data_NJ5
#
_chem_comp.id NJ5
_chem_comp.name
"[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[6-(butanoylamino)hexanoylamino]-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] hydrogen phosphate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C25 H42 N4 O18 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-11-29
_chem_comp.pdbx_modified_date 2020-02-28
_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 748.565
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NJ5
_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 6TKA
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
NJ5 C11 C1 C 0 1 N N N N N N -24.794 -31.465 -13.644 14.329 -4.771 -1.060 C11 NJ5 1
NJ5 C12 C2 C 0 1 N N N N N N -25.919 -30.582 -14.091 13.035 -4.579 -0.267 C12 NJ5 2
NJ5 C13 C3 C 0 1 N N N N N N -25.851 -30.038 -15.551 12.309 -3.329 -0.769 C13 NJ5 3
NJ5 C14 C4 C 0 1 N N N N N N -27.206 -29.818 -16.238 11.035 -3.141 0.013 C14 NJ5 4
NJ5 O1 O1 O 0 1 N N N N N N -28.227 -30.351 -15.826 10.736 -3.928 0.885 O1 NJ5 5
NJ5 N2 N1 N 0 1 N N N N N N -27.267 -29.051 -17.340 10.227 -2.096 -0.258 N2 NJ5 6
NJ5 C15 C5 C 0 1 N N N N N N -28.105 -29.368 -18.498 8.987 -1.913 0.502 C15 NJ5 7
NJ5 C16 C6 C 0 1 N N N N N N -28.407 -28.191 -19.428 8.262 -0.663 -0.000 C16 NJ5 8
NJ5 C17 C7 C 0 1 N N N N N N -27.327 -27.866 -20.465 6.968 -0.472 0.793 C17 NJ5 9
NJ5 C18 C8 C 0 1 N N N N N N -27.532 -26.547 -21.204 6.242 0.779 0.291 C18 NJ5 10
NJ5 C19 C9 C 0 1 N N N N N N -26.291 -26.026 -21.893 4.948 0.970 1.084 C19 NJ5 11
NJ5 C20 C10 C 0 1 N N N N N N -25.453 -25.042 -21.101 4.233 2.201 0.590 C20 NJ5 12
NJ5 O2 O2 O 0 1 N N N N N N -25.658 -24.808 -19.914 4.712 2.861 -0.308 O2 NJ5 13
NJ5 N3 N2 N 0 1 N N N N N N -24.434 -24.495 -21.779 3.062 2.569 1.146 N3 NJ5 14
NJ5 C21 C11 C 0 1 N N R N N N -23.464 -23.566 -21.218 2.367 3.766 0.666 C21 NJ5 15
NJ5 C22 C12 C 0 1 N N R N N N -22.146 -24.220 -20.786 1.508 3.406 -0.549 C22 NJ5 16
NJ5 O3 O3 O 0 1 N N N N N N -21.413 -24.608 -21.956 0.586 2.375 -0.191 O3 NJ5 17
NJ5 P1 P1 P 0 1 N N N N N N -21.220 -26.171 -22.292 0.043 1.282 -1.241 P1 NJ5 18
NJ5 O4 O4 O 0 1 N N N N N N -20.317 -26.395 -23.464 1.190 0.594 -1.874 O4 NJ5 19
NJ5 O5 O5 O 0 1 N N N N N N -22.567 -26.802 -22.300 -0.835 2.015 -2.374 O5 NJ5 20
NJ5 O6 O6 O 0 1 N N N N N N -20.687 -26.813 -20.955 -0.870 0.203 -0.468 O6 NJ5 21
NJ5 P2 P2 P 0 1 N N N N N N -19.277 -26.718 -20.281 -1.355 -1.295 -0.802 P2 NJ5 22
NJ5 O7 O7 O 0 1 N N N N N N -18.795 -25.317 -20.481 -1.702 -1.393 -2.238 O7 NJ5 23
NJ5 O8 O8 O 0 1 N N N N N N -19.496 -27.295 -18.950 -0.169 -2.330 -0.465 O8 NJ5 24
NJ5 O9 O9 O 0 1 N N N N N N -18.399 -27.695 -21.217 -2.648 -1.652 0.088 O9 NJ5 25
