data_XJS
#
_chem_comp.id XJS
_chem_comp.name
"2'-deoxy-5-[9-(3-{[4-(diethylamino)-4-oxobutanoyl]amino}propyl)-18-ethyl-5,8,14,17-tetraoxo-4,9,13,18-tetraazaicos-1-yn-1-yl]uridine 5'-(tetrahydrogen triphosphate)"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C38 H63 N8 O20 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-09-20
_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 1044.870
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XJS
_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 3OJS
_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
XJS C1 C1 C 0 1 N N N N N N 20.037 -16.125 -6.573 -2.390 -1.219 -3.885 C1 XJS 1
XJS N1 N1 N 0 1 N N N N N N 18.729 -19.725 -7.154 -5.587 0.572 -3.565 N1 XJS 2
XJS O1 O1 O 0 1 N N N N N N 17.841 -16.133 -11.037 -10.969 0.633 1.580 O1 XJS 3
XJS P1 P1 P 0 1 N N N N N N 19.434 -16.389 -11.354 -11.198 1.116 0.062 P1 XJS 4
XJS C2 C2 C 0 1 N N N N N N 18.384 -20.113 -5.804 -6.384 -0.133 -4.384 C2 XJS 5
XJS N2 N2 N 0 1 N N N N N N 22.400 -13.439 -6.881 0.793 -1.001 -2.640 N2 XJS 6
XJS O2 O2 O 0 1 N N N N N N 17.937 -21.190 -5.608 -7.545 0.204 -4.513 O2 XJS 7
XJS P2 P2 P 0 1 N N N N N N 16.617 -16.306 -12.121 -11.781 -0.329 2.583 P2 XJS 8
XJS C3 C3 C 0 1 N N N N N N 20.471 -15.048 -6.838 -1.266 -1.530 -3.748 C3 XJS 9
XJS N3 N3 N 0 1 N N N N N N 18.581 -19.199 -4.725 -5.934 -1.201 -5.067 N3 XJS 10
XJS O3 O3 O 0 1 N N N N N N 16.162 -14.769 -12.486 -11.347 -0.013 4.101 O3 XJS 11
XJS P3 P3 P 0 1 N N N N N N 16.792 -13.859 -13.699 -11.969 -0.375 5.541 P3 XJS 12
XJS C4 C4 C 0 1 N N N N N N 19.122 -17.908 -4.957 -4.650 -1.597 -4.944 C4 XJS 13
XJS N4 N4 N 0 1 N N N N N N 23.174 -13.707 -1.207 6.199 0.156 0.089 N4 XJS 14
XJS O4 O4 O 0 1 N N N N N N 19.298 -17.152 -4.055 -4.237 -2.562 -5.559 O4 XJS 15
XJS C5 C5 C 0 1 N N N N N N 19.467 -17.524 -6.320 -3.761 -0.839 -4.051 C5 XJS 16
XJS N5 N5 N 0 1 N N N N N N 22.865 -17.872 0.688 7.555 -4.515 0.604 N5 XJS 17
XJS O5 O5 O 0 1 N N N N N N 15.681 -13.655 -14.614 -13.443 -0.256 5.486 O5 XJS 18
XJS C6 C6 C 0 1 N N N N N N 19.268 -18.417 -7.415 -4.276 0.236 -3.385 C6 XJS 19
XJS N6 N6 N 0 1 N N N N N N 23.694 -9.701 1.742 8.698 4.340 0.494 N6 XJS 20
XJS O6 O6 O 0 1 N N N N N N 18.009 -14.631 -14.478 -11.567 -1.884 5.934 O6 XJS 21
XJS C7 C7 C 0 1 N N N N N N 21.014 -13.679 -7.272 0.143 -1.919 -3.577 C7 XJS 22
XJS N7 N7 N 0 1 N N N N N N 20.147 -20.974 4.682 9.401 -10.381 1.021 N7 XJS 23
XJS O7 O7 O 0 1 N N N N N N 17.366 -12.434 -13.126 -11.389 0.641 6.647 O7 XJS 24
XJS C8 C8 C 0 1 N N N N N N 22.629 -12.918 -5.526 2.095 -1.165 -2.329 C8 XJS 25
XJS N8 N8 N 0 1 N N N N N N 23.750 -4.552 -1.538 11.857 9.576 1.274 N8 XJS 26
XJS O8 O8 O 0 1 N N N N N N 15.525 -16.951 -11.392 -11.449 -1.866 2.239 O8 XJS 27
XJS C9 C9 C 0 1 N N N N N N 24.074 -12.910 -4.961 2.764 -0.220 -1.364 C9 XJS 28
XJS O9 O9 O 0 1 N N N N N N 16.979 -17.286 -13.369 -13.234 -0.091 2.426 O9 XJS 29
