data_SO5
#
_chem_comp.id SO5
_chem_comp.name
"(2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C24 H40 N7 O21 P3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-12-03
_chem_comp.pdbx_modified_date 2019-04-05
_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 887.595
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SO5
_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 6N96
_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
SO5 O56 O1 O 0 1 N N N N N N 31.935 12.512 15.350 -12.466 -4.282 -1.031 O56 SO5 1
SO5 SS4 S1 S 0 1 N N N N N N 31.398 13.454 16.305 -11.163 -3.916 -1.464 SS4 SO5 2
SO5 OS5 O2 O 0 1 N N N N N N 31.962 13.390 17.649 -10.499 -5.240 -1.816 OS5 SO5 3
SO5 OS4 O3 O 0 1 N N N N N N 29.962 13.292 16.313 -10.974 -3.111 -2.619 OS4 SO5 4
SO5 CS2 C1 C 0 1 N N R N N N 31.831 14.982 15.730 -10.188 -3.276 -0.075 CS2 SO5 5
SO5 CS3 C2 C 0 1 N N N N N N 33.343 15.259 15.840 -10.139 -4.322 1.039 CS3 SO5 6
SO5 CS1 C3 C 0 1 N N N N N N 31.056 15.989 16.534 -10.826 -2.015 0.448 CS1 SO5 7
SO5 OS1 O4 O 0 1 N N N N N N 31.482 16.466 17.606 -12.008 -1.824 0.285 OS1 SO5 8
SO5 OPS O5 O 0 1 N N N N N N 29.805 16.389 16.003 -10.082 -1.104 1.094 OPS SO5 9
SO5 CP1 C4 C 0 1 N N N N N N 28.925 17.184 16.830 -10.763 0.087 1.570 CP1 SO5 10
SO5 CP2 C5 C 0 1 N N N N N N 28.385 16.328 17.971 -9.760 1.001 2.276 CP2 SO5 11
SO5 NP1 N1 N 0 1 N N N N N N 27.350 17.053 18.618 -8.771 1.481 1.308 NP1 SO5 12
SO5 CP3 C6 C 0 1 N N N N N N 26.105 16.695 18.508 -7.783 2.307 1.706 CP3 SO5 13
SO5 OP1 O6 O 0 1 N N N N N N 25.745 15.787 17.750 -7.713 2.652 2.867 OP1 SO5 14
SO5 CP4 C7 C 0 1 N N N N N N 25.121 17.512 19.318 -6.766 2.801 0.710 CP4 SO5 15
SO5 CP5 C8 C 0 1 N N N N N N 24.028 17.948 18.386 -5.763 3.715 1.416 CP5 SO5 16
SO5 NP2 N2 N 0 1 N N N N N N 23.089 18.868 18.994 -4.775 4.196 0.447 NP2 SO5 17
SO5 CP6 C9 C 0 1 N N N N N N 22.129 18.454 19.840 -3.786 5.021 0.846 CP6 SO5 18
SO5 OP2 O7 O 0 1 N N N N N N 21.928 17.281 20.169 -3.769 5.440 1.984 OP2 SO5 19
SO5 CP7 C10 C 0 1 N N R N N N 21.272 19.570 20.442 -2.704 5.423 -0.122 CP7 SO5 20
SO5 OP3 O8 O 0 1 N N N N N N 21.463 20.739 19.675 -3.081 5.037 -1.446 OP3 SO5 21
SO5 CPA C11 C 0 1 N N N N N N 21.642 19.923 21.893 -1.395 4.727 0.258 CPA SO5 22
SO5 CP9 C12 C 0 1 N N N N N N 21.160 18.842 22.865 -0.914 5.252 1.612 CP9 SO5 23
SO5 CP8 C13 C 0 1 N N N N N N 23.171 20.128 21.962 -1.628 3.218 0.350 CP8 SO5 24
SO5 CPB C14 C 0 1 N N N N N N 20.982 21.238 22.273 -0.336 5.016 -0.807 CPB SO5 25
SO5 O7 O9 O 0 1 N N N N N N 19.571 21.100 22.197 0.886 4.367 -0.451 O7 SO5 26