NJ5 C23 C13 C 0 1 N N N N N N -17.398 -28.534 -20.605 -3.377 -2.872 -0.053 C23 NJ5 26
NJ5 C24 C14 C 0 1 N N R N N N -16.316 -27.692 -19.980 -4.541 -2.888 0.940 C24 NJ5 27
NJ5 O10 O10 O 0 1 N N N N N N -15.287 -28.582 -19.495 -5.496 -1.872 0.591 O10 NJ5 28
NJ5 C25 C15 C 0 1 N N R N N N -14.110 -28.399 -20.249 -6.802 -2.386 0.931 C25 NJ5 29
NJ5 N4 N3 N 0 1 N N N N N N -13.517 -29.728 -20.512 -7.844 -1.682 0.180 N4 NJ5 30
NJ5 C26 C16 C 0 1 N N N N N N -14.186 -30.671 -21.247 -7.766 -1.609 -1.184 C26 NJ5 31
NJ5 C27 C17 C 0 1 N N N N N N -13.689 -31.890 -21.470 -8.727 -0.961 -1.876 C27 NJ5 32
NJ5 C28 C18 C 0 1 N N N N N N -12.412 -32.245 -20.923 -9.801 -0.367 -1.170 C28 NJ5 33
NJ5 O11 O11 O 0 1 N N N N N N -11.848 -33.329 -21.068 -10.680 0.223 -1.772 O11 NJ5 34
NJ5 N5 N4 N 0 1 N N N N N N -11.819 -31.270 -20.153 -9.842 -0.461 0.174 N5 NJ5 35
NJ5 C29 C19 C 0 1 N N N N N N -12.296 -30.008 -19.924 -8.873 -1.118 0.838 C29 NJ5 36
NJ5 O12 O12 O 0 1 N N N N N N -11.676 -29.196 -19.264 -8.926 -1.199 2.050 O12 NJ5 37
NJ5 C30 C20 C 0 1 N N R N N N -14.520 -27.638 -21.505 -6.727 -3.874 0.503 C30 NJ5 38
NJ5 O13 O13 O 0 1 N N N N N N -13.420 -26.901 -21.998 -7.657 -4.665 1.245 O13 NJ5 39
NJ5 C31 C21 C 0 1 N N S N N N -15.581 -26.720 -20.910 -5.270 -4.245 0.871 C31 NJ5 40
NJ5 O14 O14 O 0 1 N N N N N N -14.951 -25.641 -20.217 -5.226 -4.901 2.140 O14 NJ5 41
NJ5 O15 O15 O 0 1 N N N N N N -21.468 -23.241 -20.012 0.787 4.562 -0.980 O15 NJ5 42
NJ5 C32 C22 C 0 1 N N R N N N -21.019 -22.122 -20.820 -0.108 5.091 0.000 C32 NJ5 43
NJ5 C33 C23 C 0 1 N N N N N N -20.141 -21.266 -19.934 -0.842 6.302 -0.579 C33 NJ5 44
NJ5 O16 O16 O 0 1 N N N N N N -20.786 -20.853 -18.740 -1.673 5.882 -1.663 O16 NJ5 45
NJ5 C34 C24 C 0 1 N N S N N N -22.220 -21.383 -21.418 0.686 5.518 1.237 C34 NJ5 46
NJ5 O17 O17 O 0 1 N N N N N N -21.744 -20.372 -22.313 -0.213 5.995 2.241 O17 NJ5 47
NJ5 C35 C25 C 0 1 N N R N N N -23.121 -22.389 -22.133 1.465 4.314 1.776 C35 NJ5 48
NJ5 O18 O18 O 0 1 N N N N N N -24.299 -21.788 -22.641 2.266 4.722 2.886 O18 NJ5 49
NJ5 H1 H1 H 0 1 N N N N N N -24.964 -31.777 -12.603 14.846 -5.661 -0.703 H1 NJ5 50
NJ5 H2 H2 H 0 1 N N N N N N -24.747 -32.354 -14.290 14.093 -4.887 -2.118 H2 NJ5 51
NJ5 H3 H3 H 0 1 N N N N N N -23.845 -30.912 -13.711 14.970 -3.899 -0.925 H3 NJ5 52
NJ5 H12 H4 H 0 1 N N N N N N -25.950 -29.715 -13.414 12.394 -5.450 -0.402 H12 NJ5 53
NJ5 H11 H5 H 0 1 N N N N N N -26.852 -31.157 -13.994 13.271 -4.462 0.791 H11 NJ5 54
NJ5 H14 H6 H 0 1 N N N N N N -25.278 -30.757 -16.154 12.951 -2.458 -0.634 H14 NJ5 55
NJ5 H13 H7 H 0 1 N N N N N N -25.322 -29.074 -15.529 12.073 -3.446 -1.827 H13 NJ5 56
