data_8JD
#
_chem_comp.id 8JD
_chem_comp.name
"[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-4-[(3-{[2-(ethylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H39 N7 O13 P2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "Ethyl Coenzyme A"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-02-09
_chem_comp.pdbx_modified_date 2021-03-01
_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 715.607
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 8JD
_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 5UQR
_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
8JD N6A N1 N 0 1 N N N N N N 42.769 -35.668 -33.255 8.481 6.421 2.177 N6A 8JD 1
8JD C6A C1 C 0 1 Y N N N N N 43.087 -35.621 -31.946 8.251 5.724 1.003 C6A 8JD 2
8JD N1A N2 N 0 1 Y N N N N N 44.043 -34.804 -31.456 8.413 6.310 -0.178 N1A 8JD 3
8JD C2A C2 C 0 1 Y N N N N N 44.336 -34.796 -30.138 8.196 5.653 -1.303 C2A 8JD 4
8JD N3A N3 N 0 1 Y N N N N N 43.723 -35.569 -29.206 7.812 4.395 -1.324 N3A 8JD 5
8JD C4A C3 C 0 1 Y N N N N N 42.735 -36.426 -29.589 7.624 3.725 -0.191 C4A 8JD 6
8JD C5A C4 C 0 1 Y N N N N N 42.370 -36.508 -31.011 7.847 4.378 1.033 C5A 8JD 7
8JD N9A N4 N 0 1 Y N N N N N 41.960 -37.320 -28.987 7.239 2.448 0.127 N9A 8JD 8
8JD N7A N5 N 0 1 Y N N N N N 41.390 -37.419 -31.137 7.594 3.481 2.016 N7A 8JD 9
8JD C8A C5 C 0 1 Y N N N N N 41.145 -37.902 -29.900 7.228 2.350 1.487 C8A 8JD 10
8JD C1M C6 C 0 1 N N N N N N 33.230 -34.874 -40.174 -14.824 5.677 0.745 C1M 8JD 11
8JD CP C7 C 0 1 N N N N N N 33.207 -34.112 -38.875 -13.826 4.625 1.233 CP 8JD 12
8JD O3X O1 O 0 1 N N N N N N 41.192 -37.131 -24.658 7.868 -1.347 -2.673 O3X 8JD 13
8JD S1 S1 S 0 1 N N N N N N 33.672 -34.918 -37.502 -12.794 4.080 -0.155 S1 8JD 14
8JD N4 N6 N 0 1 N N N N N N 36.672 -33.764 -35.185 -9.857 1.304 0.168 N4 8JD 15
8JD C5 C8 C 0 1 N N N N N N 37.972 -33.524 -35.390 -8.931 0.671 -0.579 C5 8JD 16
8JD O5 O2 O 0 1 N N N N N N 38.567 -33.875 -36.406 -8.832 0.919 -1.762 O5 8JD 17
8JD C6 C9 C 0 1 N N N N N N 38.711 -32.814 -34.265 -8.017 -0.346 0.056 C6 8JD 18
8JD C7 C10 C 0 1 N N N N N N 39.723 -33.747 -33.573 -7.068 -0.910 -1.003 C7 8JD 19
8JD N8 N7 N 0 1 N N N N N N 39.184 -35.035 -33.157 -6.180 -1.898 -0.386 N8 8JD 20
8JD C9 C11 C 0 1 N N N N N N 38.704 -35.260 -31.926 -5.253 -2.531 -1.132 C9 8JD 21
8JD O9 O3 O 0 1 N N N N N N 38.650 -34.388 -31.057 -5.215 -2.353 -2.331 O9 8JD 22
8JD C13 C12 C 0 1 N N N N N N 35.927 -35.634 -31.235 -2.965 -1.428 0.173 C13 8JD 23
8JD C11 C13 C 0 1 N N N N N N 36.694 -36.792 -31.880 -2.879 -2.812 -0.475 C11 8JD 24