SO5 P2 P1 P 0 1 N N N N N N 18.590 22.409 22.119 2.220 4.455 -1.349 P2 SO5 27
SO5 O21 O10 O 0 1 N N N N N N 17.233 21.880 21.818 1.916 4.015 -2.729 O21 SO5 28
SO5 O22 O11 O 0 1 N N N N N N 18.811 23.246 23.305 2.749 5.976 -1.376 O22 SO5 29
SO5 O6 O12 O 0 1 N N N N N N 19.040 23.407 21.001 3.355 3.503 -0.719 O6 SO5 30
SO5 P1 P2 P 0 1 N N N N N N 18.850 23.154 19.434 4.750 2.913 -1.266 P1 SO5 31
SO5 O11 O13 O 0 1 N N N N N N 17.600 23.913 19.112 5.892 4.042 -1.151 O11 SO5 32
SO5 O12 O14 O 0 1 N N N N N N 18.746 21.731 19.000 4.594 2.512 -2.682 O12 SO5 33
SO5 "O5'" O15 O 0 1 N N N N N N 20.092 23.918 18.806 5.172 1.632 -0.388 "O5'" SO5 34
SO5 "C5'" C15 C 0 1 N N N N N N 20.425 25.294 18.944 6.310 0.822 -0.689 "C5'" SO5 35
SO5 "C4'" C16 C 0 1 N N R N N N 21.120 25.667 17.624 6.420 -0.306 0.339 "C4'" SO5 36
SO5 "O4'" O16 O 0 1 N N N N N N 22.445 25.100 17.737 5.308 -1.206 0.199 "O4'" SO5 37
SO5 "C1'" C17 C 0 1 N N R N N N 22.688 24.335 16.576 5.795 -2.529 0.510 "C1'" SO5 38
SO5 "C2'" C18 C 0 1 N N R N N N 21.347 23.769 16.109 7.196 -2.564 -0.153 "C2'" SO5 39
SO5 "O2'" O17 O 0 1 N N N N N N 21.362 23.327 14.749 8.042 -3.516 0.494 "O2'" SO5 40
SO5 "C3'" C19 C 0 1 N N S N N N 20.535 25.033 16.366 7.703 -1.121 0.087 "C3'" SO5 41
SO5 "O3'" O18 O 0 1 N N N N N N 20.710 25.909 15.242 8.558 -1.075 1.232 "O3'" SO5 42
SO5 P3 P3 P 0 1 N N N N N N 19.487 26.930 14.836 10.083 -0.563 1.167 P3 SO5 43
SO5 O31 O19 O 0 1 N N N N N N 20.083 28.283 14.912 10.699 -0.524 2.654 O31 SO5 44
SO5 O32 O20 O 0 1 N N N N N N 18.408 26.886 15.893 10.948 -1.569 0.255 O32 SO5 45
SO5 O33 O21 O 0 1 N N N N N N 18.858 26.197 13.684 10.124 0.794 0.580 O33 SO5 46
SO5 N9 N3 N 0 1 Y N N N N N 23.661 23.289 16.952 4.922 -3.550 -0.075 N9 SO5 47
SO5 C8 C20 C 0 1 Y N N N N N 23.564 22.417 17.992 4.096 -3.387 -1.147 C8 SO5 48
SO5 N7 N4 N 0 1 Y N N N N N 24.684 21.629 18.032 3.467 -4.499 -1.396 N7 SO5 49
SO5 C5 C21 C 0 1 Y N N N N N 25.471 22.003 17.034 3.849 -5.443 -0.503 C5 SO5 50
SO5 C4 C22 C 0 1 Y N N N N N 24.839 23.129 16.359 4.792 -4.848 0.351 C4 SO5 51
SO5 C6 C23 C 0 1 Y N N N N N 26.749 21.551 16.575 3.516 -6.792 -0.287 C6 SO5 52
SO5 N6 N5 N 0 1 N N N N N N 27.433 20.546 17.197 2.599 -7.433 -1.100 N6 SO5 53
SO5 N1 N6 N 0 1 Y N N N N N 27.265 22.173 15.506 4.103 -7.436 0.716 N1 SO5 54
SO5 C2 C24 C 0 1 Y N N N N N 26.595 23.214 14.886 4.980 -6.831 1.497 C2 SO5 55
SO5 N3 N7 N 0 1 Y N N N N N 25.404 23.674 15.277 5.332 -5.575 1.324 N3 SO5 56
SO5 H1 H1 H 0 1 N N N N N N 31.528 15.037 14.674 -9.175 -3.057 -0.413 H1 SO5 57
SO5 H2 H2 H 0 1 N N N N N N 33.561 16.265 15.452 -9.677 -5.234 0.661 H2 SO5 58
