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.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 -24.794 -31.465 -13.644 14.329 -4.771 -1.060 C11 NJ5 1
NJ5 C12 C2 C 0 1 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 -25.851 -30.038 -15.551 12.309 -3.329 -0.769 C13 NJ5 3
NJ5 C14 C4 C 0 1 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 -28.227 -30.351 -15.826 10.736 -3.928 0.885 O1 NJ5 5
NJ5 N2 N1 N 0 1 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 -28.105 -29.368 -18.498 8.987 -1.913 0.502 C15 NJ5 7
NJ5 C16 C6 C 0 1 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 -27.327 -27.866 -20.465 6.968 -0.472 0.793 C17 NJ5 9
NJ5 C18 C8 C 0 1 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 -26.291 -26.026 -21.893 4.948 0.970 1.084 C19 NJ5 11
NJ5 C20 C10 C 0 1 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 -25.658 -24.808 -19.914 4.712 2.861 -0.308 O2 NJ5 13
NJ5 N3 N2 N 0 1 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 -23.464 -23.566 -21.218 2.367 3.766 0.666 C21 NJ5 15
NJ5 C22 C12 C 0 1 N N R -22.146 -24.220 -20.786 1.508 3.406 -0.549 C22 NJ5 16
NJ5 O3 O3 O 0 1 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 -21.220 -26.171 -22.292 0.043 1.282 -1.241 P1 NJ5 18
NJ5 O4 O4 O 0 1 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 -22.567 -26.802 -22.300 -0.835 2.015 -2.374 O5 NJ5 20
NJ5 O6 O6 O 0 1 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 -19.277 -26.718 -20.281 -1.355 -1.295 -0.802 P2 NJ5 22
NJ5 O7 O7 O 0 1 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 -19.496 -27.295 -18.950 -0.169 -2.330 -0.465 O8 NJ5 24
NJ5 O9 O9 O 0 1 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 -17.398 -28.534 -20.605 -3.377 -2.872 -0.053 C23 NJ5 26
NJ5 C24 C14 C 0 1 N N R -16.316 -27.692 -19.980 -4.541 -2.888 0.940 C24 NJ5 27
NJ5 O10 O10 O 0 1 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 -14.110 -28.399 -20.249 -6.802 -2.386 0.931 C25 NJ5 29
NJ5 N4 N3 N 0 1 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 -14.186 -30.671 -21.247 -7.766 -1.609 -1.184 C26 NJ5 31
NJ5 C27 C17 C 0 1 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 -12.412 -32.245 -20.923 -9.801 -0.367 -1.170 C28 NJ5 33
NJ5 O11 O11 O 0 1 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 -11.819 -31.270 -20.153 -9.842 -0.461 0.174 N5 NJ5 35
NJ5 C29 C19 C 0 1 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 -11.676 -29.196 -19.264 -8.926 -1.199 2.050 O12 NJ5 37
NJ5 C30 C20 C 0 1 N N R -14.520 -27.638 -21.505 -6.727 -3.874 0.503 C30 NJ5 38
NJ5 O13 O13 O 0 1 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 -15.581 -26.720 -20.910 -5.270 -4.245 0.871 C31 NJ5 40
NJ5 O14 O14 O 0 1 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 -21.468 -23.241 -20.012 0.787 4.562 -0.980 O15 NJ5 42
NJ5 C32 C22 C 0 1 N N R -21.019 -22.122 -20.820 -0.108 5.091 0.000 C32 NJ5 43
NJ5 C33 C23 C 0 1 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 -20.786 -20.853 -18.740 -1.673 5.882 -1.663 O16 NJ5 45
NJ5 C34 C24 C 0 1 N N S -22.220 -21.383 -21.418 0.686 5.518 1.237 C34 NJ5 46
NJ5 O17 O17 O 0 1 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 -23.121 -22.389 -22.133 1.465 4.314 1.776 C35 NJ5 48
NJ5 O18 O18 O 0 1 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 -24.964 -31.777 -12.603 14.846 -5.661 -0.703 H1 NJ5 50
NJ5 H2 H2 H 0 1 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 -23.845 -30.912 -13.711 14.970 -3.899 -0.925 H3 NJ5 52
NJ5 H12 H4 H 0 1 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 -26.852 -31.157 -13.994 13.271 -4.462 0.791 H11 NJ5 54
NJ5 H14 H6 H 0 1 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 -25.322 -29.074 -15.529 12.073 -3.446 -1.827 H13 NJ5 56
NJ5 H15 H8 H 0 1 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 -29.062 -29.762 -18.127 8.346 -2.784 0.366 H17 NJ5 58
NJ5 H16 H10 H 0 1 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 -28.555 -27.297 -18.804 8.903 0.208 0.135 H19 NJ5 60
NJ5 H18 H12 H 0 1 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 -27.310 -28.677 -21.208 6.326 -1.343 0.658 H21 NJ5 62
NJ5 H20 H14 H 0 1 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 -27.866 -25.792 -20.477 6.883 1.650 0.426 H23 NJ5 64
NJ5 H22 H16 H 0 1 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 -25.655 -26.889 -22.137 4.307 0.099 0.949 H24 NJ5 66
NJ5 H25 H18 H 0 1 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 -24.333 -24.744 -22.742 2.679 2.042 1.865 H26 NJ5 68
NJ5 H27 H20 H 0 1 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 -22.374 -25.103 -20.171 2.150 3.056 -1.357 H28 NJ5 70
NJ5 H4 H22 H 0 1 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 -19.286 -26.649 -18.286 0.111 -2.320 0.461 H5 NJ5 72
NJ5 H29 H24 H 0 1 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 -16.953 -29.185 -21.372 -2.717 -3.716 0.147 H30 NJ5 74
NJ5 H31 H26 H 0 1 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 -13.390 -27.786 -19.687 -6.980 -2.303 2.003 H32 NJ5 76
NJ5 H33 H28 H 0 1 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 -14.245 -32.604 -22.059 -8.677 -0.895 -2.953 H34 NJ5 78
NJ5 H35 H30 H 0 1 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 -14.955 -28.314 -22.256 -6.897 -3.980 -0.568 H36 NJ5 80
NJ5 H37 H32 H 0 1 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 -16.260 -26.359 -21.697 -4.831 -4.877 0.100 H38 NJ5 82
NJ5 H39 H34 H 0 1 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 -20.405 -22.502 -21.650 -0.833 4.326 0.280 H40 NJ5 84
NJ5 H41 H36 H 0 1 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 -19.843 -20.370 -20.498 -0.115 7.029 -0.940 H42 NJ5 86
NJ5 H43 H38 H 0 1 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 -22.790 -20.921 -20.599 1.383 6.312 0.966 H44 NJ5 88
NJ5 H45 H40 H 0 1 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 -22.545 -22.795 -22.978 0.766 3.540 2.093 H46 NJ5 90
NJ5 H47 H42 H 0 1 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
##