8JD C14 C14 C 0 1 N N N N N N 36.447 -36.789 -33.383 -2.379 -2.671 -1.914 C14 8JD 25
8JD C12 C15 C 0 1 N N N N N N 36.234 -38.126 -31.300 -1.907 -3.687 0.320 C12 8JD 26
8JD P1A P1 P 0 1 N N N N N N 38.687 -40.709 -28.380 3.553 -3.139 0.825 P1A 8JD 27
8JD O2A O4 O 0 1 N N N N N N 39.824 -41.046 -29.312 3.842 -4.458 0.220 O2A 8JD 28
8JD O1A O5 O 0 1 N N N N N N 37.925 -41.856 -27.757 4.030 -3.137 2.363 O1A 8JD 29
8JD O3A O6 O 0 1 N N N N N N 37.738 -39.633 -29.140 1.970 -2.851 0.753 O3A 8JD 30
8JD O5X O7 O 0 1 N N N N N N 39.294 -39.767 -27.246 4.344 -1.993 0.017 O5X 8JD 31
8JD C4X C16 C 0 1 N N R N N N 41.247 -39.124 -25.995 6.180 -0.790 -0.994 C4X 8JD 32
8JD O4X O8 O 0 1 N N N N N N 42.117 -38.878 -27.110 6.044 0.404 -0.193 O4X 8JD 33
8JD C1X C17 C 0 1 N N R N N N 41.945 -37.530 -27.525 6.900 1.383 -0.821 C1X 8JD 34
8JD C2X C18 C 0 1 N N R N N N 40.580 -37.065 -26.998 8.168 0.599 -1.224 C2X 8JD 35
8JD O2X O9 O 0 1 N N N N N N 40.491 -35.639 -26.831 8.666 1.063 -2.480 O2X 8JD 36
8JD C3X C19 C 0 1 N N S N N N 40.499 -37.822 -25.694 7.684 -0.864 -1.341 C3X 8JD 37
8JD C5X C20 C 0 1 N N N N N N 40.313 -40.255 -26.377 5.757 -2.023 -0.193 C5X 8JD 38
8JD P2A P2 P 0 1 N N N N N N 36.181 -39.260 -28.876 0.658 -3.730 1.066 P2A 8JD 39
8JD O4A O10 O 0 1 N N N N N N 35.327 -40.410 -29.324 0.863 -5.112 0.579 O4A 8JD 40
8JD O5A O11 O 0 1 N N N N N N 35.984 -38.669 -27.505 0.396 -3.754 2.655 O5A 8JD 41
8JD O6A O12 O 0 1 N N N N N N 36.039 -38.017 -29.893 -0.613 -3.080 0.322 O6A 8JD 42
8JD C10 C21 C 0 1 N N R N N N 38.198 -36.648 -31.598 -4.264 -3.461 -0.477 C10 8JD 43
8JD O10 O13 O 0 1 N N N N N N 38.921 -37.684 -32.295 -4.672 -3.719 0.868 O10 8JD 44
8JD C3 C22 C 0 1 N N N N N N 35.886 -34.632 -36.055 -10.745 2.292 -0.450 C3 8JD 45
8JD C2 C23 C 0 1 N N N N N N 35.075 -33.902 -37.091 -11.694 2.856 0.609 C2 8JD 46
8JD H1 H1 H 0 1 N N N N N N 43.341 -35.022 -33.761 8.763 7.348 2.143 H1 8JD 47
8JD H2 H2 H 0 1 N N N N N N 42.923 -36.593 -33.602 8.355 5.983 3.033 H2 8JD 48
8JD H3 H3 H 0 1 N N N N N N 45.114 -34.127 -29.801 8.340 6.168 -2.242 H3 8JD 49
8JD H4 H4 H 0 1 N N N N N N 40.401 -38.650 -29.670 6.967 1.462 2.042 H4 8JD 50
8JD H5 H5 H 0 1 N N N N N N 32.899 -34.216 -40.991 -14.282 6.530 0.338 H5 8JD 51
8JD H6 H6 H 0 1 N N N N N N 34.253 -35.223 -40.376 -15.457 5.245 -0.030 H6 8JD 52
8JD H7 H7 H 0 1 N N N N N N 32.554 -35.739 -40.103 -15.444 6.004 1.579 H7 8JD 53
8JD H8 H8 H 0 1 N N N N N N 33.875 -33.246 -38.990 -13.193 5.057 2.008 H8 8JD 54
8JD H9 H9 H 0 1 N N N N N N 32.176 -33.762 -38.717 -14.368 3.771 1.641 H9 8JD 55
