data_HY8
#
_chem_comp.id HY8
_chem_comp.name "(2~{S})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[[9-[(2~{S},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]propyl]amino]-2-azanyl-butanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C27 H38 N12 O9"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-01-03
_chem_comp.pdbx_modified_date 2019-03-22
_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 674.666
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HY8
_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 6QDX
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
# #
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
HY8 C4 C1 C 0 1 N N S 10.068 5.238 17.178 7.678 1.043 -0.328 C4 HY8 1
HY8 C14 C2 C 0 1 N N N 14.911 0.810 19.575 -4.120 -1.961 -1.415 C14 HY8 2
HY8 C5 C3 C 0 1 N N N 10.215 8.728 17.574 10.468 1.000 2.020 C5 HY8 3
HY8 C6 C4 C 0 1 Y N N 11.228 3.412 15.710 5.312 0.594 -1.109 C6 HY8 4
HY8 C11 C5 C 0 1 N N N 13.950 -0.120 16.336 0.631 -0.710 -1.521 C11 HY8 5
HY8 C7 C6 C 0 1 Y N N 12.192 2.430 15.959 4.181 0.022 -0.504 C7 HY8 6
HY8 C8 C7 C 0 1 Y N N 11.805 3.542 17.799 5.782 -0.016 0.958 C8 HY8 7
HY8 C9 C8 C 0 1 Y N N 11.112 2.703 13.505 4.100 0.912 -3.035 C9 HY8 8
HY8 C10 C9 C 0 1 Y N N 12.599 1.577 14.892 2.999 -0.069 -1.260 C10 HY8 9
HY8 C12 C10 C 0 1 N N N 15.399 0.194 16.750 -0.479 -1.359 -0.692 C12 HY8 10
HY8 C13 C11 C 0 1 N N N 15.909 -0.758 17.852 -1.756 -1.448 -1.531 C13 HY8 11
HY8 N1 N1 N 0 1 Y N N 10.996 4.062 16.877 6.306 0.557 -0.163 N1 HY8 12
HY8 N2 N2 N 0 1 Y N N 12.527 2.556 17.269 4.535 -0.329 0.755 N2 HY8 13
HY8 C3 C12 C 0 1 N N R 8.797 5.185 17.389 8.559 -0.044 -0.982 C3 HY8 14
HY8 N3 N3 N 0 1 Y N N 10.709 3.525 14.474 5.227 1.022 -2.364 N3 HY8 15
HY8 C1 C13 C 0 1 N N S 9.793 7.213 17.568 9.710 1.267 0.718 C1 HY8 16
HY8 C15 C14 C 0 1 N N N 15.490 -1.396 20.159 -2.503 -3.473 -0.433 C15 HY8 17
HY8 C16 C15 C 0 1 N N N 16.763 -1.948 20.821 -3.400 -3.967 0.703 C16 HY8 18
HY8 C17 C16 C 0 1 N N S 16.629 -2.238 22.330 -2.979 -5.381 1.108 C17 HY8 19
HY8 C18 C17 C 0 1 N N N 17.164 -1.004 23.021 -3.780 -5.821 2.306 C18 HY8 20
HY8 C19 C18 C 0 1 N N S 15.481 2.289 19.475 -4.652 -0.535 -1.269 C19 HY8 21
HY8 C2 C19 C 0 1 N N S 8.584 6.805 17.766 9.926 0.106 -0.278 C2 HY8 22
HY8 C20 C20 C 0 1 N N S 15.692 3.026 20.558 -5.982 -0.366 -2.048 C20 HY8 23
HY8 C21 C21 C 0 1 N N R 16.737 4.229 19.983 -6.649 0.813 -1.300 C21 HY8 24
HY8 C22 C22 C 0 1 N N R 16.810 4.022 18.748 -5.954 0.830 0.075 C22 HY8 25
HY8 C23 C23 C 0 1 Y N N 15.472 4.642 16.712 -5.766 3.272 0.717 C23 HY8 26
HY8 C24 C24 C 0 1 Y N N 14.325 5.377 16.468 -4.710 4.198 0.719 C24 HY8 27