XJS "C1'" C1* C 0 1 N N R N N N 18.490 -20.677 -8.259 -6.134 1.730 -2.853 C1* XJS 30
XJS C10 C10 C 0 1 N N N N N N 24.174 -12.805 -3.418 4.228 -0.625 -1.187 C10 XJS 31
XJS O10 O10 O 0 1 N N N N N N 20.214 -15.379 -10.611 -12.280 2.308 0.034 O10 XJS 32
XJS C11 C11 C 0 1 N N N N N N 23.483 -13.948 -2.628 4.898 0.320 -0.222 C11 XJS 33
XJS O11 O11 O 0 1 N N N N N N 19.826 -16.264 -12.933 -11.695 -0.020 -0.747 O11 XJS 34
XJS C12 C12 C 0 1 N N N N N N 23.069 -14.876 -0.287 6.962 -0.941 -0.511 C12 XJS 35
XJS O12 O12 O 0 1 N N N N N N 16.197 -19.463 -10.929 -8.379 4.430 -3.647 O12 XJS 36
XJS C13 C13 C 0 1 N N N N N N 23.466 -12.344 -0.667 6.849 1.075 1.026 C13 XJS 37
XJS O13 O13 O 0 1 N N N N N N 21.692 -12.654 -4.844 2.727 -2.073 -2.825 O13 XJS 38
XJS C14 C14 C 0 1 N N N N N N 21.762 -15.735 -0.280 6.858 -2.181 0.379 C14 XJS 39
XJS O14 O14 O 0 1 N N N N N N 23.337 -15.026 -3.099 4.265 1.228 0.274 O14 XJS 40
XJS C15 C15 C 0 1 N N N N N N 21.734 -16.924 0.732 7.655 -3.327 -0.248 C15 XJS 41
XJS O15 O15 O 0 1 N N N N N N 23.508 -20.090 0.792 8.830 -5.695 -0.775 O15 XJS 42
XJS C16 C16 C 0 1 N N N N N N 23.779 -12.159 0.846 7.446 2.253 0.254 C16 XJS 43
XJS O16 O16 O 0 1 N N N N N N 21.950 -8.600 0.717 9.462 5.264 2.361 O16 XJS 44
XJS C17 C17 C 0 1 N N N N N N 23.030 -11.013 1.590 8.126 3.212 1.234 C17 XJS 45
XJS O17 O17 O 0 1 N N N N N N 25.302 -5.304 0.020 11.092 8.653 -0.593 O17 XJS 46
XJS C18 C18 C 0 1 N N N N N N 22.598 -19.336 0.689 8.182 -5.654 0.250 C18 XJS 47
XJS O18 O18 O 0 1 N N N N N N 18.841 -21.085 2.795 8.125 -9.201 2.400 O18 XJS 48
XJS C19 C19 C 0 1 N N N N N N 22.947 -8.484 1.337 9.349 5.318 1.155 C19 XJS 49
XJS "C2'" C2* C 0 1 N N N N N N 17.087 -20.498 -8.790 -6.540 2.821 -3.863 C2* XJS 50
XJS C20 C20 C 0 1 N N N N N N 21.170 -19.835 1.054 8.079 -6.875 1.126 C20 XJS 51
XJS C21 C21 C 0 1 N N N N N N 23.559 -7.071 1.522 9.938 6.479 0.395 C21 XJS 52
XJS C22 C22 C 0 1 N N N N N N 21.129 -20.737 2.313 8.877 -8.021 0.500 C22 XJS 53
XJS C23 C23 C 0 1 N N N N N N 23.074 -6.013 0.498 10.617 7.438 1.374 C23 XJS 54
XJS C24 C24 C 0 1 N N N N N N 24.169 -5.323 -0.353 11.205 8.599 0.613 C24 XJS 55
XJS C25 C25 C 0 1 N N N N N N 19.881 -20.752 3.240 8.773 -9.243 1.376 C25 XJS 56
XJS C26 C26 C 0 1 N N N N N N 22.343 -4.593 -1.971 12.429 10.704 0.535 C26 XJS 57
XJS C27 C27 C 0 1 N N N N N N 21.642 -5.957 -2.019 11.390 11.822 0.426 C27 XJS 58
XJS C28 C28 C 0 1 N N N N N N 24.714 -3.757 -2.286 11.993 9.510 2.731 C28 XJS 59
XJS C29 C29 C 0 1 N N N N N N 25.766 -2.965 -1.502 13.279 8.762 3.090 C29 XJS 60
XJS "C3'" C3* C 0 1 N N S N N N 17.261 -19.570 -10.004 -8.050 3.040 -3.599 C3* XJS 61
XJS C30 C30 C 0 1 N N N N N N 19.145 -21.633 5.526 9.300 -11.569 1.873 C30 XJS 62
XJS C31 C31 C 0 1 N N N N N N 21.493 -20.809 5.191 10.183 -10.432 -0.216 C31 XJS 63
XJS C32 C32 C 0 1 N N N N N N 19.663 -22.620 6.582 10.439 -11.562 2.895 C32 XJS 64
XJS C33 C33 C 0 1 N N N N N N 22.321 -19.641 4.655 9.282 -10.870 -1.372 C33 XJS 65