NJ5 H15 H8 H 0 1 N N N N N N -26.711 -28.220 -17.371 10.466 -1.466 -0.956 H15 NJ5 57
NJ5 H17 H9 H 0 1 N N N N N N -29.062 -29.762 -18.127 8.346 -2.784 0.366 H17 NJ5 58
NJ5 H16 H10 H 0 1 N N N N N N -27.592 -30.143 -19.086 9.224 -1.796 1.559 H16 NJ5 59
NJ5 H19 H11 H 0 1 N N N N N N -28.555 -27.297 -18.804 8.903 0.208 0.135 H19 NJ5 60
NJ5 H18 H12 H 0 1 N N N N N N -29.337 -28.419 -19.969 8.026 -0.780 -1.058 H18 NJ5 61
NJ5 H21 H13 H 0 1 N N N N N N -27.310 -28.677 -21.208 6.326 -1.343 0.658 H21 NJ5 62
NJ5 H20 H14 H 0 1 N N N N N N -26.357 -27.822 -19.948 7.204 -0.355 1.851 H20 NJ5 63
NJ5 H23 H15 H 0 1 N N N N N N -27.866 -25.792 -20.477 6.883 1.650 0.426 H23 NJ5 64
NJ5 H22 H16 H 0 1 N N N N N N -28.313 -26.695 -21.964 6.006 0.662 -0.766 H22 NJ5 65
NJ5 H24 H17 H 0 1 N N N N N N -25.655 -26.889 -22.137 4.307 0.099 0.949 H24 NJ5 66
NJ5 H25 H18 H 0 1 N N N N N N -26.606 -25.528 -22.822 5.184 1.087 2.142 H25 NJ5 67
NJ5 H26 H19 H 0 1 N N N N N N -24.333 -24.744 -22.742 2.679 2.042 1.865 H26 NJ5 68
NJ5 H27 H20 H 0 1 N N N N N N -23.910 -23.135 -20.309 3.099 4.523 0.383 H27 NJ5 69
NJ5 H28 H21 H 0 1 N N N N N N -22.374 -25.103 -20.171 2.150 3.056 -1.357 H28 NJ5 70
NJ5 H4 H22 H 0 1 N N N N N N -22.681 -27.296 -23.103 -1.606 2.487 -2.030 H4 NJ5 71
NJ5 H5 H23 H 0 1 N N N N N N -19.286 -26.649 -18.286 0.111 -2.320 0.461 H5 NJ5 72
NJ5 H29 H24 H 0 1 N N N N N N -17.870 -29.153 -19.828 -3.766 -2.948 -1.069 H29 NJ5 73
NJ5 H30 H25 H 0 1 N N N N N N -16.953 -29.185 -21.372 -2.717 -3.716 0.147 H30 NJ5 74
NJ5 H31 H26 H 0 1 N N N N N N -16.744 -27.123 -19.142 -4.169 -2.716 1.950 H31 NJ5 75
NJ5 H32 H27 H 0 1 N N N N N N -13.390 -27.786 -19.687 -6.980 -2.303 2.003 H32 NJ5 76
NJ5 H33 H28 H 0 1 N N N N N N -15.151 -30.419 -21.661 -6.938 -2.068 -1.705 H33 NJ5 77
NJ5 H34 H29 H 0 1 N N N N N N -14.245 -32.604 -22.059 -8.677 -0.895 -2.953 H34 NJ5 78
NJ5 H35 H30 H 0 1 N N N N N N -10.951 -31.508 -19.717 -10.575 -0.057 0.664 H35 NJ5 79
NJ5 H36 H31 H 0 1 N N N N N N -14.955 -28.314 -22.256 -6.897 -3.980 -0.568 H36 NJ5 80
NJ5 H37 H32 H 0 1 N N N N N N -12.776 -27.497 -22.362 -7.587 -5.615 1.079 H37 NJ5 81
NJ5 H38 H33 H 0 1 N N N N N N -16.260 -26.359 -21.697 -4.831 -4.877 0.100 H38 NJ5 82
NJ5 H39 H34 H 0 1 N N N N N N -15.615 -25.071 -19.847 -5.719 -5.733 2.170 H39 NJ5 83
NJ5 H40 H35 H 0 1 N N N N N N -20.405 -22.502 -21.650 -0.833 4.326 0.280 H40 NJ5 84
NJ5 H41 H36 H 0 1 N N N N N N -19.245 -21.845 -19.665 -1.458 6.758 0.196 H41 NJ5 85
NJ5 H42 H37 H 0 1 N N N N N N -19.843 -20.370 -20.498 -0.115 7.029 -0.940 H42 NJ5 86
NJ5 H43 H38 H 0 1 N N N N N N -20.190 -20.321 -18.225 -2.170 6.600 -2.079 H43 NJ5 87