8JD H10 H10 H 0 1 N N N N N N 41.127 -37.625 -23.849 8.794 -1.414 -2.943 H10 8JD 56
8JD H11 H11 H 0 1 N N N N N N 36.221 -33.331 -34.404 -9.936 1.105 1.114 H11 8JD 57
8JD H12 H12 H 0 1 N N N N N N 39.249 -31.950 -34.681 -7.437 0.131 0.846 H12 8JD 58
8JD H13 H13 H 0 1 N N N N N N 37.979 -32.467 -33.521 -8.612 -1.155 0.479 H13 8JD 59
8JD H14 H14 H 0 1 N N N N N N 40.551 -33.933 -34.273 -7.647 -1.387 -1.794 H14 8JD 60
8JD H15 H15 H 0 1 N N N N N N 40.107 -33.233 -32.680 -6.473 -0.101 -1.426 H15 8JD 61
8JD H16 H16 H 0 1 N N N N N N 39.172 -35.784 -33.819 -6.258 -2.097 0.561 H16 8JD 62
8JD H17 H17 H 0 1 N N N N N N 36.105 -35.635 -30.149 -3.321 -1.528 1.198 H17 8JD 63
8JD H18 H18 H 0 1 N N N N N N 36.274 -34.682 -31.662 -1.978 -0.965 0.175 H18 8JD 64
8JD H19 H19 H 0 1 N N N N N N 34.851 -35.753 -31.430 -3.657 -0.804 -0.393 H19 8JD 65
8JD H20 H20 H 0 1 N N N N N N 35.369 -36.892 -33.578 -3.028 -1.985 -2.459 H20 8JD 66
8JD H21 H21 H 0 1 N N N N N N 36.808 -35.843 -33.812 -1.361 -2.281 -1.908 H21 8JD 67
8JD H22 H22 H 0 1 N N N N N N 36.985 -37.630 -33.845 -2.391 -3.646 -2.400 H22 8JD 68
8JD H23 H23 H 0 1 N N N N N N 35.286 -38.420 -31.775 -2.263 -3.787 1.345 H23 8JD 69
8JD H24 H24 H 0 1 N N N N N N 36.998 -38.891 -31.501 -1.845 -4.672 -0.141 H24 8JD 70
8JD H25 H25 H 0 1 N N N N N N 38.290 -42.680 -28.057 3.870 -2.302 2.823 H25 8JD 71
8JD H26 H26 H 0 1 N N N N N N 41.830 -39.417 -25.110 5.585 -0.706 -1.903 H26 8JD 72
8JD H27 H27 H 0 1 N N N N N N 42.722 -36.900 -27.067 6.414 1.801 -1.702 H27 8JD 73
8JD H28 H28 H 0 1 N N N N N N 39.792 -37.422 -27.677 8.934 0.689 -0.454 H28 8JD 74
8JD H29 H29 H 0 1 N N N N N N 39.629 -35.411 -26.504 9.462 0.604 -2.782 H29 8JD 75
8JD H30 H30 H 0 1 N N N N N N 39.453 -38.031 -25.426 8.210 -1.498 -0.627 H30 8JD 76
8JD H31 H31 H 0 1 N N N N N N 39.851 -40.670 -25.469 6.267 -2.023 0.770 H31 8JD 77
8JD H32 H32 H 0 1 N N N N N N 40.884 -41.043 -26.890 6.023 -2.924 -0.746 H32 8JD 78
8JD H33 H33 H 0 1 N N N N N N 35.288 -39.134 -27.056 0.253 -2.881 3.043 H33 8JD 79
8JD H34 H34 H 0 1 N N N N N N 38.338 -36.800 -30.518 -4.225 -4.398 -1.031 H34 8JD 80
8JD H35 H35 H 0 1 N N N N N N 38.567 -38.533 -32.057 -4.729 -2.927 1.420 H35 8JD 81
8JD H36 H36 H 0 1 N N N N N N 35.197 -35.216 -35.427 -10.150 3.101 -0.873 H36 8JD 82
8JD H37 H37 H 0 1 N N N N N N 36.575 -35.314 -36.575 -11.325 1.815 -1.241 H37 8JD 83
8JD H38 H38 H 0 1 N N N N N N 35.686 -33.727 -37.989 -11.115 3.332 1.400 H38 8JD 84
8JD H39 H39 H 0 1 N N N N N N 34.733 -32.938 -36.687 -12.290 2.047 1.032 H39 8JD 85