XJS "C4'" C4* C 0 1 N N R N N N 18.638 -20.098 -10.566 -8.212 2.483 -2.161 C4* XJS 66
XJS "O4'" O4* O 0 1 N N N N N N 19.396 -20.413 -9.328 -7.319 1.347 -2.135 O4* XJS 67
XJS "C5'" C5* C 0 1 N N N N N N 19.359 -19.084 -11.475 -9.655 2.041 -1.915 C5* XJS 68
XJS "O5'" O5* O 0 1 N N N N N N 19.691 -17.920 -10.751 -9.805 1.642 -0.551 O5* XJS 69
XJS HN2 HN2 H 0 1 N N N N N N 23.159 -13.621 -7.506 0.288 -0.274 -2.243 HN2 XJS 70
XJS HN3 HN3 H 0 1 N N N N N N 18.335 -19.472 -3.795 -6.536 -1.688 -5.651 HN3 XJS 71
XJS HN5 HN5 H 0 1 N N N N N N 23.805 -17.532 0.658 7.037 -4.482 1.424 HN5 XJS 72
XJS H6 H6 H 0 1 N N N N N N 19.518 -18.116 -8.422 -3.651 0.816 -2.722 H6 XJS 73
XJS HN6 HN6 H 0 1 N N N N N N 24.622 -9.635 2.108 8.607 4.384 -0.470 HN6 XJS 74
XJS HO6 HO6 H 0 1 N N N N N N 17.754 -14.797 -15.378 -10.614 -2.036 5.989 HO6 XJS 75
XJS H7 H7 H 0 1 N N N N N N 20.390 -12.903 -6.805 0.651 -1.876 -4.541 H7 XJS 76
XJS H7A H7A H 0 1 N N N N N N 20.956 -13.623 -8.369 0.194 -2.935 -3.185 H7A XJS 77
XJS HO7 HO7 H 0 1 N N N N N N 16.865 -11.718 -13.498 -11.722 0.481 7.541 HO7 XJS 78
XJS HO8 HO8 H 0 1 N N N N N N 15.299 -17.769 -11.818 -10.512 -2.094 2.321 HO8 XJS 79
XJS H9 H9 H 0 1 N N N N N N 24.556 -13.852 -5.263 2.713 0.796 -1.757 H9 XJS 80
XJS H9A H9A H 0 1 N N N N N N 24.595 -12.041 -5.389 2.255 -0.263 -0.401 H9A XJS 81
XJS "H1'" H1* H 0 1 N N N N N N 18.632 -21.699 -7.878 -5.391 2.124 -2.160 H1* XJS 82
XJS H10 H10 H 0 1 N N N N N N 25.242 -12.817 -3.153 4.279 -1.641 -0.794 H10 XJS 83
XJS H10A H10A H 0 0 N N N N N N 23.698 -11.860 -3.118 4.737 -0.581 -2.150 H10A XJS 84
XJS HO10 HO10 H 0 0 N N N N N N 20.761 -14.892 -11.217 -12.020 3.087 0.545 HO10 XJS 85
XJS H12 H12 H 0 1 N N N N N N 23.885 -15.560 -0.563 6.560 -1.167 -1.498 H12 XJS 86
XJS HO12 HO12 H 0 0 N N N N N N 16.439 -18.861 -11.623 -8.209 4.845 -4.504 HO12 XJS 87
XJS H13 H13 H 0 1 N N N N N N 24.353 -11.984 -1.209 6.115 1.444 1.742 H13 XJS 88
XJS H13A H13A H 0 0 N N N N N N 22.572 -11.737 -0.870 7.642 0.549 1.558 H13A XJS 89
XJS H14 H14 H 0 1 N N N N N N 20.929 -15.064 -0.023 7.260 -1.955 1.366 H14 XJS 90
XJS H15 H15 H 0 1 N N N N N N 20.822 -17.502 0.524 8.701 -3.034 -0.340 H15 XJS 91
XJS H15A H15A H 0 0 N N N N N N 21.720 -16.487 1.741 7.252 -3.553 -1.235 H15A XJS 92
XJS H16 H16 H 0 1 N N N N N N 23.508 -13.100 1.348 8.181 1.884 -0.461 H16 XJS 93
XJS H16A H16A H 0 0 N N N N N N 24.855 -11.947 0.928 6.653 2.778 -0.278 H16A XJS 94
XJS H17 H17 H 0 1 N N N N N N 22.105 -10.829 1.025 8.919 2.687 1.766 H17 XJS 95
XJS H17A H17A H 0 0 N N N N N N 22.833 -11.381 2.608 7.391 3.582 1.949 H17A XJS 96
XJS "H2'" H2* H 0 1 N N N N N N 16.645 -21.462 -9.084 -5.983 3.739 -3.677 H2* XJS 97
XJS "H2'A" H2*A H 0 0 N N N N N N 16.428 -20.047 -8.034 -6.375 2.477 -4.884 H2*A XJS 98
XJS H20 H20 H 0 1 N N N N N N 20.539 -18.954 1.244 8.482 -6.649 2.113 H20 XJS 99
XJS H20A H20A H 0 0 N N N N N N 20.784 -20.417 0.204 7.033 -7.169 1.218 H20A XJS 100