NJ5 H44 H39 H 0 1 N N N N N N -22.790 -20.921 -20.599 1.383 6.312 0.966 H44 NJ5 88
NJ5 H45 H40 H 0 1 N N N N N N -21.189 -19.765 -21.839 -0.743 6.755 1.965 H45 NJ5 89
NJ5 H46 H41 H 0 1 N N N N N N -22.545 -22.795 -22.978 0.766 3.540 2.093 H46 NJ5 90
NJ5 H47 H42 H 0 1 N N N N N N -24.828 -22.446 -23.076 1.759 5.086 3.625 H47 NJ5 91
#
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
NJ5 O4 P1 DOUB N N 1
NJ5 O18 C35 SING N N 2
NJ5 O17 C34 SING N N 3
NJ5 O5 P1 SING N N 4
NJ5 P1 O3 SING N N 5
NJ5 P1 O6 SING N N 6
NJ5 C35 C34 SING N N 7
NJ5 C35 C21 SING N N 8
NJ5 O13 C30 SING N N 9
NJ5 O3 C22 SING N N 10
NJ5 C19 C18 SING N N 11
NJ5 C19 C20 SING N N 12
NJ5 N3 C21 SING N N 13
NJ5 N3 C20 SING N N 14
NJ5 C30 C31 SING N N 15
NJ5 C30 C25 SING N N 16
NJ5 C27 C26 DOUB N N 17
NJ5 C27 C28 SING N N 18
NJ5 C34 C32 SING N N 19
NJ5 C26 N4 SING N N 20
NJ5 C21 C22 SING N N 21
NJ5 O9 C23 SING N N 22
NJ5 O9 P2 SING N N 23
NJ5 C18 C17 SING N N 24
NJ5 C20 O2 DOUB N N 25
NJ5 O11 C28 DOUB N N 26
NJ5 O6 P2 SING N N 27
NJ5 C28 N5 SING N N 28
NJ5 C31 O14 SING N N 29
NJ5 C31 C24 SING N N 30
NJ5 C32 O15 SING N N 31
NJ5 C32 C33 SING N N 32
NJ5 C22 O15 SING N N 33
NJ5 C23 C24 SING N N 34
NJ5 N4 C25 SING N N 35
NJ5 N4 C29 SING N N 36
NJ5 O7 P2 DOUB N N 37
NJ5 C17 C16 SING N N 38
NJ5 P2 O8 SING N N 39
NJ5 C25 O10 SING N N 40
NJ5 N5 C29 SING N N 41
NJ5 C24 O10 SING N N 42
NJ5 C33 O16 SING N N 43
NJ5 C29 O12 DOUB N N 44
NJ5 C16 C15 SING N N 45
NJ5 C15 N2 SING N N 46
NJ5 N2 C14 SING N N 47
NJ5 C14 O1 DOUB N N 48
NJ5 C14 C13 SING N N 49
NJ5 C13 C12 SING N N 50
NJ5 C12 C11 SING N N 51
NJ5 C11 H1 SING N N 52
NJ5 C11 H2 SING N N 53
NJ5 C11 H3 SING N N 54
NJ5 C12 H12 SING N N 55
NJ5 C12 H11 SING N N 56
NJ5 C13 H14 SING N N 57
NJ5 C13 H13 SING N N 58
NJ5 N2 H15 SING N N 59
NJ5 C15 H17 SING N N 60
NJ5 C15 H16 SING N N 61
NJ5 C16 H19 SING N N 62
NJ5 C16 H18 SING N N 63
NJ5 C17 H21 SING N N 64
NJ5 C17 H20 SING N N 65
NJ5 C18 H23 SING N N 66
NJ5 C18 H22 SING N N 67
NJ5 C19 H24 SING N N 68
NJ5 C19 H25 SING N N 69
NJ5 N3 H26 SING N N 70
NJ5 C21 H27 SING N N 71
NJ5 C22 H28 SING N N 72
NJ5 O5 H4 SING N N 73
NJ5 O8 H5 SING N N 74
NJ5 C23 H29 SING N N 75
NJ5 C23 H30 SING N N 76
NJ5 C24 H31 SING N N 77
NJ5 C25 H32 SING N N 78
NJ5 C26 H33 SING N N 79
NJ5 C27 H34 SING N N 80
NJ5 N5 H35 SING N N 81
NJ5 C30 H36 SING N N 82
NJ5 O13 H37 SING N N 83
NJ5 C31 H38 SING N N 84
NJ5 O14 H39 SING N N 85
NJ5 C32 H40 SING N N 86
NJ5 C33 H41 SING N N 87
NJ5 C33 H42 SING N N 88
NJ5 O16 H43 SING N N 89
NJ5 C34 H44 SING N N 90
NJ5 O17 H45 SING N N 91
NJ5 C35 H46 SING N N 92
NJ5 O18 H47 SING N N 93
#
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
