O11 H25 SING N N 81
52O N6 H26 SING N N 82
52O C17 H27 SING N N 83
52O C17 H28 SING N N 84
52O C18 H29 SING N N 85
52O C18 H30 SING N N 86
52O N7 H31 SING N N 87
52O C20 H32 SING N N 88
52O C20 H33 SING N N 89
52O C21 H34 SING N N 90
52O C21 H35 SING N N 91
52O C24 H36 SING N N 92
52O C24 H37 SING N N 93
52O C24 H38 SING N N 94
52O C25 H39 SING N N 95
52O C25 H40 SING N N 96
52O C25 H41 SING N N 97
52O C26 H42 SING N N 98
52O C26 H43 SING N N 99
52O C26 H44 SING N N 100
#
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
52O SMILES ACDLabs 12.01 OC3C(n1c2c(nc1)c(N)ncn2)OC(COP(OP(OCC(C)(C(O)C(NCCC(NCCSC(C(C)(C)C)=O)=O)=O)C)(=O)O)(O)=O)C3OP(O)(=O)O
52O InChI InChI 1.03 InChI=1S/C26H44N7O17P3S/c1-25(2,3)24(38)54-9-8-28-15(34)6-7-29-22(37)19(36)26(4,5)11-47-53(44,45)50-52(42,43)46-10-14-18(49-51(39,40)41)17(35)23(48-14)33-13-32-16-20(27)30-12-31-21(16)33/h12-14,17-19,23,35-36H,6-11H2,1-5H3,(H,28,34)(H,29,37)(H,42,43)(H,44,45)(H2,27,30,31)(H2,39,40,41)/t14-,17-,18-,19+,23-/m1/s1
52O InChIKey InChI 1.03 FCMKBHDFOPWWQK-NDZSKPAWSA-N
52O SMILES_CANONICAL CACTVS 3.385 CC(C)(C)C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
52O SMILES CACTVS 3.385 CC(C)(C)C(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
52O SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 CC(C)(C)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
52O SMILES "OpenEye OEToolkits" 1.9.2 CC(C)(C)C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
#
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
52O "SYSTEMATIC NAME" ACDLabs 12.01 "S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2,2-dimethylpropanethioate (non-preferred name)"
52O "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 2,2-dimethylpropanethioate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
52O 'Create component' 2015-07-16 RCSB
52O 'Initial release' 2015-09-09 RCSB
#
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
52O O3 O 26.340 -8.010 1
52O C4 C 23.701 -7.587 2
52O C5 C 23.244 -3.733 3
52O O4 O 21.777 -3.418 4
52O C6 C 21.815 -9.470 5
52O N1 N 23.235 -9.013 6
52O C7 C 24.110 -10.220 7
52O C8 C 21.815 -10.970 8
52O N2 N 23.235 -11.427 9
52O C9 C 15.994 1.807 10
52O O5 O 27.683 -3.100 11
52O C10 C 14.527 2.121 12
52O O6 O 26.037 -1.762 13
52O C11 C 17.460 1.492 14
52O C12 C 20.516 -11.720 15
52O N3 N 20.516 -8.720 16
52O C13 C 16.308 3.274 17
52O O7 O 20.855 -0.564 18
52O C14 C 15.679 0.340 19
52O O8 O 17.922 0.065 20
52O C15 C 19.217 -9.470 21
52O N4 N 19.217 -10.970 22
52O O9 O 24.699 -3.409 23
52O P1 P 26.191 -3.255 24
52O O2 O 26.346 -4.747 25
52O C1 C 25.131 -5.626 26
52O C2 C 25.128 -7.126 27
52O N5 N 20.516 -13.220 28
52O O1 O 22.821 -6.372 29
52O C3 C 23.705 -5.160 30
52O P2 P 21.316 -1.991 31
52O O12 O 19.889 -2.452 32
52O O10 O 22.743 -1.530 33
52O P3 P 19.388 -0.249 34
52O O14 O 19.074 -1.716 35
52O O13 O 19.703 1.217 36
52O O11 O 13.521 1.008 37
52O C16 C 14.066 3.549 38
52O O15 O 15.072 4.662 39
52O N6 N 12.599 3.863 40
52O C17 C 12.138 5.290 41
52O C18 C 10.672 5.605 42
52O C19 C 10.211 7.032 43