XJS H21 H21 H 0 1 N N N N N N 23.284 -6.716 2.526 10.672 6.109 -0.321 H21 XJS 101
XJS H21A H21A H 0 0 N N N N N N 24.650 -7.162 1.418 9.144 7.004 -0.138 H21A XJS 102
XJS H22 H22 H 0 1 N N N N N N 21.245 -21.768 1.948 8.474 -8.247 -0.488 H22 XJS 103
XJS H22A H22A H 0 0 N N N N N N 21.969 -20.411 2.944 9.922 -7.727 0.407 H22A XJS 104
XJS H23 H23 H 0 1 N N N N N N 22.393 -6.523 -0.199 9.882 7.807 2.089 H23 XJS 105
XJS H23A H23A H 0 0 N N N N N N 22.558 -5.224 1.065 11.410 6.913 1.906 H23A XJS 106
XJS H26 H26 H 0 1 N N N N N N 21.776 -3.971 -1.263 13.308 11.075 1.061 H26 XJS 107
XJS H27 H27 H 0 1 N N N N N N 20.604 -5.825 -2.359 11.815 12.661 -0.124 H27 XJS 108
XJS H27A H27A H 0 0 N N N N N N 22.175 -6.619 -2.718 10.510 11.451 -0.100 H27A XJS 109
XJS H28 H28 H 0 1 N N N N N N 25.264 -4.456 -2.933 12.035 10.521 3.138 H28 XJS 110
XJS H29 H29 H 0 1 N N N N N N 26.415 -2.421 -2.204 13.381 8.714 4.174 H29 XJS 111
XJS H29A H29A H 0 0 N N N N N N 25.264 -2.248 -0.836 13.237 7.752 2.683 H29A XJS 112
XJS "H3'" H3* H 0 1 N N N N N N 17.253 -18.504 -9.731 -8.655 2.474 -4.306 H3* XJS 113
XJS H30 H30 H 0 1 N N N N N N 18.605 -20.840 6.064 8.344 -11.562 2.395 H30 XJS 114
XJS H31 H31 H 0 1 N N N N N N 21.406 -20.664 6.278 10.591 -9.443 -0.429 H31 XJS 115
XJS H32 H32 H 0 1 N N N N N N 18.813 -23.039 7.141 10.365 -12.445 3.528 H32 XJS 116
XJS H32A H32A H 0 0 N N N N N N 20.212 -23.433 6.085 11.396 -11.569 2.372 H32A XJS 117
XJS H33 H33 H 0 1 N N N N N N 23.313 -19.645 5.130 8.874 -11.858 -1.160 H33 XJS 118
XJS H33A H33A H 0 0 N N N N N N 22.436 -19.743 3.566 8.466 -10.157 -1.487 H33A XJS 119
XJS "H4'" H4* H 0 1 N N N N N N 18.521 -20.965 -11.232 -7.906 3.227 -1.425 H4* XJS 120
XJS "H5'" H5* H 0 1 N N N N N N 20.280 -19.541 -11.865 -10.331 2.870 -2.127 H5* XJS 121
XJS "H5'A" H5*A H 0 0 N N N N N N 18.696 -18.813 -12.309 -9.895 1.201 -2.567 H5*A XJS 122
XJS H54 H54 H 0 1 N N N N N N 23.181 -14.477 0.732 8.008 -0.648 -0.603 H54 XJS 123
XJS H55 H55 H 0 1 N N N N N N 21.641 -16.158 -1.288 5.812 -2.475 0.471 H55 XJS 124
XJS H56 H56 H 0 1 N N N N N N 22.315 -4.187 -2.993 12.715 10.376 -0.464 H56 XJS 125
XJS H57 H57 H 0 1 N N N N N N 21.645 -6.406 -1.015 11.103 12.150 1.425 H57 XJS 126
XJS H58 H58 H 0 1 N N N N N N 24.135 -3.023 -2.866 11.137 8.984 3.153 H58 XJS 127
XJS H59 H59 H 0 1 N N N N N N 26.375 -3.658 -0.903 14.135 9.289 2.668 H59 XJS 128
XJS H60 H60 H 0 1 N N N N N N 18.480 -22.198 4.856 9.371 -12.465 1.257 H60 XJS 129
XJS H61 H61 H 0 1 N N N N N N 22.042 -21.729 4.940 10.999 -11.145 -0.102 H61 XJS 130
XJS H62 H62 H 0 1 N N N N N N 20.335 -22.094 7.276 10.368 -10.665 3.511 H62 XJS 131
XJS H63 H63 H 0 1 N N N N N N 21.810 -18.694 4.883 9.864 -10.907 -2.293 H63 XJS 132
#
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
XJS C1 C5 SING N N 1
XJS N1 C2 SING N N 2
XJS P1 O1 SING N N 3
XJS P1 "O5'" SING N N 4
XJS P1 O10 SING N N 5
XJS C2 O2 DOUB N N 6
XJS C2 N3 SING N N 7
XJS N2 C8 SING N N 8
XJS N2 HN2 SING N N 9