NJ5 InChI InChI 1.03 InChI=1S/C25H42N4O18P2/c1-2-6-15(31)26-9-5-3-4-7-16(32)27-18-21(36)19(34)13(11-30)45-24(18)46-49(41,42)47-48(39,40)43-12-14-20(35)22(37)23(44-14)29-10-8-17(33)28-25(29)38/h8,10,13-14,18-24,30,34-37H,2-7,9,11-12H2,1H3,(H,26,31)(H,27,32)(H,39,40)(H,41,42)(H,28,33,38)/t13-,14-,18-,19-,20-,21-,22-,23-,24-/m1/s1
NJ5 InChIKey InChI 1.03 MGZXRAPGBJHSCZ-HDEQREAESA-N
NJ5 SMILES_CANONICAL CACTVS 3.385 CCCC(=O)NCCCCCC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
NJ5 SMILES CACTVS 3.385 CCCC(=O)NCCCCCC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
NJ5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CCCC(=O)NCCCCCC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
NJ5 SMILES "OpenEye OEToolkits" 2.0.7 CCCC(=O)NCCCCCC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
#
_pdbx_chem_comp_identifier.comp_id NJ5
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
"[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[6-(butanoylamino)hexanoylamino]-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] 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
NJ5 'Create component' 2019-11-29 PDBE
NJ5 'Initial release' 2020-03-04 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
NJ5 C11 C 23.291 -6.785 1
NJ5 C12 C 21.992 -7.535 2
NJ5 C13 C 20.693 -6.785 3
NJ5 C14 C 19.394 -7.535 4
NJ5 O1 O 19.394 -9.035 5
NJ5 N2 N 18.095 -6.785 6
NJ5 C15 C 16.796 -7.535 7
NJ5 C16 C 15.497 -6.785 8
NJ5 C17 C 14.198 -7.535 9
NJ5 C18 C 12.899 -6.785 10
NJ5 C19 C 11.600 -7.535 11
NJ5 C20 C 10.301 -6.785 12
NJ5 O2 O 10.301 -5.285 13
NJ5 N3 N 9.002 -7.535 14
NJ5 C21 C 7.702 -6.785 15
NJ5 C22 C 7.702 -5.285 16
NJ5 O3 O 9.002 -4.535 17
NJ5 P1 P 9.002 -3.035 18
NJ5 O4 O 10.502 -3.035 19
NJ5 O5 O 7.502 -3.035 20
NJ5 O6 O 9.002 -1.535 21
NJ5 P2 P 10.301 -0.785 22
NJ5 O7 O 9.551 0.514 23
NJ5 O8 O 11.051 -2.084 24
NJ5 O9 O 11.600 -0.035 25
NJ5 C23 C 11.600 1.465 26
NJ5 C24 C 12.899 2.215 27
NJ5 O10 O 13.055 3.707 28
NJ5 C25 C 14.523 4.019 29
NJ5 N4 N 15.133 5.389 30
NJ5 C26 C 14.251 6.603 31
NJ5 C27 C 14.861 7.973 32
NJ5 C28 C 16.353 8.130 33
NJ5 O11 O 16.963 9.500 34
NJ5 N5 N 17.235 6.916 35
NJ5 C29 C 16.625 5.546 36
NJ5 O12 O 17.506 4.332 37
NJ5 C30 C 15.273 2.720 38
NJ5 O13 O 16.765 2.563 39
NJ5 C31 C 14.269 1.605 40
NJ5 O14 O 14.581 0.138 41
NJ5 O15 O 6.404 -4.535 42
NJ5 C32 C 5.104 -5.285 43
NJ5 C33 C 3.805 -4.535 44
NJ5 O16 O 3.805 -3.035 45
NJ5 C34 C 5.104 -6.785 46
NJ5 O17 O 3.805 -7.535 47
NJ5 C35 C 6.404 -7.535 48
NJ5 O18 O 6.404 -9.035 49
#
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
NJ5 O4 P1 DOUBLE NONE 1
NJ5 C35 O18 SINGLE BEGINWEDGE 2
NJ5 C34 O17 SINGLE BEGINDASH 3
NJ5 P1 O5 SINGLE BEGINWEDGE 4
NJ5 P1 O3 SINGLE NONE 5