HY8 C25 C25 C 0 1 Y N N 14.689 5.381 18.607 -3.915 2.316 -0.007 C25 HY8 28
HY8 C26 C26 C 0 1 Y N N 15.705 4.231 14.436 -7.174 4.902 1.517 C26 HY8 29
HY8 C27 C27 C 0 1 Y N N 13.905 5.513 15.129 -4.977 5.508 1.153 C27 HY8 30
HY8 N10 N4 N 0 1 Y N N 16.127 4.087 15.680 -6.970 3.664 1.117 N10 HY8 31
HY8 N11 N5 N 0 1 Y N N 14.608 4.930 14.162 -6.213 5.806 1.541 N11 HY8 32
HY8 N12 N6 N 0 1 N N N 12.724 6.263 14.813 -3.977 6.464 1.178 N12 HY8 33
HY8 N4 N7 N 0 1 Y N N 12.034 1.753 13.697 3.009 0.390 -2.507 N4 HY8 34
HY8 N5 N8 N 0 1 N N N 13.629 0.512 15.048 1.853 -0.624 -0.718 N5 HY8 35
HY8 N6 N9 N 0 1 N N N 15.875 -0.261 19.257 -2.822 -2.071 -0.735 N6 HY8 36
HY8 N7 N10 N 0 1 N N N 15.279 -2.557 22.755 -3.224 -6.304 -0.009 N7 HY8 37
HY8 N8 N11 N 0 1 Y N N 15.668 4.668 18.050 -5.235 2.094 0.255 N8 HY8 38
HY8 N9 N12 N 0 1 Y N N 13.868 5.815 17.661 -3.609 3.551 0.266 N9 HY8 39
HY8 O1 O1 O 0 1 N N N 10.205 6.490 16.267 8.286 1.285 0.960 O1 HY8 40
HY8 O2 O2 O 0 1 N N N 11.609 8.607 17.885 10.351 2.134 2.881 O2 HY8 41
HY8 O3 O3 O 0 1 N N N 7.601 7.370 16.852 10.266 -1.094 0.418 O3 HY8 42
HY8 O4 O4 O 0 1 N N N 7.972 4.897 16.200 8.013 -1.343 -0.742 O4 HY8 43
HY8 O5 O5 O 0 1 N N N 18.183 -0.455 22.494 -4.733 -6.549 2.162 O5 HY8 44
HY8 O6 O6 O 0 1 N N N 16.605 -0.554 24.077 -3.434 -5.403 3.534 O6 HY8 45
HY8 O7 O7 O 0 1 N N N 16.743 2.411 18.617 -5.028 -0.270 0.100 O7 HY8 46
HY8 O8 O8 O 0 1 N N N 16.331 2.428 21.688 -6.781 -1.547 -1.954 O8 HY8 47
HY8 O9 O9 O 0 1 N N N 18.041 4.029 20.612 -8.051 0.581 -1.148 O9 HY8 48
HY8 H1 H1 H 0 1 N N N 10.479 5.611 18.128 7.688 1.952 -0.929 H1 HY8 49
HY8 H2 H2 H 0 1 N N N 14.065 0.724 18.877 -4.825 -2.661 -0.966 H2 HY8 50
HY8 H3 H3 H 0 1 N N N 14.555 0.652 20.604 -3.997 -2.197 -2.472 H3 HY8 51
HY8 H4 H4 H 0 1 N N N 10.057 9.198 16.592 10.046 0.124 2.513 H4 HY8 52
HY8 H5 H5 H 0 1 N N N 9.675 9.298 18.344 11.520 0.820 1.797 H5 HY8 53
HY8 H6 H6 H 0 1 N N N 13.264 0.261 17.106 0.821 -1.313 -2.409 H6 HY8 54
HY8 H7 H7 H 0 1 N N N 13.829 -1.209 16.244 0.322 0.292 -1.821 H7 HY8 55
HY8 H8 H8 H 0 1 N N N 11.866 3.872 18.826 6.322 -0.185 1.877 H8 HY8 56
HY8 H9 H9 H 0 1 N N N 10.675 2.809 12.523 4.064 1.274 -4.052 H9 HY8 57
HY8 H10 H10 H 0 1 N N N 16.049 0.095 15.868 -0.171 -2.360 -0.392 H10 HY8 58
HY8 H11 H11 H 0 1 N N N 15.444 1.227 17.125 -0.670 -0.756 0.196 H11 HY8 59
HY8 H12 H12 H 0 1 N N N 15.296 -1.670 17.810 -2.065 -0.447 -1.831 H12 HY8 60
HY8 H13 H13 H 0 1 N N N 16.954 -1.007 17.615 -1.566 -2.051 -2.418 H13 HY8 61
HY8 H14 H14 H 0 1 N N N 8.494 4.574 18.252 8.658 0.137 -2.052 H14 HY8 62
HY8 H15 H15 H 0 1 N N N 10.423 6.756 18.345 10.033 2.210 0.278 H15 HY8 63