#
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
8JD C1M CP SING N N 1
8JD CP S1 SING N N 2
8JD S1 C2 SING N N 3
8JD C2 C3 SING N N 4
8JD O5 C5 DOUB N N 5
8JD C3 N4 SING N N 6
8JD C5 N4 SING N N 7
8JD C5 C6 SING N N 8
8JD C6 C7 SING N N 9
8JD C7 N8 SING N N 10
8JD C14 C11 SING N N 11
8JD N6A C6A SING N N 12
8JD N8 C9 SING N N 13
8JD O10 C10 SING N N 14
8JD C6A N1A DOUB Y N 15
8JD C6A C5A SING Y N 16
8JD C9 C10 SING N N 17
8JD C9 O9 DOUB N N 18
8JD C11 C10 SING N N 19
8JD C11 C12 SING N N 20
8JD C11 C13 SING N N 21
8JD N1A C2A SING Y N 22
8JD C12 O6A SING N N 23
8JD N7A C5A SING Y N 24
8JD N7A C8A DOUB Y N 25
8JD C5A C4A DOUB Y N 26
8JD C2A N3A DOUB Y N 27
8JD C8A N9A SING Y N 28
8JD O6A P2A SING N N 29
8JD C4A N3A SING Y N 30
8JD C4A N9A SING Y N 31
8JD O4A P2A DOUB N N 32
8JD O2A P1A DOUB N N 33
8JD O3A P2A SING N N 34
8JD O3A P1A SING N N 35
8JD N9A C1X SING N N 36
8JD P2A O5A SING N N 37
8JD P1A O1A SING N N 38
8JD P1A O5X SING N N 39
8JD C1X O4X SING N N 40
8JD C1X C2X SING N N 41
8JD O5X C5X SING N N 42
8JD O4X C4X SING N N 43
8JD C2X O2X SING N N 44
8JD C2X C3X SING N N 45
8JD C5X C4X SING N N 46
8JD C4X C3X SING N N 47
8JD C3X O3X SING N N 48
8JD N6A H1 SING N N 49
8JD N6A H2 SING N N 50
8JD C2A H3 SING N N 51
8JD C8A H4 SING N N 52
8JD C1M H5 SING N N 53
8JD C1M H6 SING N N 54
8JD C1M H7 SING N N 55
8JD CP H8 SING N N 56
8JD CP H9 SING N N 57
8JD O3X H10 SING N N 58
8JD N4 H11 SING N N 59
8JD C6 H12 SING N N 60
8JD C6 H13 SING N N 61
8JD C7 H14 SING N N 62
8JD C7 H15 SING N N 63
8JD N8 H16 SING N N 64
8JD C13 H17 SING N N 65
8JD C13 H18 SING N N 66
8JD C13 H19 SING N N 67
8JD C14 H20 SING N N 68
8JD C14 H21 SING N N 69
8JD C14 H22 SING N N 70
8JD C12 H23 SING N N 71
8JD C12 H24 SING N N 72
8JD O1A H25 SING N N 73
8JD C4X H26 SING N N 74
8JD C1X H27 SING N N 75
8JD C2X H28 SING N N 76
8JD O2X H29 SING N N 77
8JD C3X H30 SING N N 78
8JD C5X H31 SING N N 79
8JD C5X H32 SING N N 80
8JD O5A H33 SING N N 81
8JD C10 H34 SING N N 82
8JD O10 H35 SING N N 83
8JD C3 H36 SING N N 84
8JD C3 H37 SING N N 85
8JD C2 H38 SING N N 86
8JD C2 H39 SING N N 87
#
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
8JD SMILES ACDLabs 12.01 Nc2ncnc3n(C1OC(C(O)C1O)COP(O)(=O)OP(O)(=O)OCC(C)(C(C(NCCC(NCCSCC)=O)=O)O)C)cnc23
8JD InChI InChI 1.03 InChI=1S/C23H39N7O13P2S/c1-4-46-8-7-25-14(31)5-6-26-21(35)18(34)23(2,3)10-41-45(38,39)43-44(36,37)40-9-13-16(32)17(33)22(42-13)30-12-29-15-19(24)27-11-28-20(15)30/h11-13,16-18,22,32-34H,4-10H2,1-3H3,(H,25,31)(H,26,35)(H,36,37)(H,38,39)(H2,24,27,28)/t13-,16-,17-,18+,22-/m1/s1