SO5 H3 H3 H 0 1 N N N N N N 33.651 15.198 16.894 -9.552 -3.937 1.874 H3 SO5 59
SO5 H4 H4 H 0 1 N N N N N N 33.896 14.511 15.253 -11.152 -4.541 1.377 H4 SO5 60
SO5 H5 H5 H 0 1 N N N N N N 29.483 18.037 17.244 -11.204 0.615 0.725 H5 SO5 61
SO5 H6 H6 H 0 1 N N N N N N 28.087 17.555 16.222 -11.549 -0.199 2.270 H6 SO5 62
SO5 H7 H7 H 0 1 N N N N N N 27.985 15.384 17.572 -10.286 1.851 2.711 H7 SO5 63
SO5 H8 H8 H 0 1 N N N N N N 29.191 16.111 18.687 -9.255 0.444 3.066 H8 SO5 64
SO5 H9 H9 H 0 1 N N N N N N 27.583 17.854 19.169 -8.828 1.206 0.379 H9 SO5 65
SO5 H10 H10 H 0 1 N N N N N N 25.624 18.392 19.745 -6.240 1.951 0.275 H10 SO5 66
SO5 H11 H11 H 0 1 N N N N N N 24.701 16.899 20.130 -7.272 3.357 -0.079 H11 SO5 67
SO5 H12 H12 H 0 1 N N N N N N 23.477 17.056 18.053 -6.289 4.565 1.850 H12 SO5 68
SO5 H13 H13 H 0 1 N N N N N N 24.487 18.441 17.517 -5.258 3.159 2.205 H13 SO5 69
SO5 H14 H14 H 0 1 N N N N N N 23.157 19.842 18.778 -4.831 3.920 -0.481 H14 SO5 70
SO5 H15 H15 H 0 1 N N N N N N 20.217 19.260 20.413 -2.565 6.503 -0.084 H15 SO5 71
SO5 H16 H16 H 0 1 N N N N N N 20.619 21.100 19.431 -3.221 4.086 -1.553 H16 SO5 72
SO5 H17 H17 H 0 1 N N N N N N 21.438 19.121 23.892 -1.632 4.978 2.385 H17 SO5 73
SO5 H18 H18 H 0 1 N N N N N N 20.066 18.747 22.794 0.057 4.815 1.847 H18 SO5 74
SO5 H19 H19 H 0 1 N N N N N N 21.629 17.881 22.607 -0.823 6.338 1.570 H19 SO5 75
SO5 H20 H20 H 0 1 N N N N N N 23.461 20.382 22.992 -1.971 2.844 -0.615 H20 SO5 76
SO5 H21 H21 H 0 1 N N N N N N 23.679 19.202 21.656 -0.696 2.722 0.621 H21 SO5 77
SO5 H22 H22 H 0 1 N N N N N N 23.462 20.946 21.287 -2.383 3.012 1.109 H22 SO5 78
SO5 H23 H23 H 0 1 N N N N N N 21.269 21.509 23.300 -0.679 4.642 -1.771 H23 SO5 79
SO5 H24 H24 H 0 1 N N N N N N 21.311 22.027 21.580 -0.170 6.092 -0.872 H24 SO5 80
SO5 H25 H25 H 0 1 N N N N N N 17.992 23.356 23.773 2.968 6.332 -0.503 H25 SO5 81
SO5 H26 H26 H 0 1 N N N N N N 16.977 23.334 18.689 6.048 4.353 -0.248 H26 SO5 82
SO5 H27 H27 H 0 1 N N N N N N 21.105 25.444 19.795 6.198 0.395 -1.686 H27 SO5 83
SO5 H28 H28 H 0 1 N N N N N N 19.518 25.899 19.088 7.211 1.434 -0.655 H28 SO5 84
SO5 H29 H29 H 0 1 N N N N N N 21.160 26.761 17.515 6.435 0.111 1.346 H29 SO5 85
SO5 H30 H30 H 0 1 N N N N N N 23.109 24.964 15.778 5.874 -2.665 1.588 H30 SO5 86
SO5 H31 H31 H 0 1 N N N N N N 21.021 22.967 16.788 7.117 -2.776 -1.219 H31 SO5 87
SO5 H32 H32 H 0 1 N N N N N N 21.887 22.539 14.678 7.765 -4.435 0.373 H32 SO5 88
SO5 H33 H33 H 0 1 N N N N N N 19.476 24.781 16.523 8.225 -0.749 -0.795 H33 SO5 89
SO5 H34 H34 H 0 1 N N N N N N 20.027 28.702 14.061 11.618 -0.224 2.691 H34 SO5 90