HY8 H16 H16 H 0 1 N N N 14.796 -1.036 20.933 -1.458 -3.551 -0.131 H16 HY8 64
HY8 H17 H17 H 0 1 N N N 15.004 -2.189 19.571 -2.671 -4.083 -1.321 H17 HY8 65
HY8 H18 H18 H 0 1 N N N 17.034 -2.886 20.314 -3.302 -3.300 1.560 H18 HY8 66
HY8 H19 H19 H 0 1 N N N 17.568 -1.211 20.684 -4.437 -3.979 0.369 H19 HY8 67
HY8 H20 H20 H 0 1 N N N 17.291 -3.083 22.572 -1.918 -5.387 1.358 H20 HY8 68
HY8 H21 H21 H 0 1 N N N 14.713 2.818 18.892 -3.912 0.187 -1.613 H21 HY8 69
HY8 H22 H22 H 0 1 N N N 8.248 6.878 18.811 10.701 0.363 -1.001 H22 HY8 70
HY8 H23 H23 H 0 1 N N N 14.772 3.537 20.879 -5.792 -0.109 -3.090 H23 HY8 71
HY8 H24 H24 H 0 1 N N N 16.313 5.206 20.259 -6.474 1.750 -1.830 H24 HY8 72
HY8 H25 H25 H 0 1 N N N 17.757 4.361 18.301 -6.694 0.709 0.866 H25 HY8 73
HY8 H26 H26 H 0 1 N N N 14.581 5.575 19.664 -3.226 1.575 -0.384 H26 HY8 74
HY8 H27 H27 H 0 1 N N N 16.260 3.774 13.630 -8.165 5.188 1.837 H27 HY8 75
HY8 H28 H28 H 0 1 N N N 12.573 6.247 13.825 -3.078 6.233 0.893 H28 HY8 76
HY8 H29 H29 H 0 1 N N N 11.937 5.856 15.277 -4.173 7.364 1.480 H29 HY8 77
HY8 H30 H30 H 0 1 N N N 13.349 -0.231 14.441 1.859 -0.956 0.193 H30 HY8 78
HY8 H32 H32 H 0 1 N N N 15.272 -2.732 23.740 -4.201 -6.316 -0.260 H32 HY8 79
HY8 H33 H33 H 0 1 N N N 14.674 -1.788 22.548 -2.649 -6.068 -0.805 H33 HY8 80
HY8 H35 H35 H 0 1 N N N 12.002 9.471 17.922 10.808 2.035 3.727 H35 HY8 81
HY8 H36 H36 H 0 1 N N N 7.471 8.289 17.055 11.116 -1.055 0.878 H36 HY8 82
HY8 H37 H37 H 0 1 N N N 7.055 4.877 16.448 8.526 -2.064 -1.131 H37 HY8 83
HY8 H38 H38 H 0 1 N N N 17.067 0.221 24.375 -3.978 -5.711 4.272 H38 HY8 84
HY8 H39 H39 H 0 1 N N N 16.414 3.071 22.382 -7.623 -1.491 -2.426 H39 HY8 85
HY8 H40 H40 H 0 1 N N N 17.971 4.189 21.546 -8.529 0.503 -1.985 H40 HY8 86
# #
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
HY8 C9 N4 DOUB Y N 1
HY8 C9 N3 SING Y N 2
HY8 N4 C10 SING Y N 3
HY8 N11 C26 DOUB Y N 4
HY8 N11 C27 SING Y N 5
HY8 C26 N10 SING Y N 6
HY8 N3 C6 DOUB Y N 7
HY8 N12 C27 SING N N 8
HY8 C10 N5 SING N N 9
HY8 C10 C7 DOUB Y N 10
HY8 N5 C11 SING N N 11
HY8 C27 C24 DOUB Y N 12
HY8 N10 C23 DOUB Y N 13
HY8 C6 C7 SING Y N 14
HY8 C6 N1 SING Y N 15
HY8 C7 N2 SING Y N 16
HY8 O4 C3 SING N N 17
HY8 O1 C4 SING N N 18
HY8 O1 C1 SING N N 19
HY8 C11 C12 SING N N 20
HY8 C24 C23 SING Y N 21
HY8 C24 N9 SING Y N 22
HY8 C23 N8 SING Y N 23
HY8 C12 C13 SING N N 24
HY8 O3 C2 SING N N 25
HY8 N1 C4 SING N N 26
HY8 N1 C8 SING Y N 27
HY8 C4 C3 SING N N 28
HY8 N2 C8 DOUB Y N 29
HY8 C3 C2 SING N N 30
HY8 C1 C5 SING N N 31
HY8 C1 C2 SING N N 32
HY8 C5 O2 SING N N 33
HY8 N9 C25 DOUB Y N 34
HY8 C13 N6 SING N N 35
HY8 N8 C25 SING Y N 36
HY8 N8 C22 SING N N 37
HY8 O7 C22 SING N N 38
HY8 O7 C19 SING N N 39