8JD InChIKey InChI 1.03 ZYQGAGMIMDQCKA-ZSJPKINUSA-N
8JD SMILES_CANONICAL CACTVS 3.385 CCSCCNC(=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)n2cnc3c(N)ncnc23
8JD SMILES CACTVS 3.385 CCSCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
8JD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CCSCCNC(=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)O)O
8JD SMILES "OpenEye OEToolkits" 2.0.6 CCSCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)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
8JD "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-4-[(3-{[2-(ethylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)"
8JD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-(2-ethylsulfanylethylamino)-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] 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
8JD 'Create component' 2017-02-09 RCSB
8JD 'Other modification' 2018-02-27 RCSB
8JD 'Initial release' 2018-03-14 RCSB
8JD 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 8JD
_pdbx_chem_comp_synonyms.name "Ethyl Coenzyme A"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id 8JD
_pdbe_chem_comp_synonyms.name 'Ethyl Coenzyme A'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
8JD N6A N 4.299 -5.333 1
8JD C6A C 4.299 -3.833 2
8JD N1A N 3.000 -3.083 3
8JD C2A C 3.000 -1.583 4
8JD N3A N 4.299 -0.833 5
8JD C4A C 5.598 -1.583 6
8JD C5A C 5.598 -3.083 7
8JD N9A N 7.018 -1.126 8
8JD N7A N 7.018 -3.540 9
8JD C8A C 7.893 -2.333 10
8JD C1M C 34.757 4.932 11
8JD CP C 33.541 4.053 12
8JD O3X O 7.027 4.155 13
8JD S1 S 32.172 4.665 14
8JD N4 N 28.373 3.518 15
8JD C5 C 27.004 4.131 16
8JD O5 O 26.849 5.623 17
8JD C6 C 25.788 3.251 18
8JD C7 C 24.419 3.864 19
8JD N8 N 23.204 2.984 20
8JD C9 C 21.835 3.597 21
8JD O9 O 21.681 5.089 22
8JD C13 C 18.638 1.960 23
8JD C11 C 19.251 3.330 24
8JD C14 C 19.863 4.699 25
8JD C12 C 17.881 3.942 26
8JD P1A P 12.713 3.408 27
8JD O2A O 13.592 2.193 28
8JD O1A O 11.833 4.623 29
8JD O3A O 13.928 4.288 30
8JD O5X O 11.498 2.528 31
8JD C4X C 8.913 2.261 32
8JD O4X O 8.911 0.761 33
8JD C1X C 7.483 0.300 34
8JD C2X C 6.604 1.515 35
8JD O2X O 5.104 1.518 36
8JD C3X C 7.487 2.727 37
8JD C5X C 10.129 3.141 38
8JD P2A P 15.297 3.675 39
8JD O4A O 15.909 5.044 40
8JD O5A O 14.684 2.306 41
8JD O6A O 16.666 3.062 42
8JD C10 C 20.620 2.717 43
8JD O10 O 20.774 1.225 44
8JD C3 C 29.588 4.398 45
8JD C2 C 30.957 3.785 46
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
8JD C1M CP SINGLE NONE 1