SO5 H35 H35 H 0 1 N N N N N N 17.651 26.423 15.554 10.966 -2.479 0.581 H35 SO5 91
SO5 H36 H36 H 0 1 N N N N N N 22.733 22.356 18.679 3.979 -2.470 -1.706 H36 SO5 92
SO5 H37 H37 H 0 1 N N N N N N 28.304 20.396 16.730 2.177 -6.953 -1.830 H37 SO5 93
SO5 H38 H38 H 0 1 N N N N N N 27.605 20.799 18.149 2.377 -8.364 -0.941 H38 SO5 94
SO5 H39 H39 H 0 1 N N N N N N 27.065 23.683 14.034 5.438 -7.393 2.297 H39 SO5 95
SO5 H40 H40 H 0 1 N N N N N N 31.265 13.252 18.279 -10.917 -5.706 -2.553 H40 SO5 96
#
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
SO5 O33 P3 DOUB N N 1
SO5 "O2'" "C2'" SING N N 2
SO5 P3 O31 SING N N 3
SO5 P3 "O3'" SING N N 4
SO5 P3 O32 SING N N 5
SO5 C2 N3 DOUB Y N 6
SO5 C2 N1 SING Y N 7
SO5 "O3'" "C3'" SING N N 8
SO5 N3 C4 SING Y N 9
SO5 O56 SS4 DOUB N N 10
SO5 N1 C6 DOUB Y N 11
SO5 CS2 CS3 SING N N 12
SO5 CS2 SS4 SING N N 13
SO5 CS2 CS1 SING N N 14
SO5 OPS CS1 SING N N 15
SO5 OPS CP1 SING N N 16
SO5 "C2'" "C3'" SING N N 17
SO5 "C2'" "C1'" SING N N 18
SO5 SS4 OS4 DOUB N N 19
SO5 SS4 OS5 SING N N 20
SO5 C4 N9 SING Y N 21
SO5 C4 C5 DOUB Y N 22
SO5 "C3'" "C4'" SING N N 23
SO5 CS1 OS1 DOUB N N 24
SO5 C6 C5 SING Y N 25
SO5 C6 N6 SING N N 26
SO5 "C1'" N9 SING N N 27
SO5 "C1'" "O4'" SING N N 28
SO5 CP1 CP2 SING N N 29
SO5 N9 C8 SING Y N 30
SO5 C5 N7 SING Y N 31
SO5 "C4'" "O4'" SING N N 32
SO5 "C4'" "C5'" SING N N 33
SO5 OP1 CP3 DOUB N N 34
SO5 CP2 NP1 SING N N 35
SO5 C8 N7 DOUB Y N 36
SO5 CP5 NP2 SING N N 37
SO5 CP5 CP4 SING N N 38
SO5 CP3 NP1 SING N N 39
SO5 CP3 CP4 SING N N 40
SO5 "O5'" "C5'" SING N N 41
SO5 "O5'" P1 SING N N 42
SO5 NP2 CP6 SING N N 43
SO5 O12 P1 DOUB N N 44
SO5 O11 P1 SING N N 45
SO5 P1 O6 SING N N 46
SO5 OP3 CP7 SING N N 47
SO5 CP6 OP2 DOUB N N 48
SO5 CP6 CP7 SING N N 49
SO5 CP7 CPA SING N N 50
SO5 O6 P2 SING N N 51
SO5 O21 P2 DOUB N N 52
SO5 CPA CP8 SING N N 53
SO5 CPA CPB SING N N 54
SO5 CPA CP9 SING N N 55
SO5 P2 O7 SING N N 56
SO5 P2 O22 SING N N 57
SO5 O7 CPB SING N N 58
SO5 CS2 H1 SING N N 59
SO5 CS3 H2 SING N N 60
SO5 CS3 H3 SING N N 61
SO5 CS3 H4 SING N N 62
SO5 CP1 H5 SING N N 63
SO5 CP1 H6 SING N N 64
SO5 CP2 H7 SING N N 65
SO5 CP2 H8 SING N N 66
SO5 NP1 H9 SING N N 67
SO5 CP4 H10 SING N N 68
SO5 CP4 H11 SING N N 69
SO5 CP5 H12 SING N N 70
SO5 CP5 H13 SING N N 71
SO5 NP2 H14 SING N N 72
SO5 CP7 H15 SING N N 73
SO5 OP3 H16 SING N N 74
SO5 CP9 H17 SING N N 75
SO5 CP9 H18 SING N N 76
SO5 CP9 H19 SING N N 77
SO5 CP8 H20 SING N N 78
SO5 CP8 H21 SING N N 79
SO5 CP8 H22 SING N N 80
SO5 CPB H23 SING N N 81
SO5 CPB H24 SING N N 82
SO5 O22 H25 SING N N 83
SO5 O11 H26 SING N N 84