XJS P2 O1 SING N N 10
XJS P2 O8 SING N N 11
XJS C3 C1 TRIP N N 12
XJS N3 HN3 SING N N 13
XJS O3 P2 SING N N 14
XJS P3 O3 SING N N 15
XJS P3 O7 SING N N 16
XJS C4 N3 SING N N 17
XJS C4 O4 DOUB N N 18
XJS N4 C13 SING N N 19
XJS N4 C12 SING N N 20
XJS C5 C4 SING N N 21
XJS N5 C18 SING N N 22
XJS N5 C15 SING N N 23
XJS N5 HN5 SING N N 24
XJS O5 P3 DOUB N N 25
XJS C6 N1 SING N N 26
XJS C6 C5 DOUB N N 27
XJS C6 H6 SING N N 28
XJS N6 HN6 SING N N 29
XJS O6 P3 SING N N 30
XJS O6 HO6 SING N N 31
XJS C7 N2 SING N N 32
XJS C7 C3 SING N N 33
XJS C7 H7 SING N N 34
XJS C7 H7A SING N N 35
XJS N7 C31 SING N N 36
XJS N7 C30 SING N N 37
XJS O7 HO7 SING N N 38
XJS C8 C9 SING N N 39
XJS C8 O13 DOUB N N 40
XJS N8 C24 SING N N 41
XJS O8 HO8 SING N N 42
XJS C9 C10 SING N N 43
XJS C9 H9 SING N N 44
XJS C9 H9A SING N N 45
XJS O9 P2 DOUB N N 46
XJS "C1'" N1 SING N N 47
XJS "C1'" "H1'" SING N N 48
XJS C10 C11 SING N N 49
XJS C10 H10 SING N N 50
XJS C10 H10A SING N N 51
XJS O10 HO10 SING N N 52
XJS C11 N4 SING N N 53
XJS O11 P1 DOUB N N 54
XJS C12 C14 SING N N 55
XJS C12 H12 SING N N 56
XJS O12 "C3'" SING N N 57
XJS O12 HO12 SING N N 58
XJS C13 C16 SING N N 59
XJS C13 H13 SING N N 60
XJS C13 H13A SING N N 61
XJS C14 C15 SING N N 62
XJS C14 H14 SING N N 63
XJS O14 C11 DOUB N N 64
XJS C15 H15 SING N N 65
XJS C15 H15A SING N N 66
XJS C16 C17 SING N N 67
XJS C16 H16 SING N N 68
XJS C16 H16A SING N N 69
XJS O16 C19 DOUB N N 70
XJS C17 N6 SING N N 71
XJS C17 H17 SING N N 72
XJS C17 H17A SING N N 73
XJS C18 O15 DOUB N N 74
XJS C18 C20 SING N N 75
XJS O18 C25 DOUB N N 76
XJS C19 N6 SING N N 77
XJS C19 C21 SING N N 78
XJS "C2'" "C1'" SING N N 79
XJS "C2'" "H2'" SING N N 80
XJS "C2'" "H2'A" SING N N 81
XJS C20 C22 SING N N 82
XJS C20 H20 SING N N 83
XJS C20 H20A SING N N 84
XJS C21 H21 SING N N 85
XJS C21 H21A SING N N 86
XJS C22 C25 SING N N 87
XJS C22 H22 SING N N 88
XJS C22 H22A SING N N 89
XJS C23 C21 SING N N 90
XJS C23 H23 SING N N 91
XJS C23 H23A SING N N 92
XJS C24 O17 DOUB N N 93
XJS C24 C23 SING N N 94
XJS C25 N7 SING N N 95
XJS C26 N8 SING N N 96
XJS C26 H26 SING N N 97
XJS C27 C26 SING N N 98
XJS C27 H27 SING N N 99
XJS C27 H27A SING N N 100
XJS C28 N8 SING N N 101
XJS C28 C29 SING N N 102
XJS C28 H28 SING N N 103
XJS C29 H29 SING N N 104
XJS C29 H29A SING N N 105
XJS "C3'" "C2'" SING N N 106
XJS "C3'" "H3'" SING N N 107
XJS C30 C32 SING N N 108
XJS C30 H30 SING N N 109
XJS C31 H31 SING N N 110
XJS C32 H32 SING N N 111
XJS C32 H32A SING N N 112
XJS C33 C31 SING N N 113
XJS C33 H33 SING N N 114
XJS C33 H33A SING N N 115
XJS "C4'" "C3'" SING N N 116
XJS "C4'" "O4'" SING N N 117
XJS "C4'" "H4'" SING N N 118
XJS "O4'" "C1'" SING N N 119
XJS "C5'" "C4'" SING N N 120
XJS "C5'" "O5'" SING N N 121
XJS "C5'" "H5'" SING N N 122
XJS "C5'" "H5'A" SING N N 123
XJS C12 H54 SING N N 124
XJS C14 H55 SING N N 125
XJS C26 H56 SING N N 126
XJS C27 H57 SING N N 127
XJS C28 H58 SING N N 128
XJS C29 H59 SING N N 129