52O O16 O 11.216 8.145 44
52O N7 N 8.744 7.347 45
52O C20 C 8.283 8.774 46
52O C21 C 6.816 9.088 47
52O S1 S 6.355 10.516 48
52O C22 C 4.888 10.830 49
52O O17 O 3.883 9.717 50
52O C23 C 4.427 12.258 51
52O C24 C 5.855 12.719 52
52O C25 C 3.000 11.797 53
52O C26 C 3.966 13.685 54
#
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
52O C15 N3 SINGLE NONE 1
52O C15 N4 DOUBLE NONE 2
52O N3 C6 DOUBLE NONE 3
52O N4 C12 SINGLE NONE 4
52O O6 P1 DOUBLE NONE 5
52O C2 O3 SINGLE BEGINWEDGE 6
52O O5 P1 SINGLE NONE 7
52O C6 C8 SINGLE NONE 8
52O C6 N1 SINGLE NONE 9
52O C12 N5 SINGLE NONE 10
52O C12 C8 DOUBLE NONE 11
52O C2 C4 SINGLE NONE 12
52O C2 C1 SINGLE NONE 13
52O P1 O9 SINGLE NONE 14
52O P1 O2 SINGLE NONE 15
52O C4 N1 SINGLE BEGINDASH 16
52O C4 O1 SINGLE NONE 17
52O C8 N2 SINGLE NONE 18
52O N1 C7 SINGLE NONE 19
52O C1 O2 SINGLE BEGINWEDGE 20
52O C1 C3 SINGLE NONE 21
52O O1 C3 SINGLE NONE 22
52O N2 C7 DOUBLE NONE 23
52O C3 C5 SINGLE BEGINDASH 24
52O C5 O4 SINGLE NONE 25
52O O4 P2 SINGLE NONE 26
52O O12 P2 DOUBLE NONE 27
52O P2 O7 SINGLE NONE 28
52O P2 O10 SINGLE BEGINDASH 29
52O O7 P3 SINGLE NONE 30
52O P3 O13 DOUBLE NONE 31
52O P3 O14 SINGLE BEGINDASH 32
52O P3 O8 SINGLE NONE 33
52O O8 C11 SINGLE NONE 34
52O C13 C9 SINGLE NONE 35
52O C11 C9 SINGLE NONE 36
52O C9 C14 SINGLE NONE 37
52O C9 C10 SINGLE NONE 38
52O C10 O11 SINGLE BEGINWEDGE 39
52O C10 C16 SINGLE NONE 40
52O O15 C16 DOUBLE NONE 41
52O C16 N6 SINGLE NONE 42
52O N6 C17 SINGLE NONE 43
52O C17 C18 SINGLE NONE 44
52O C18 C19 SINGLE NONE 45
52O O16 C19 DOUBLE NONE 46
52O C19 N7 SINGLE NONE 47
52O N7 C20 SINGLE NONE 48
52O C20 C21 SINGLE NONE 49
52O C21 S1 SINGLE NONE 50
52O S1 C22 SINGLE NONE 51
52O O17 C22 DOUBLE NONE 52
52O C22 C23 SINGLE NONE 53
52O C23 C26 SINGLE NONE 54
52O C23 C25 SINGLE NONE 55
52O C23 C24 SINGLE NONE 56
#
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
52O MurckoScaffold S1 scaffold 'c1ncc2ncn([C@H]3CCCO3)c2n1' InChI=1S/C9H10N4O/c1-2-8(14-3-1)13-6-12-7-4-10-5-11-9(7)13/h4-6,8H,1-3H2/t8-/m1/s1 DAKONNSVCLKUJN-MRVPVSSYSA-N
52O adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
52O amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
52O imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
52O phosphate F4 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
52O purine F5 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
52O pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
52O ribose F7 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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
52O C4 S1 1
52O C6 S1 1
52O N1 S1 1
52O C7 S1 1
52O C8 S1 1
52O N2 S1 1
52O C12 S1 1
52O N3 S1 1
52O C15 S1 1
52O N4 S1 1
52O C1 S1 1
52O C2 S1 1
52O O1 S1 1
52O C3 S1 1
52O N4 F1 1
52O C12 F1 1
52O C8 F1 1
52O C6 F1 1
52O N3 F1 1
52O C15 F1 1
52O N1 F1 1
52O C7 F1 1
52O N2 F1 1
52O N5 F1 1
52O N6 F2 1
52O C16 F2 1
52O O15 F2 1
52O C10 F2 1
52O N7 F2 2
52O C19 F2 2
52O O16 F2 2
52O C18 F2 2
52O C6 F3 1
52O C8 F3 1
52O N2 F3 1
52O C7 F3 1
52O N1 F3 1
52O O4 F4 1
52O P2 F4 1