SO5 "C5'" H27 SING N N 85
SO5 "C5'" H28 SING N N 86
SO5 "C4'" H29 SING N N 87
SO5 "C1'" H30 SING N N 88
SO5 "C2'" H31 SING N N 89
SO5 "O2'" H32 SING N N 90
SO5 "C3'" H33 SING N N 91
SO5 O31 H34 SING N N 92
SO5 O32 H35 SING N N 93
SO5 C8 H36 SING N N 94
SO5 N6 H37 SING N N 95
SO5 N6 H38 SING N N 96
SO5 C2 H39 SING N N 97
SO5 OS5 H40 SING N N 98
#
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
SO5 SMILES ACDLabs 12.01 O=S(=O)(O)C(C)C(=O)OCCNC(CCNC(=O)C(C(C)(COP(O)(=O)OP(O)(=O)OCC3OC(n1cnc2c1ncnc2N)C(C3OP(O)(O)=O)O)C)O)=O
SO5 InChI InChI 1.03 InChI=1S/C24H40N7O21P3S/c1-12(56(44,45)46)23(36)47-7-6-26-14(32)4-5-27-21(35)18(34)24(2,3)9-49-55(42,43)52-54(40,41)48-8-13-17(51-53(37,38)39)16(33)22(50-13)31-11-30-15-19(25)28-10-29-20(15)31/h10-13,16-18,22,33-34H,4-9H2,1-3H3,(H,26,32)(H,27,35)(H,40,41)(H,42,43)(H2,25,28,29)(H2,37,38,39)(H,44,45,46)/t12-,13-,16-,17-,18+,22-/m1/s1
SO5 InChIKey InChI 1.03 BEMUOEZGNHFKKE-AGCMQPJKSA-N
SO5 SMILES_CANONICAL CACTVS 3.385 C[C@H](C(=O)OCCNC(=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[P](O)(O)=O)n2cnc3c(N)ncnc23)[S](O)(=O)=O
SO5 SMILES CACTVS 3.385 C[CH](C(=O)OCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[S](O)(=O)=O
SO5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C[C@H](C(=O)OCCNC(=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)OP(=O)(O)O)O)S(=O)(=O)O
SO5 SMILES "OpenEye OEToolkits" 2.0.6 CC(C(=O)OCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)S(=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
SO5 "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,5R,9R,20R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,19-trioxo-2,4,6,18-tetraoxa-11,15-diaza-3,5-diphosphahenicosane-20-sulfonic acid 3,5-dioxide (non-preferred name)"
SO5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic 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
SO5 'Create component' 2018-12-03 RCSB
SO5 'Initial release' 2019-04-10 RCSB
#
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
SO5 O56 O 37.495 2.973 1
SO5 SS4 S 36.126 3.586 2
SO5 OS5 O 35.513 2.216 3
SO5 OS4 O 36.738 4.955 4
SO5 CS2 C 34.757 4.198 5
SO5 CS3 C 34.602 5.690 6
SO5 CS1 C 33.541 3.319 7
SO5 OS1 O 33.696 1.827 8
SO5 OPS O 32.172 3.931 9
SO5 CP1 C 30.957 3.052 10
SO5 CP2 C 29.588 3.664 11
SO5 NP1 N 28.373 2.785 12
SO5 CP3 C 27.004 3.397 13
SO5 OP1 O 26.849 4.889 14
SO5 CP4 C 25.788 2.517 15
SO5 CP5 C 24.419 3.130 16
SO5 NP2 N 23.204 2.250 17
SO5 CP6 C 21.835 2.863 18
SO5 OP2 O 21.681 4.355 19
SO5 CP7 C 20.620 1.983 20
SO5 OP3 O 20.774 0.491 21
SO5 CPA C 19.251 2.596 22
SO5 CP9 C 18.638 1.226 23