8JD CP S1 SINGLE NONE 2
8JD S1 C2 SINGLE NONE 3
8JD C2 C3 SINGLE NONE 4
8JD O5 C5 DOUBLE NONE 5
8JD C3 N4 SINGLE NONE 6
8JD C5 N4 SINGLE NONE 7
8JD C5 C6 SINGLE NONE 8
8JD C6 C7 SINGLE NONE 9
8JD C7 N8 SINGLE NONE 10
8JD C14 C11 SINGLE NONE 11
8JD N6A C6A SINGLE NONE 12
8JD N8 C9 SINGLE NONE 13
8JD C10 O10 SINGLE BEGINDASH 14
8JD C6A N1A DOUBLE NONE 15
8JD C6A C5A SINGLE NONE 16
8JD C9 C10 SINGLE NONE 17
8JD C9 O9 DOUBLE NONE 18
8JD C11 C10 SINGLE NONE 19
8JD C11 C12 SINGLE NONE 20
8JD C11 C13 SINGLE NONE 21
8JD N1A C2A SINGLE NONE 22
8JD C12 O6A SINGLE NONE 23
8JD N7A C5A SINGLE NONE 24
8JD N7A C8A DOUBLE NONE 25
8JD C5A C4A DOUBLE NONE 26
8JD C2A N3A DOUBLE NONE 27
8JD C8A N9A SINGLE NONE 28
8JD O6A P2A SINGLE NONE 29
8JD C4A N3A SINGLE NONE 30
8JD C4A N9A SINGLE NONE 31
8JD O4A P2A DOUBLE NONE 32
8JD O2A P1A DOUBLE NONE 33
8JD O3A P2A SINGLE NONE 34
8JD O3A P1A SINGLE NONE 35
8JD C1X N9A SINGLE BEGINWEDGE 36
8JD P2A O5A SINGLE BEGINWEDGE 37
8JD P1A O1A SINGLE BEGINDASH 38
8JD P1A O5X SINGLE NONE 39
8JD C1X O4X SINGLE NONE 40
8JD C1X C2X SINGLE NONE 41
8JD O5X C5X SINGLE NONE 42
8JD O4X C4X SINGLE NONE 43
8JD C2X O2X SINGLE BEGINDASH 44
8JD C2X C3X SINGLE NONE 45
8JD C4X C5X SINGLE BEGINWEDGE 46
8JD C4X C3X SINGLE NONE 47
8JD C3X O3X SINGLE BEGINDASH 48
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
8JD 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
8JD 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
8JD amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
8JD imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
8JD 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
8JD 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
8JD pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
8JD 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
8JD C6A S1 1
8JD N1A S1 1
8JD C2A S1 1
8JD N3A S1 1
8JD C4A S1 1
8JD C5A S1 1
8JD N9A S1 1
8JD N7A S1 1
8JD C8A S1 1
8JD C4X S1 1
8JD O4X S1 1
8JD C1X S1 1
8JD C2X S1 1
8JD C3X S1 1
8JD N1A F1 1
8JD C6A F1 1
8JD C5A F1 1
8JD C4A F1 1
8JD N3A F1 1
8JD C2A F1 1
8JD N9A F1 1
8JD C8A F1 1
8JD N7A F1 1
8JD N6A F1 1
8JD N4 F2 1
8JD C5 F2 1
8JD O5 F2 1
8JD C6 F2 1
8JD N8 F2 2
8JD C9 F2 2
8JD O9 F2 2
8JD C10 F2 2
8JD C4A F3 1
8JD C5A F3 1
8JD N7A F3 1
8JD C8A F3 1
8JD N9A F3 1
8JD O1A F4 1
8JD P1A F4 1
8JD O2A F4 1
8JD O3A F4 1
8JD O5X F4 1
8JD O3A F4 2
8JD P2A F4 2
8JD O4A F4 2
8JD O6A F4 2
8JD O5A F4 2
8JD N7A F5 1
8JD C8A F5 1
8JD N9A F5 1
8JD C4A F5 1
8JD C5A F5 1
8JD C6A F5 1
8JD N1A F5 1
8JD C2A F5 1
8JD N3A F5 1
8JD C5A F6 1