HY8 C22 C21 SING N N 40
HY8 N6 C14 SING N N 41
HY8 N6 C15 SING N N 42
HY8 C19 C14 SING N N 43
HY8 C19 C20 SING N N 44
HY8 C21 C20 SING N N 45
HY8 C21 O9 SING N N 46
HY8 C15 C16 SING N N 47
HY8 C20 O8 SING N N 48
HY8 C16 C17 SING N N 49
HY8 C17 N7 SING N N 50
HY8 C17 C18 SING N N 51
HY8 O5 C18 DOUB N N 52
HY8 C18 O6 SING N N 53
HY8 C4 H1 SING N N 54
HY8 C14 H2 SING N N 55
HY8 C14 H3 SING N N 56
HY8 C5 H4 SING N N 57
HY8 C5 H5 SING N N 58
HY8 C11 H6 SING N N 59
HY8 C11 H7 SING N N 60
HY8 C8 H8 SING N N 61
HY8 C9 H9 SING N N 62
HY8 C12 H10 SING N N 63
HY8 C12 H11 SING N N 64
HY8 C13 H12 SING N N 65
HY8 C13 H13 SING N N 66
HY8 C3 H14 SING N N 67
HY8 C1 H15 SING N N 68
HY8 C15 H16 SING N N 69
HY8 C15 H17 SING N N 70
HY8 C16 H18 SING N N 71
HY8 C16 H19 SING N N 72
HY8 C17 H20 SING N N 73
HY8 C19 H21 SING N N 74
HY8 C2 H22 SING N N 75
HY8 C20 H23 SING N N 76
HY8 C21 H24 SING N N 77
HY8 C22 H25 SING N N 78
HY8 C25 H26 SING N N 79
HY8 C26 H27 SING N N 80
HY8 N12 H28 SING N N 81
HY8 N12 H29 SING N N 82
HY8 N5 H30 SING N N 83
HY8 N7 H32 SING N N 84
HY8 N7 H33 SING N N 85
HY8 O2 H35 SING N N 86
HY8 O3 H36 SING N N 87
HY8 O4 H37 SING N N 88
HY8 O6 H38 SING N N 89
HY8 O8 H39 SING N N 90
HY8 O9 H40 SING N N 91
# #
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
HY8 InChI InChI 1.03 "InChI=1S/C27H38N12O9/c28-12(27(45)46)2-5-37(6-13-17(41)19(43)25(47-13)38-10-35-15-21(29)31-8-33-23(15)38)4-1-3-30-22-16-24(34-9-32-22)39(11-36-16)26-20(44)18(42)14(7-40)48-26/h8-14,17-20,25-26,40-44H,1-7,28H2,(H,45,46)(H2,29,31,33)(H,30,32,34)/t12-,13-,14-,17+,18+,19+,20+,25+,26-/m0/s1"
HY8 InChIKey InChI 1.03 BNMNWGQODJWABC-JIDNCIPASA-N
HY8 SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCN(CCCNc1ncnc2n(cnc12)[C@H]3O[C@@H](CO)[C@@H](O)[C@H]3O)C[C@@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)C(O)=O"
HY8 SMILES CACTVS 3.385 "N[CH](CCN(CCCNc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O)C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)C(O)=O"
HY8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@@H](O3)CN(CCCNc4c5c(ncn4)n(cn5)[C@@H]6[C@@H]([C@@H]([C@@H](O6)CO)O)O)CC[C@@H](C(=O)O)N)O)O)N"
HY8 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCNc4c5c(ncn4)n(cn5)C6C(C(C(O6)CO)O)O)CCC(C(=O)O)N)O)O)N"
#
_pdbx_chem_comp_identifier.comp_id HY8
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier "(2~{S})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[[9-[(2~{S},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]propyl]amino]-2-azanyl-butanoic acid"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HY8 "Create component" 2019-01-03 EBI
HY8 "Initial release" 2019-03-27 RCSB
##