52O O12 F4 1
52O O7 F4 1
52O O10 F4 1
52O O5 F4 2
52O P1 F4 2
52O O6 F4 2
52O O9 F4 2
52O O2 F4 2
52O O7 F4 3
52O P3 F4 3
52O O13 F4 3
52O O14 F4 3
52O O8 F4 3
52O N2 F5 1
52O C7 F5 1
52O N1 F5 1
52O C6 F5 1
52O C8 F5 1
52O C12 F5 1
52O N4 F5 1
52O C15 F5 1
52O N3 F5 1
52O C8 F6 1
52O C6 F6 1
52O N3 F6 1
52O C15 F6 1
52O N4 F6 1
52O C12 F6 1
52O C2 F7 1
52O C1 F7 1
52O C3 F7 1
52O O1 F7 1
52O C4 F7 1
52O C5 F7 1
52O O4 F7 1
52O O2 F7 1
52O O3 F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 52O
_pdbe_chem_comp_rdkit_properties.exactmw 851.173
_pdbe_chem_comp_rdkit_properties.amw 851.659
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 24
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 28
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 23
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 54
_pdbe_chem_comp_rdkit_properties.NumAtoms 98
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 28
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.692
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 7
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 374.449
_pdbe_chem_comp_rdkit_properties.tpsa 363.630
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.098
_pdbe_chem_comp_rdkit_properties.CrippenMR 183.523
_pdbe_chem_comp_rdkit_properties.chi0v 28.320
_pdbe_chem_comp_rdkit_properties.chi1v 17.469
_pdbe_chem_comp_rdkit_properties.chi2v 8.010
_pdbe_chem_comp_rdkit_properties.chi3v 8.010
_pdbe_chem_comp_rdkit_properties.chi4v 5.094
_pdbe_chem_comp_rdkit_properties.chi0n 68.821
_pdbe_chem_comp_rdkit_properties.chi1n 33.509
_pdbe_chem_comp_rdkit_properties.chi2n 4.689
_pdbe_chem_comp_rdkit_properties.chi3n 4.689
_pdbe_chem_comp_rdkit_properties.chi4n 2.678
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.440
_pdbe_chem_comp_rdkit_properties.kappa1 13.848
_pdbe_chem_comp_rdkit_properties.kappa2 18.219
_pdbe_chem_comp_rdkit_properties.kappa3 13.351
_pdbe_chem_comp_rdkit_properties.Phi 4.672
#
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
52O UniChem PDBe 52O
52O UniChem ChEBI 137545
52O UniChem ZINC ZINC000195883426
52O UniChem SureChEMBL SCHEMBL7524149
52O UniChem PubChem 9543321
52O UniChem MetaboLights MTBLC137545
52O UniChem BRENDA 214081
52O UniChem Nikkaji J3.487.819F
#
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
52O O3 7.475 4.768 -1.371 ETKDGv3 1
52O C4 7.276 2.900 0.176 ETKDGv3 2
52O C5 3.786 2.325 -0.121 ETKDGv3 3
52O O4 3.205 2.456 1.154 ETKDGv3 4
52O C6 9.363 1.411 0.068 ETKDGv3 5
52O N1 7.971 1.614 0.209 ETKDGv3 6
52O C7 7.431 0.337 -0.197 ETKDGv3 7
52O C8 9.578 0.079 -0.363 ETKDGv3 8
52O N2 8.321 -0.564 -0.523 ETKDGv3 9
52O C9 -1.915 -1.410 1.527 ETKDGv3 10
52O O5 4.136 2.363 -4.300 ETKDGv3 11
52O C10 -3.193 -0.892 2.274 ETKDGv3 12
52O O6 6.601 3.271 -4.417 ETKDGv3 13
52O C11 -1.408 -0.299 0.567 ETKDGv3 14
52O C12 10.800 -0.329 -0.702 ETKDGv3 15
52O N3 10.310 2.296 0.132 ETKDGv3 16
52O C13 -2.222 -2.686 0.709 ETKDGv3 17
52O O7 0.722 1.936 0.020 ETKDGv3 18
52O C14 -0.801 -1.727 2.554 ETKDGv3 19