XJS C30 H60 SING N N 130
XJS C31 H61 SING N N 131
XJS C32 H62 SING N N 132
XJS C33 H63 SING N N 133
#
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
XJS SMILES ACDLabs 12.01 "O=C(N(CC)CC)CCC(=O)NCCCN(C(=O)CCC(=O)NCC#CC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)CCCNC(=O)CCC(=O)N(CC)CC"
XJS SMILES_CANONICAL CACTVS 3.370 "CCN(CC)C(=O)CCC(=O)NCCCN(CCCNC(=O)CCC(=O)N(CC)CC)C(=O)CCC(=O)NCC#CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"
XJS SMILES CACTVS 3.370 "CCN(CC)C(=O)CCC(=O)NCCCN(CCCNC(=O)CCC(=O)N(CC)CC)C(=O)CCC(=O)NCC#CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"
XJS SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CCN(CC)C(=O)CCC(=O)NCCCN(CCCNC(=O)CCC(=O)N(CC)CC)C(=O)CCC(=O)NCC#CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O"
XJS SMILES "OpenEye OEToolkits" 1.7.0 "CCN(CC)C(=O)CCC(=O)NCCCN(CCCNC(=O)CCC(=O)N(CC)CC)C(=O)CCC(=O)NCC#CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O"
XJS InChI InChI 1.03 InChI=1S/C38H63N8O20P3/c1-5-43(6-2)33(51)16-13-31(49)40-20-10-22-45(23-11-21-41-32(50)14-17-34(52)44(7-3)8-4)35(53)18-15-30(48)39-19-9-12-27-25-46(38(55)42-37(27)54)36-24-28(47)29(64-36)26-63-68(59,60)66-69(61,62)65-67(56,57)58/h25,28-29,36,47H,5-8,10-11,13-24,26H2,1-4H3,(H,39,48)(H,40,49)(H,41,50)(H,59,60)(H,61,62)(H,42,54,55)(H2,56,57,58)/t28-,29+,36+/m0/s1
XJS InChIKey InChI 1.03 FRKZJUQJYOJKOB-CMUUVTEDSA-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
XJS "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5-[12-(3-{[4-(diethylamino)-4-oxobutanoyl]amino}propyl)-3-ethyl-4,7,13,16-tetraoxo-3,8,12,17-tetraazaicos-19-yn-20-yl]uridine 5'-(tetrahydrogen triphosphate)"
XJS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[[(2R,3S,5R)-5-[5-[3-[[4-[bis[3-[[4-(diethylamino)-4-oxo-butanoyl]amino]propyl]amino]-4-oxo-butanoyl]amino]prop-1-ynyl]-2,4-dioxo-pyrimidin-1-yl]-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XJS 'Create component' 2010-09-20 RCSB
XJS 'Modify descriptor' 2011-06-04 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
XJS C1 C 23.785 -4.297 1
XJS N1 N 26.383 -7.297 2
XJS O1 O 31.269 -14.589 3
XJS P1 P 30.388 -13.376 4
XJS C2 C 27.682 -6.547 5
XJS N2 N 21.187 -1.297 6
XJS O2 O 28.981 -7.297 7
XJS P2 P 32.761 -14.433 8
XJS C3 C 22.486 -3.547 9
XJS N3 N 27.682 -5.047 10
XJS O3 O 34.253 -14.276 11
XJS P3 P 35.135 -15.489 12
XJS C4 C 26.383 -4.297 13
XJS N4 N 17.290 3.953 14
XJS O4 O 26.383 -2.797 15
XJS C5 C 25.084 -5.047 16
XJS N5 N 12.093 3.953 17
XJS O5 O 36.348 -14.608 18
XJS C6 C 25.084 -6.547 19
XJS N6 N 14.691 8.453 20
XJS O6 O 33.921 -16.371 21
XJS C7 C 21.187 -2.797 22
XJS N7 N 5.598 3.203 23
XJS O7 O 36.017 -16.703 24
XJS C8 C 19.887 -0.547 25
XJS N8 N 12.093 14.453 26
XJS O8 O 32.918 -15.924 27
XJS C9 C 19.887 0.953 28
XJS O9 O 32.604 -12.941 29
XJS "C1'" C 26.383 -8.797 30
XJS C10 C 18.588 1.703 31
XJS O10 O 31.601 -12.494 32
XJS C11 C 18.588 3.203 33
XJS O11 O 29.174 -14.258 34