SO5 CP8 C 19.863 3.965 24
SO5 CPB C 17.881 3.208 25
SO5 O7 O 16.666 2.329 26
SO5 P2 P 15.297 2.941 27
SO5 O21 O 15.909 4.310 28
SO5 O22 O 14.684 1.572 29
SO5 O6 O 13.928 3.554 30
SO5 P1 P 12.713 2.674 31
SO5 O11 O 11.833 3.889 32
SO5 O12 O 13.592 1.459 33
SO5 "O5'" O 11.498 1.794 34
SO5 "C5'" C 10.129 2.407 35
SO5 "C4'" C 8.913 1.527 36
SO5 "O4'" O 8.911 0.027 37
SO5 "C1'" C 7.483 -0.434 38
SO5 "C2'" C 6.604 0.781 39
SO5 "O2'" O 5.104 0.784 40
SO5 "C3'" C 7.487 1.993 41
SO5 "O3'" O 7.027 3.421 42
SO5 P3 P 8.032 4.534 43
SO5 O31 O 6.919 5.539 44
SO5 O32 O 9.145 3.528 45
SO5 O33 O 9.038 5.647 46
SO5 N9 N 7.018 -1.860 47
SO5 C8 C 7.893 -3.067 48
SO5 N7 N 7.018 -4.274 49
SO5 C5 C 5.598 -3.817 50
SO5 C4 C 5.598 -2.317 51
SO5 C6 C 4.299 -4.567 52
SO5 N6 N 4.299 -6.067 53
SO5 N1 N 3.000 -3.817 54
SO5 C2 C 3.000 -2.317 55
SO5 N3 N 4.299 -1.567 56
#
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
SO5 O33 P3 DOUBLE NONE 1
SO5 "C2'" "O2'" SINGLE BEGINDASH 2
SO5 P3 O31 SINGLE NONE 3
SO5 P3 "O3'" SINGLE NONE 4
SO5 P3 O32 SINGLE NONE 5
SO5 C2 N3 DOUBLE NONE 6
SO5 C2 N1 SINGLE NONE 7
SO5 "C3'" "O3'" SINGLE BEGINDASH 8
SO5 N3 C4 SINGLE NONE 9
SO5 O56 SS4 DOUBLE NONE 10
SO5 N1 C6 DOUBLE NONE 11
SO5 CS2 CS3 SINGLE BEGINWEDGE 12
SO5 CS2 SS4 SINGLE NONE 13
SO5 CS2 CS1 SINGLE NONE 14
SO5 OPS CS1 SINGLE NONE 15
SO5 OPS CP1 SINGLE NONE 16
SO5 "C2'" "C3'" SINGLE NONE 17
SO5 "C2'" "C1'" SINGLE NONE 18
SO5 SS4 OS4 DOUBLE NONE 19
SO5 SS4 OS5 SINGLE NONE 20
SO5 C4 N9 SINGLE NONE 21
SO5 C4 C5 DOUBLE NONE 22
SO5 "C3'" "C4'" SINGLE NONE 23
SO5 CS1 OS1 DOUBLE NONE 24
SO5 C6 C5 SINGLE NONE 25
SO5 C6 N6 SINGLE NONE 26
SO5 "C1'" N9 SINGLE BEGINWEDGE 27
SO5 "C1'" "O4'" SINGLE NONE 28
SO5 CP1 CP2 SINGLE NONE 29
SO5 N9 C8 SINGLE NONE 30
SO5 C5 N7 SINGLE NONE 31
SO5 "C4'" "O4'" SINGLE NONE 32
SO5 "C4'" "C5'" SINGLE BEGINWEDGE 33
SO5 OP1 CP3 DOUBLE NONE 34
SO5 CP2 NP1 SINGLE NONE 35
SO5 C8 N7 DOUBLE NONE 36
SO5 CP5 NP2 SINGLE NONE 37
SO5 CP5 CP4 SINGLE NONE 38
SO5 CP3 NP1 SINGLE NONE 39
SO5 CP3 CP4 SINGLE NONE 40
SO5 "O5'" "C5'" SINGLE NONE 41
SO5 "O5'" P1 SINGLE NONE 42
SO5 NP2 CP6 SINGLE NONE 43
SO5 O12 P1 DOUBLE NONE 44
SO5 P1 O11 SINGLE BEGINWEDGE 45
SO5 P1 O6 SINGLE NONE 46
SO5 CP7 OP3 SINGLE BEGINDASH 47
SO5 CP6 OP2 DOUBLE NONE 48
SO5 CP6 CP7 SINGLE NONE 49
SO5 CP7 CPA SINGLE NONE 50
SO5 O6 P2 SINGLE NONE 51
SO5 O21 P2 DOUBLE NONE 52
SO5 CPA CP8 SINGLE NONE 53
SO5 CPA CPB SINGLE NONE 54
SO5 CPA CP9 SINGLE NONE 55
SO5 P2 O7 SINGLE NONE 56
SO5 P2 O22 SINGLE BEGINDASH 57
SO5 O7 CPB SINGLE NONE 58
#
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