8JD C6A F6 1
8JD N1A F6 1
8JD C2A F6 1
8JD N3A F6 1
8JD C4A F6 1
8JD C2X F7 1
8JD C3X F7 1
8JD C4X F7 1
8JD O4X F7 1
8JD C1X F7 1
8JD C5X F7 1
8JD O5X F7 1
8JD O3X F7 1
8JD O2X F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 8JD
_pdbe_chem_comp_rdkit_properties.exactmw 715.180
_pdbe_chem_comp_rdkit_properties.amw 715.616
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 20
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 27
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 19
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 46
_pdbe_chem_comp_rdkit_properties.NumAtoms 85
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 23
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.696
_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 322.624
_pdbe_chem_comp_rdkit_properties.tpsa 300.030
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.768
_pdbe_chem_comp_rdkit_properties.CrippenMR 158.692
_pdbe_chem_comp_rdkit_properties.chi0v 23.846
_pdbe_chem_comp_rdkit_properties.chi1v 14.324
_pdbe_chem_comp_rdkit_properties.chi2v 6.664
_pdbe_chem_comp_rdkit_properties.chi3v 6.664
_pdbe_chem_comp_rdkit_properties.chi4v 4.218
_pdbe_chem_comp_rdkit_properties.chi0n 60.240
_pdbe_chem_comp_rdkit_properties.chi1n 29.417
_pdbe_chem_comp_rdkit_properties.chi2n 4.138
_pdbe_chem_comp_rdkit_properties.chi3n 4.138
_pdbe_chem_comp_rdkit_properties.chi4n 2.386
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.260
_pdbe_chem_comp_rdkit_properties.kappa1 11.127
_pdbe_chem_comp_rdkit_properties.kappa2 16.227
_pdbe_chem_comp_rdkit_properties.kappa3 10.369
_pdbe_chem_comp_rdkit_properties.Phi 3.925
#
_pdbe_chem_comp_external_mappings.comp_id 8JD
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 132471741
#
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
8JD N6A 10.548 3.512 -1.530 ETKDGv3 1
8JD C6A 9.301 2.918 -1.170 ETKDGv3 2
8JD N1A 8.183 3.578 -1.320 ETKDGv3 3
8JD C2A 6.909 2.996 -0.944 ETKDGv3 4
8JD N3A 6.854 1.791 -0.441 ETKDGv3 5
8JD C4A 8.074 1.055 -0.290 ETKDGv3 6
8JD C5A 9.232 1.559 -0.618 ETKDGv3 7
8JD N9A 8.252 -0.195 0.352 ETKDGv3 8
8JD N7A 10.290 0.706 -0.199 ETKDGv3 9
8JD C8A 9.684 -0.298 0.367 ETKDGv3 10
8JD C1M -4.567 2.842 0.745 ETKDGv3 11
8JD CP -6.008 2.356 0.679 ETKDGv3 12
8JD O3X 5.387 0.425 4.000 ETKDGv3 13
8JD S1 -6.517 2.169 -1.064 ETKDGv3 14
8JD N4 -7.913 -0.677 -1.521 ETKDGv3 15
8JD C5 -8.052 -2.104 -1.480 ETKDGv3 16
8JD O5 -8.682 -2.653 -0.535 ETKDGv3 17
8JD C6 -7.427 -2.962 -2.542 ETKDGv3 18
8JD C7 -6.205 -3.722 -2.013 ETKDGv3 19