XJS C12 C 15.990 3.203 35
XJS O12 O 24.751 -12.319 36
XJS C13 C 17.290 5.453 37
XJS O13 O 18.588 -1.297 38
XJS C14 C 14.691 3.953 39
XJS O14 O 19.887 3.953 40
XJS C15 C 13.392 3.203 41
XJS O15 O 10.794 1.703 42
XJS C16 C 15.990 6.203 43
XJS O16 O 15.990 10.703 44
XJS C17 C 15.990 7.703 45
XJS O17 O 10.794 12.203 46
XJS C18 C 10.794 3.203 47
XJS O18 O 6.897 5.453 48
XJS C19 C 14.691 9.953 49
XJS "C2'" C 25.169 -9.679 50
XJS C20 C 9.495 3.953 51
XJS C21 C 13.392 10.703 52
XJS C22 C 8.196 3.203 53
XJS C23 C 13.392 12.203 54
XJS C24 C 12.093 12.953 55
XJS C25 C 6.897 3.953 56
XJS C26 C 10.794 15.203 57
XJS C27 C 10.794 16.703 58
XJS C28 C 13.392 15.203 59
XJS C29 C 13.392 16.703 60
XJS "C3'" C 25.633 -11.105 61
XJS C30 C 5.598 1.703 62
XJS C31 C 4.299 3.953 63
XJS C32 C 4.299 0.953 64
XJS C33 C 3.000 3.203 65
XJS "C4'" C 27.133 -11.105 66
XJS "O4'" O 27.596 -9.679 67
XJS "C5'" C 28.014 -12.319 68
XJS "O5'" O 29.506 -12.162 69
#
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
XJS C1 C5 SINGLE NONE 1
XJS N1 C2 SINGLE NONE 2
XJS P1 O1 SINGLE NONE 3
XJS P1 "O5'" SINGLE NONE 4
XJS P1 O10 SINGLE BEGINWEDGE 5
XJS C2 O2 DOUBLE NONE 6
XJS C2 N3 SINGLE NONE 7
XJS N2 C8 SINGLE NONE 8
XJS P2 O1 SINGLE NONE 9
XJS P2 O8 SINGLE BEGINWEDGE 10
XJS C3 C1 TRIPLE NONE 11
XJS O3 P2 SINGLE NONE 12
XJS P3 O3 SINGLE NONE 13
XJS P3 O7 SINGLE NONE 14
XJS C4 N3 SINGLE NONE 15
XJS C4 O4 DOUBLE NONE 16
XJS N4 C13 SINGLE NONE 17
XJS N4 C12 SINGLE NONE 18
XJS C5 C4 SINGLE NONE 19
XJS N5 C18 SINGLE NONE 20
XJS N5 C15 SINGLE NONE 21
XJS O5 P3 DOUBLE NONE 22
XJS C6 N1 SINGLE NONE 23
XJS C6 C5 DOUBLE NONE 24
XJS O6 P3 SINGLE NONE 25
XJS C7 N2 SINGLE NONE 26
XJS C7 C3 SINGLE NONE 27
XJS N7 C31 SINGLE NONE 28
XJS N7 C30 SINGLE NONE 29
XJS C8 C9 SINGLE NONE 30
XJS C8 O13 DOUBLE NONE 31
XJS N8 C24 SINGLE NONE 32
XJS C9 C10 SINGLE NONE 33
XJS O9 P2 DOUBLE NONE 34
XJS "C1'" N1 SINGLE BEGINDASH 35
XJS C10 C11 SINGLE NONE 36
XJS C11 N4 SINGLE NONE 37
XJS O11 P1 DOUBLE NONE 38
XJS C12 C14 SINGLE NONE 39
XJS "C3'" O12 SINGLE BEGINWEDGE 40
XJS C13 C16 SINGLE NONE 41
XJS C14 C15 SINGLE NONE 42
XJS O14 C11 DOUBLE NONE 43
XJS C16 C17 SINGLE NONE 44
XJS O16 C19 DOUBLE NONE 45
XJS C17 N6 SINGLE NONE 46
XJS C18 O15 DOUBLE NONE 47
XJS C18 C20 SINGLE NONE 48
XJS O18 C25 DOUBLE NONE 49
XJS C19 N6 SINGLE NONE 50
XJS C19 C21 SINGLE NONE 51
XJS "C2'" "C1'" SINGLE NONE 52
XJS C20 C22 SINGLE NONE 53
XJS C22 C25 SINGLE NONE 54
XJS C23 C21 SINGLE NONE 55
XJS C24 O17 DOUBLE NONE 56
XJS C24 C23 SINGLE NONE 57
XJS C25 N7 SINGLE NONE 58
XJS C26 N8 SINGLE NONE 59
XJS C27 C26 SINGLE NONE 60
XJS C28 N8 SINGLE NONE 61
XJS C28 C29 SINGLE NONE 62
XJS "C3'" "C2'" SINGLE NONE 63
XJS C30 C32 SINGLE NONE 64
XJS C33 C31 SINGLE NONE 65
XJS "C4'" "C3'" SINGLE NONE 66
XJS "C4'" "O4'" SINGLE NONE 67
XJS "O4'" "C1'" SINGLE NONE 68
XJS "C4'" "C5'" SINGLE BEGINDASH 69
XJS "C5'" "O5'" SINGLE NONE 70
#
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