SO5 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
SO5 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
SO5 amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
SO5 imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
SO5 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
SO5 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
SO5 pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
SO5 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
SO5 "C4'" S1 1
SO5 "O4'" S1 1
SO5 "C1'" S1 1
SO5 "C2'" S1 1
SO5 "C3'" S1 1
SO5 N9 S1 1
SO5 C8 S1 1
SO5 N7 S1 1
SO5 C5 S1 1
SO5 C4 S1 1
SO5 C6 S1 1
SO5 N1 S1 1
SO5 C2 S1 1
SO5 N3 S1 1
SO5 N1 F1 1
SO5 C6 F1 1
SO5 C5 F1 1
SO5 C4 F1 1
SO5 N3 F1 1
SO5 C2 F1 1
SO5 N9 F1 1
SO5 C8 F1 1
SO5 N7 F1 1
SO5 N6 F1 1
SO5 NP1 F2 1
SO5 CP3 F2 1
SO5 OP1 F2 1
SO5 CP4 F2 1
SO5 NP2 F2 2
SO5 CP6 F2 2
SO5 OP2 F2 2
SO5 CP7 F2 2
SO5 C5 F3 1
SO5 C4 F3 1
SO5 N9 F3 1
SO5 C8 F3 1
SO5 N7 F3 1
SO5 O7 F4 1
SO5 P2 F4 1
SO5 O21 F4 1
SO5 O6 F4 1
SO5 O22 F4 1
SO5 O6 F4 2
SO5 P1 F4 2
SO5 O12 F4 2
SO5 "O5'" F4 2
SO5 O11 F4 2
SO5 "O3'" F4 3
SO5 P3 F4 3
SO5 O33 F4 3
SO5 O31 F4 3
SO5 O32 F4 3
SO5 N7 F5 1
SO5 C8 F5 1
SO5 N9 F5 1
SO5 C4 F5 1
SO5 C5 F5 1
SO5 C6 F5 1
SO5 N1 F5 1
SO5 C2 F5 1
SO5 N3 F5 1
SO5 C5 F6 1
SO5 C4 F6 1
SO5 N3 F6 1
SO5 C2 F6 1
SO5 N1 F6 1
SO5 C6 F6 1
SO5 "C2'" F7 1
SO5 "C3'" F7 1
SO5 "C4'" F7 1
SO5 "O4'" F7 1
SO5 "C1'" F7 1
SO5 "C5'" F7 1
SO5 "O5'" F7 1
SO5 "O3'" F7 1
SO5 "O2'" F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SO5
_pdbe_chem_comp_rdkit_properties.exactmw 887.121
_pdbe_chem_comp_rdkit_properties.amw 887.601
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 28
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 11
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 32
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 26
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 56
_pdbe_chem_comp_rdkit_properties.NumAtoms 96
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 32
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 8
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 372.805
_pdbe_chem_comp_rdkit_properties.tpsa 427.230
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.585
_pdbe_chem_comp_rdkit_properties.CrippenMR 178.573
_pdbe_chem_comp_rdkit_properties.chi0v 28.953
_pdbe_chem_comp_rdkit_properties.chi1v 18.265
_pdbe_chem_comp_rdkit_properties.chi2v 8.121
_pdbe_chem_comp_rdkit_properties.chi3v 8.121
_pdbe_chem_comp_rdkit_properties.chi4v 5.075
_pdbe_chem_comp_rdkit_properties.chi0n 65.454
_pdbe_chem_comp_rdkit_properties.chi1n 31.622