52O O8 -0.219 -0.705 -0.075 ETKDGv3 20
52O C15 11.654 1.859 -0.179 ETKDGv3 21
52O N4 11.879 0.625 -0.571 ETKDGv3 22
52O O9 4.706 4.959 -5.016 ETKDGv3 23
52O P1 5.190 3.664 -4.041 ETKDGv3 24
52O O2 5.120 4.153 -2.406 ETKDGv3 25
52O C1 5.679 3.148 -1.581 ETKDGv3 26
52O C2 7.136 3.403 -1.267 ETKDGv3 27
52O N5 11.045 -1.641 -1.208 ETKDGv3 28
52O O1 5.993 2.752 0.749 ETKDGv3 29
52O C3 5.044 3.193 -0.196 ETKDGv3 30
52O P2 1.836 1.443 1.219 ETKDGv3 31
52O O12 1.181 1.614 2.570 ETKDGv3 32
52O O10 2.335 -0.172 1.066 ETKDGv3 33
52O P3 0.385 0.606 -0.985 ETKDGv3 34
52O O14 1.798 0.127 -1.786 ETKDGv3 35
52O O13 -0.637 1.021 -2.021 ETKDGv3 36
52O O11 -4.188 -0.505 1.356 ETKDGv3 37
52O C16 -3.783 -1.904 3.227 ETKDGv3 38
52O O15 -3.415 -1.906 4.433 ETKDGv3 39
52O N6 -4.754 -2.860 2.770 ETKDGv3 40
52O C17 -5.501 -3.725 3.684 ETKDGv3 41
52O C18 -6.512 -2.920 4.509 ETKDGv3 42
52O C19 -7.406 -2.106 3.622 ETKDGv3 43
52O O16 -7.194 -0.870 3.495 ETKDGv3 44
52O N7 -8.452 -2.741 2.873 ETKDGv3 45
52O C20 -9.125 -2.073 1.762 ETKDGv3 46
52O C21 -8.211 -2.039 0.539 ETKDGv3 47
52O S1 -8.976 -1.048 -0.786 ETKDGv3 48
52O C22 -7.670 -1.405 -1.978 ETKDGv3 49
52O O17 -7.791 -2.405 -2.670 ETKDGv3 50
52O C23 -6.440 -0.518 -2.152 ETKDGv3 51
52O C24 -5.184 -1.338 -1.805 ETKDGv3 52
52O C25 -6.358 -0.053 -3.620 ETKDGv3 53
52O C26 -6.490 0.730 -1.245 ETKDGv3 54
52O H1 6.909 5.278 -0.733 ETKDGv3 55
52O H2 7.853 3.629 0.787 ETKDGv3 56
52O H3 3.077 2.672 -0.908 ETKDGv3 57
52O H4 4.073 1.266 -0.318 ETKDGv3 58
52O H5 6.369 0.140 -0.254 ETKDGv3 59
52O H6 4.682 1.549 -4.154 ETKDGv3 60
52O H7 -2.899 -0.007 2.891 ETKDGv3 61
52O H8 -1.242 0.628 1.162 ETKDGv3 62
52O H9 -2.190 -0.094 -0.200 ETKDGv3 63
52O H10 -1.325 -3.019 0.145 ETKDGv3 64
52O H11 -2.521 -3.524 1.372 ETKDGv3 65
52O H12 -3.037 -2.500 -0.021 ETKDGv3 66
52O H13 0.129 -2.060 2.046 ETKDGv3 67
52O H14 -1.110 -2.544 3.240 ETKDGv3 68
52O H15 -0.561 -0.828 3.162 ETKDGv3 69
52O H16 12.477 2.555 -0.099 ETKDGv3 70
52O H17 3.789 5.174 -4.711 ETKDGv3 71
52O H18 5.570 2.114 -1.990 ETKDGv3 72
52O H19 7.785 2.830 -1.967 ETKDGv3 73
52O H20 12.013 -1.923 -1.478 ETKDGv3 74
52O H21 10.270 -2.334 -1.313 ETKDGv3 75
52O H22 4.764 4.242 0.055 ETKDGv3 76
52O H23 3.015 -0.295 1.774 ETKDGv3 77
52O H24 1.554 -0.714 -2.248 ETKDGv3 78
52O H25 -4.100 0.473 1.211 ETKDGv3 79
52O H26 -4.960 -2.934 1.749 ETKDGv3 80
52O H27 -4.797 -4.255 4.360 ETKDGv3 81
52O H28 -6.045 -4.495 3.094 ETKDGv3 82
52O H29 -7.131 -3.619 5.112 ETKDGv3 83
52O H30 -5.975 -2.253 5.218 ETKDGv3 84
52O H31 -8.711 -3.729 3.097 ETKDGv3 85
52O H32 -9.414 -1.043 2.063 ETKDGv3 86
52O H33 -10.053 -2.630 1.506 ETKDGv3 87
52O H34 -8.039 -3.077 0.181 ETKDGv3 88
52O H35 -7.234 -1.590 0.813 ETKDGv3 89
52O H36 -5.257 -1.735 -0.771 ETKDGv3 90
52O H37 -4.268 -0.712 -1.881 ETKDGv3 91
52O H38 -5.070 -2.202 -2.496 ETKDGv3 92
52O H39 -7.265 0.526 -3.895 ETKDGv3 93
52O H40 -6.277 -0.923 -4.308 ETKDGv3 94
52O H41 -5.467 0.593 -3.778 ETKDGv3 95
52O H42 -6.510 0.446 -0.172 ETKDGv3 96
52O H43 -7.390 1.343 -1.468 ETKDGv3 97
52O H44 -5.593 1.367 -1.406 ETKDGv3 98
#