NJ5 P1 O6 SINGLE NONE 6
NJ5 C35 C34 SINGLE NONE 7
NJ5 C35 C21 SINGLE NONE 8
NJ5 C30 O13 SINGLE BEGINDASH 9
NJ5 C22 O3 SINGLE BEGINDASH 10
NJ5 C19 C18 SINGLE NONE 11
NJ5 C19 C20 SINGLE NONE 12
NJ5 C21 N3 SINGLE BEGINDASH 13
NJ5 N3 C20 SINGLE NONE 14
NJ5 C30 C31 SINGLE NONE 15
NJ5 C30 C25 SINGLE NONE 16
NJ5 C27 C26 DOUBLE NONE 17
NJ5 C27 C28 SINGLE NONE 18
NJ5 C34 C32 SINGLE NONE 19
NJ5 C26 N4 SINGLE NONE 20
NJ5 C21 C22 SINGLE NONE 21
NJ5 O9 C23 SINGLE NONE 22
NJ5 O9 P2 SINGLE NONE 23
NJ5 C18 C17 SINGLE NONE 24
NJ5 C20 O2 DOUBLE NONE 25
NJ5 O11 C28 DOUBLE NONE 26
NJ5 O6 P2 SINGLE NONE 27
NJ5 C28 N5 SINGLE NONE 28
NJ5 C31 O14 SINGLE BEGINDASH 29
NJ5 C31 C24 SINGLE NONE 30
NJ5 C32 O15 SINGLE NONE 31
NJ5 C32 C33 SINGLE BEGINWEDGE 32
NJ5 C22 O15 SINGLE NONE 33
NJ5 C24 C23 SINGLE BEGINWEDGE 34
NJ5 C25 N4 SINGLE BEGINWEDGE 35
NJ5 N4 C29 SINGLE NONE 36
NJ5 O7 P2 DOUBLE NONE 37
NJ5 C17 C16 SINGLE NONE 38
NJ5 P2 O8 SINGLE BEGINWEDGE 39
NJ5 C25 O10 SINGLE NONE 40
NJ5 N5 C29 SINGLE NONE 41
NJ5 C24 O10 SINGLE NONE 42
NJ5 C33 O16 SINGLE NONE 43
NJ5 C29 O12 DOUBLE NONE 44
NJ5 C16 C15 SINGLE NONE 45
NJ5 C15 N2 SINGLE NONE 46
NJ5 N2 C14 SINGLE NONE 47
NJ5 C14 O1 DOUBLE NONE 48
NJ5 C14 C13 SINGLE NONE 49
NJ5 C13 C12 SINGLE NONE 50
NJ5 C12 C11 SINGLE NONE 51
#
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
NJ5 MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CC[C@@H](CO[PH](=O)O[PH](=O)O[C@@H]3CCCCO3)O2)c(=O)[nH]1' InChI=1S/C14H22N2O9P2/c17-11-6-7-16(14(18)15-11)12-5-4-10(23-12)9-22-26(19)25-27(20)24-13-3-1-2-8-21-13/h6-7,10,12-13,26-27H,1-5,8-9H2,(H,15,17,18)/t10-,12+,13+/m0/s1 AKKVBKIXAFLMCT-CYZMBNFOSA-N
NJ5 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
NJ5 phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
NJ5 pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
NJ5 pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
NJ5 ribose F5 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
NJ5 C21 S1 1
NJ5 C22 S1 1
NJ5 O3 S1 1
NJ5 P1 S1 1
NJ5 O4 S1 1
NJ5 O6 S1 1
NJ5 P2 S1 1
NJ5 O7 S1 1
NJ5 O9 S1 1
NJ5 C23 S1 1
NJ5 C24 S1 1
NJ5 O10 S1 1
NJ5 C25 S1 1
NJ5 N4 S1 1
NJ5 C26 S1 1
NJ5 C27 S1 1
NJ5 C28 S1 1
NJ5 O11 S1 1
NJ5 N5 S1 1
NJ5 C29 S1 1
NJ5 O12 S1 1
NJ5 C30 S1 1
NJ5 C31 S1 1
NJ5 O15 S1 1
NJ5 C32 S1 1
NJ5 C34 S1 1
NJ5 C35 S1 1
NJ5 N2 F1 1
NJ5 C14 F1 1
NJ5 O1 F1 1
NJ5 C13 F1 1
NJ5 N3 F1 2
NJ5 C20 F1 2
NJ5 O2 F1 2
NJ5 C19 F1 2
NJ5 O3 F2 1
NJ5 P1 F2 1
NJ5 O4 F2 1
NJ5 O5 F2 1
NJ5 O6 F2 1
NJ5 O6 F2 2
NJ5 P2 F2 2
NJ5 O7 F2 2
NJ5 O9 F2 2
NJ5 O8 F2 2
NJ5 C34 F3 1
NJ5 C32 F3 1
NJ5 O15 F3 1
NJ5 C22 F3 1
NJ5 C21 F3 1
NJ5 C35 F3 1
NJ5 O3 F3 1
NJ5 C27 F4 1
NJ5 C26 F4 1
NJ5 N4 F4 1
NJ5 C29 F4 1
NJ5 N5 F4 1