8JD N8 -5.105 -2.805 -1.715 ETKDGv3 20
8JD C9 -4.978 -2.131 -0.453 ETKDGv3 21
8JD O9 -5.730 -2.443 0.510 ETKDGv3 22
8JD C13 -1.885 -2.504 -0.720 ETKDGv3 23
8JD C11 -2.582 -1.574 0.300 ETKDGv3 24
8JD C14 -2.809 -2.365 1.611 ETKDGv3 25
8JD C12 -1.647 -0.378 0.631 ETKDGv3 26
8JD P1A 2.020 0.277 -0.497 ETKDGv3 27
8JD O2A 2.629 1.271 -1.462 ETKDGv3 28
8JD O1A 1.077 -0.833 -1.361 ETKDGv3 29
8JD O3A 1.080 1.095 0.666 ETKDGv3 30
8JD O5X 3.268 -0.584 0.285 ETKDGv3 31
8JD C4X 5.153 -0.425 1.754 ETKDGv3 32
8JD O4X 6.035 -0.861 0.745 ETKDGv3 33
8JD C1X 7.340 -0.849 1.289 ETKDGv3 34
8JD C2X 7.326 -0.118 2.641 ETKDGv3 35
8JD O2X 7.585 -1.004 3.705 ETKDGv3 36
8JD C3X 5.932 0.470 2.707 ETKDGv3 37
8JD C5X 3.961 0.305 1.129 ETKDGv3 38
8JD P2A -0.327 1.659 -0.109 ETKDGv3 39
8JD O4A -1.061 2.586 0.834 ETKDGv3 40
8JD O5A 0.073 2.528 -1.506 ETKDGv3 41
8JD O6A -1.344 0.357 -0.535 ETKDGv3 42
8JD C10 -3.945 -1.043 -0.257 ETKDGv3 43
8JD O10 -3.744 -0.357 -1.468 ETKDGv3 44
8JD C3 -8.350 0.160 -0.402 ETKDGv3 45
8JD C2 -8.240 1.653 -0.728 ETKDGv3 46
8JD H1 10.579 4.480 -1.918 ETKDGv3 47
8JD H2 11.442 2.986 -1.411 ETKDGv3 48
8JD H3 6.000 3.567 -1.070 ETKDGv3 49
8JD H4 10.218 -1.117 0.830 ETKDGv3 50
8JD H5 -4.248 2.924 1.805 ETKDGv3 51
8JD H6 -3.896 2.127 0.224 ETKDGv3 52
8JD H7 -4.478 3.840 0.265 ETKDGv3 53
8JD H8 -6.085 1.383 1.205 ETKDGv3 54
8JD H9 -6.664 3.096 1.185 ETKDGv3 55
8JD H10 5.846 1.134 4.522 ETKDGv3 56
8JD H11 -7.479 -0.239 -2.365 ETKDGv3 57
8JD H12 -7.130 -2.343 -3.416 ETKDGv3 58
8JD H13 -8.183 -3.696 -2.895 ETKDGv3 59
8JD H14 -6.469 -4.323 -1.115 ETKDGv3 60
8JD H15 -5.872 -4.436 -2.796 ETKDGv3 61
8JD H16 -4.413 -2.611 -2.472 ETKDGv3 62
8JD H17 -2.494 -3.414 -0.908 ETKDGv3 63
8JD H18 -1.724 -1.987 -1.690 ETKDGv3 64
8JD H19 -0.895 -2.832 -0.336 ETKDGv3 65
8JD H20 -1.839 -2.662 2.066 ETKDGv3 66
8JD H21 -3.364 -1.747 2.350 ETKDGv3 67
8JD H22 -3.384 -3.296 1.426 ETKDGv3 68
8JD H23 -2.156 0.273 1.379 ETKDGv3 69
8JD H24 -0.710 -0.771 1.088 ETKDGv3 70
8JD H25 1.720 -1.314 -1.941 ETKDGv3 71
8JD H26 4.775 -1.319 2.302 ETKDGv3 72
8JD H27 7.671 -1.903 1.419 ETKDGv3 73
8JD H28 8.080 0.699 2.677 ETKDGv3 74
8JD H29 6.907 -1.731 3.675 ETKDGv3 75
8JD H30 5.952 1.520 2.328 ETKDGv3 76
8JD H31 3.296 0.654 1.951 ETKDGv3 77
8JD H32 4.340 1.184 0.558 ETKDGv3 78
8JD H33 -0.795 2.714 -1.945 ETKDGv3 79
8JD H34 -4.359 -0.325 0.488 ETKDGv3 80
8JD H35 -4.587 0.124 -1.675 ETKDGv3 81
8JD H36 -7.749 -0.084 0.498 ETKDGv3 82
8JD H37 -9.415 -0.066 -0.174 ETKDGv3 83
8JD H38 -8.663 2.250 0.109 ETKDGv3 84
8JD H39 -8.850 1.871 -1.630 ETKDGv3 85
#