XJS MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CCCO2)c(=O)[nH]1' InChI=1S/C8H10N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h3-4,7H,1-2,5H2,(H,9,11,12)/t7-/m1/s1 CWWIKVUHBBTKHC-SSDOTTSWSA-N
XJS amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
XJS deoxyribose F2 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N
XJS phosphate F3 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
XJS pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
XJS N1 S1 1
XJS C2 S1 1
XJS O2 S1 1
XJS N3 S1 1
XJS C4 S1 1
XJS O4 S1 1
XJS C5 S1 1
XJS C6 S1 1
XJS "C1'" S1 1
XJS "C2'" S1 1
XJS "C3'" S1 1
XJS "C4'" S1 1
XJS "O4'" S1 1
XJS N2 F1 1
XJS C8 F1 1
XJS O13 F1 1
XJS C9 F1 1
XJS N4 F1 2
XJS C11 F1 2
XJS O14 F1 2
XJS C10 F1 2
XJS N5 F1 3
XJS C18 F1 3
XJS O15 F1 3
XJS C20 F1 3
XJS N6 F1 4
XJS C19 F1 4
XJS O16 F1 4
XJS C21 F1 4
XJS N7 F1 5
XJS C25 F1 5
XJS O18 F1 5
XJS C22 F1 5
XJS N8 F1 6
XJS C24 F1 6
XJS O17 F1 6
XJS C23 F1 6
XJS "C1'" F2 1
XJS "C2'" F2 1
XJS "C3'" F2 1
XJS O12 F2 1
XJS "C4'" F2 1
XJS "O4'" F2 1
XJS "C5'" F2 1
XJS "O5'" F2 1
XJS O1 F3 1
XJS P1 F3 1
XJS O11 F3 1
XJS "O5'" F3 1
XJS O10 F3 1
XJS O1 F3 2
XJS P2 F3 2
XJS O9 F3 2
XJS O8 F3 2
XJS O3 F3 2
XJS O3 F3 3
XJS P3 F3 3
XJS O5 F3 3
XJS O7 F3 3
XJS O6 F3 3
XJS C5 F4 1
XJS C4 F4 1
XJS N3 F4 1
XJS C2 F4 1
XJS N1 F4 1
XJS C6 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id XJS
_pdbe_chem_comp_rdkit_properties.exactmw 1044.337
_pdbe_chem_comp_rdkit_properties.amw 1044.880
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 28
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 39
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 21
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 69
_pdbe_chem_comp_rdkit_properties.NumAtoms 132
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 31
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 6
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.684
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 485.956
_pdbe_chem_comp_rdkit_properties.tpsa 392.370
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.660
_pdbe_chem_comp_rdkit_properties.CrippenMR 240.902
_pdbe_chem_comp_rdkit_properties.chi0v 34.768
_pdbe_chem_comp_rdkit_properties.chi1v 19.994
_pdbe_chem_comp_rdkit_properties.chi2v 8.868
_pdbe_chem_comp_rdkit_properties.chi3v 8.868
_pdbe_chem_comp_rdkit_properties.chi4v 5.609
_pdbe_chem_comp_rdkit_properties.chi0n 95.084
_pdbe_chem_comp_rdkit_properties.chi1n 46.443
_pdbe_chem_comp_rdkit_properties.chi2n 5.353
_pdbe_chem_comp_rdkit_properties.chi3n 5.353
_pdbe_chem_comp_rdkit_properties.chi4n 2.934
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -4.610
_pdbe_chem_comp_rdkit_properties.kappa1 15.696
_pdbe_chem_comp_rdkit_properties.kappa2 29.543
_pdbe_chem_comp_rdkit_properties.kappa3 23.239
_pdbe_chem_comp_rdkit_properties.Phi 6.721
#
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
XJS UniChem PDBe XJS
XJS UniChem PubChem 49795055
#