NJ5 C28 F4 1
NJ5 C30 F5 1
NJ5 C31 F5 1
NJ5 C24 F5 1
NJ5 O10 F5 1
NJ5 C25 F5 1
NJ5 C23 F5 1
NJ5 O9 F5 1
NJ5 O14 F5 1
NJ5 O13 F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id NJ5
_pdbe_chem_comp_rdkit_properties.exactmw 748.197
_pdbe_chem_comp_rdkit_properties.amw 748.569
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 22
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 26
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 19
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 49
_pdbe_chem_comp_rdkit_properties.NumAtoms 91
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 24
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.760
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 11
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 337.495
_pdbe_chem_comp_rdkit_properties.tpsa 334.960
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.393
_pdbe_chem_comp_rdkit_properties.CrippenMR 161.312
_pdbe_chem_comp_rdkit_properties.chi0v 24.321
_pdbe_chem_comp_rdkit_properties.chi1v 14.206
_pdbe_chem_comp_rdkit_properties.chi2v 6.620
_pdbe_chem_comp_rdkit_properties.chi3v 6.620
_pdbe_chem_comp_rdkit_properties.chi4v 4.330
_pdbe_chem_comp_rdkit_properties.chi0n 64.532
_pdbe_chem_comp_rdkit_properties.chi1n 31.484
_pdbe_chem_comp_rdkit_properties.chi2n 4.315
_pdbe_chem_comp_rdkit_properties.chi3n 4.315
_pdbe_chem_comp_rdkit_properties.chi4n 2.562
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.400
_pdbe_chem_comp_rdkit_properties.kappa1 11.805
_pdbe_chem_comp_rdkit_properties.kappa2 18.198
_pdbe_chem_comp_rdkit_properties.kappa3 11.830
_pdbe_chem_comp_rdkit_properties.Phi 4.384
#
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
NJ5 UniChem PDBe NJ5
NJ5 UniChem PubChem 146018706
#
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
NJ5 C11 9.571 3.060 0.156 ETKDGv3 1
NJ5 C12 8.854 2.199 -0.879 ETKDGv3 2
NJ5 C13 8.050 3.062 -1.856 ETKDGv3 3
NJ5 C14 7.357 2.198 -2.865 ETKDGv3 4
NJ5 O1 7.849 2.072 -4.019 ETKDGv3 5
NJ5 N2 6.162 1.492 -2.503 ETKDGv3 6
NJ5 C15 5.519 0.520 -3.387 ETKDGv3 7
NJ5 C16 6.355 -0.762 -3.516 ETKDGv3 8
NJ5 C17 6.623 -1.471 -2.176 ETKDGv3 9
NJ5 C18 5.361 -2.096 -1.545 ETKDGv3 10
NJ5 C19 4.830 -1.269 -0.367 ETKDGv3 11
NJ5 C20 3.582 -1.886 0.186 ETKDGv3 12
NJ5 O2 3.656 -2.653 1.183 ETKDGv3 13
NJ5 N3 2.319 -1.639 -0.450 ETKDGv3 14
NJ5 C21 1.056 -2.171 0.076 ETKDGv3 15
NJ5 C22 0.617 -1.375 1.323 ETKDGv3 16
NJ5 O3 0.563 0.006 1.020 ETKDGv3 17
NJ5 P1 0.229 0.912 2.434 ETKDGv3 18
NJ5 O4 1.178 2.089 2.498 ETKDGv3 19
NJ5 O5 0.442 -0.017 3.835 ETKDGv3 20
NJ5 O6 -1.386 1.452 2.391 ETKDGv3 21
NJ5 P2 -1.531 2.570 1.112 ETKDGv3 22
NJ5 O7 -0.876 3.874 1.508 ETKDGv3 23
NJ5 O8 -0.805 1.991 -0.306 ETKDGv3 24
NJ5 O9 -3.182 2.870 0.811 ETKDGv3 25
NJ5 C23 -3.795 1.650 0.465 ETKDGv3 26
NJ5 C24 -5.269 1.890 0.131 ETKDGv3 27
NJ5 O10 -5.865 0.679 -0.273 ETKDGv3 28
NJ5 C25 -7.218 0.706 0.139 ETKDGv3 29
NJ5 N4 -7.548 -0.542 0.848 ETKDGv3 30
NJ5 C26 -6.629 -1.072 1.828 ETKDGv3 31
NJ5 C27 -6.892 -2.195 2.502 ETKDGv3 32
NJ5 C28 -8.149 -2.920 2.279 ETKDGv3 33
NJ5 O11 -8.383 -3.987 2.904 ETKDGv3 34
NJ5 N5 -9.108 -2.403 1.356 ETKDGv3 35
NJ5 C29 -8.819 -1.196 0.649 ETKDGv3 36
NJ5 O12 -9.678 -0.714 -0.137 ETKDGv3 37
NJ5 C30 -7.453 1.922 1.048 ETKDGv3 38
NJ5 O13 -8.264 2.886 0.415 ETKDGv3 39
NJ5 C31 -6.054 2.434 1.318 ETKDGv3 40
NJ5 O14 -5.994 3.836 1.364 ETKDGv3 41
NJ5 O15 -0.621 -1.868 1.818 ETKDGv3 42
NJ5 C32 -1.670 -1.710 0.875 ETKDGv3 43
NJ5 C33 -2.985 -2.144 1.539 ETKDGv3 44
NJ5 O16 -3.212 -1.399 2.705 ETKDGv3 45
NJ5 C34 -1.391 -2.543 -0.397 ETKDGv3 46
NJ5 O17 -2.403 -2.329 -1.348 ETKDGv3 47
NJ5 C35 -0.042 -2.120 -1.001 ETKDGv3 48
NJ5 O18 0.303 -2.984 -2.054 ETKDGv3 49
NJ5 H1 8.835 3.646 0.746 ETKDGv3 50
NJ5 H2 10.144 2.408 0.849 ETKDGv3 51
NJ5 H3 10.279 3.755 -0.344 ETKDGv3 52
NJ5 H12 9.609 1.604 -1.439 ETKDGv3 53
NJ5 H11 8.174 1.495 -0.351 ETKDGv3 54
NJ5 H14 7.291 3.654 -1.300 ETKDGv3 55
NJ5 H13 8.728 3.773 -2.377 ETKDGv3 56
NJ5 H15 5.714 1.702 -1.583 ETKDGv3 57
NJ5 H17 4.509 0.271 -2.998 ETKDGv3 58
NJ5 H16 5.376 0.972 -4.392 ETKDGv3 59
NJ5 H19 7.331 -0.513 -3.985 ETKDGv3 60
NJ5 H18 5.838 -1.462 -4.209 ETKDGv3 61
NJ5 H21 7.134 -0.781 -1.469 ETKDGv3 62
NJ5 H20 7.346 -2.291 -2.380 ETKDGv3 63
NJ5 H23 5.618 -3.110 -1.166 ETKDGv3 64
NJ5 H22 4.563 -2.227 -2.308 ETKDGv3 65
NJ5 H24 5.602 -1.215 0.431 ETKDGv3 66
NJ5 H25 4.603 -0.233 -0.689 ETKDGv3 67
NJ5 H26 2.312 -1.067 -1.325 ETKDGv3 68
NJ5 H27 1.204 -3.236 0.366 ETKDGv3 69
NJ5 H28 1.394 -1.556 2.098 ETKDGv3 70
NJ5 H4 0.103 0.553 4.570 ETKDGv3 71
NJ5 H5 -1.014 2.673 -0.994 ETKDGv3 72
NJ5 H29 -3.313 1.207 -0.437 ETKDGv3 73
NJ5 H30 -3.731 0.923 1.306 ETKDGv3 74
NJ5 H31 -5.327 2.607 -0.721 ETKDGv3 75
NJ5 H32 -7.839 0.790 -0.781 ETKDGv3 76
NJ5 H33 -5.702 -0.554 2.031 ETKDGv3 77
NJ5 H34 -6.175 -2.569 3.223 ETKDGv3 78
NJ5 H35 -10.015 -2.899 1.205 ETKDGv3 79
NJ5 H36 -7.941 1.631 2.005 ETKDGv3 80
NJ5 H37 -7.825 3.149 -0.437 ETKDGv3 81
NJ5 H38 -5.673 1.995 2.271 ETKDGv3 82
NJ5 H39 -6.391 4.105 2.233 ETKDGv3 83
NJ5 H40 -1.787 -0.641 0.592 ETKDGv3 84
NJ5 H41 -3.832 -1.962 0.844 ETKDGv3 85
NJ5 H42 -2.964 -3.234 1.771 ETKDGv3 86
NJ5 H43 -2.696 -1.835 3.432 ETKDGv3 87
NJ5 H44 -1.329 -3.625 -0.123 ETKDGv3 88
NJ5 H45 -3.075 -3.050 -1.230 ETKDGv3 89
NJ5 H46 -0.126 -1.073 -1.380 ETKDGv3 90
NJ5 H47 -0.210 -2.688 -2.850 ETKDGv3 91
#