_pdbe_chem_comp_rdkit_properties.chi2n 4.819
_pdbe_chem_comp_rdkit_properties.chi3n 4.819
_pdbe_chem_comp_rdkit_properties.chi4n 2.750
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.080
_pdbe_chem_comp_rdkit_properties.kappa1 15.833
_pdbe_chem_comp_rdkit_properties.kappa2 18.668
_pdbe_chem_comp_rdkit_properties.kappa3 13.509
_pdbe_chem_comp_rdkit_properties.Phi 5.278
#
_pdbe_chem_comp_external_mappings.comp_id SO5
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 137700789
#
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
SO5 O56 14.569 3.106 -1.810 ETKDGv3 1
SO5 SS4 13.607 2.308 -0.976 ETKDGv3 2
SO5 OS5 14.035 0.683 -1.036 ETKDGv3 3
SO5 OS4 13.677 2.781 0.448 ETKDGv3 4
SO5 CS2 11.943 2.514 -1.605 ETKDGv3 5
SO5 CS3 11.500 3.975 -1.505 ETKDGv3 6
SO5 CS1 10.998 1.613 -0.868 ETKDGv3 7
SO5 OS1 10.761 1.809 0.357 ETKDGv3 8
SO5 OPS 10.405 0.542 -1.546 ETKDGv3 9
SO5 CP1 9.463 -0.343 -0.942 ETKDGv3 10
SO5 CP2 8.098 0.336 -0.811 ETKDGv3 11
SO5 NP1 7.114 -0.594 -0.264 ETKDGv3 12
SO5 CP3 7.081 -0.953 1.125 ETKDGv3 13
SO5 OP1 7.925 -0.469 1.928 ETKDGv3 14
SO5 CP4 6.022 -1.882 1.644 ETKDGv3 15
SO5 CP5 4.924 -1.116 2.391 ETKDGv3 16
SO5 NP2 4.159 -0.253 1.490 ETKDGv3 17
SO5 CP6 3.083 0.564 1.972 ETKDGv3 18
SO5 OP2 2.794 0.560 3.200 ETKDGv3 19
SO5 CP7 2.276 1.406 1.004 ETKDGv3 20
SO5 OP3 1.959 2.657 1.571 ETKDGv3 21
SO5 CPA 1.009 0.677 0.432 ETKDGv3 22
SO5 CP9 0.281 1.634 -0.541 ETKDGv3 23
SO5 CP8 1.449 -0.576 -0.364 ETKDGv3 24
SO5 CPB 0.027 0.248 1.558 ETKDGv3 25
SO5 O7 -1.091 -0.411 1.005 ETKDGv3 26
SO5 P2 -2.083 -0.974 2.274 ETKDGv3 27
SO5 O21 -1.352 -2.060 3.036 ETKDGv3 28
SO5 O22 -2.470 0.310 3.312 ETKDGv3 29
SO5 O6 -3.508 -1.595 1.579 ETKDGv3 30
SO5 P1 -4.418 -2.335 2.815 ETKDGv3 31
SO5 O11 -4.568 -1.321 4.165 ETKDGv3 32
SO5 O12 -3.749 -3.625 3.233 ETKDGv3 33
SO5 "O5'" -5.968 -2.706 2.213 ETKDGv3 34
SO5 "C5'" -6.603 -1.499 1.858 ETKDGv3 35
SO5 "C4'" -7.959 -1.804 1.207 ETKDGv3 36
SO5 "O4'" -8.650 -0.590 0.996 ETKDGv3 37
SO5 "C1'" -8.804 -0.411 -0.394 ETKDGv3 38
SO5 "C2'" -7.902 -1.402 -1.120 ETKDGv3 39
SO5 "O2'" -8.463 -1.823 -2.336 ETKDGv3 40
SO5 "C3'" -7.801 -2.536 -0.133 ETKDGv3 41
SO5 "O3'" -8.884 -3.430 -0.324 ETKDGv3 42
SO5 P3 -8.420 -5.007 0.137 ETKDGv3 43
SO5 O31 -7.259 -5.602 -0.944 ETKDGv3 44
SO5 O32 -7.797 -5.006 1.711 ETKDGv3 45
SO5 O33 -9.636 -5.904 0.090 ETKDGv3 46
SO5 N9 -8.474 0.966 -0.755 ETKDGv3 47
SO5 C8 -7.298 1.696 -0.372 ETKDGv3 48
SO5 N7 -7.002 2.676 -1.177 ETKDGv3 49
SO5 C5 -8.014 2.620 -2.177 ETKDGv3 50
SO5 C4 -8.841 1.638 -1.944 ETKDGv3 51
SO5 C6 -8.119 3.375 -3.431 ETKDGv3 52
SO5 N6 -7.227 4.448 -3.731 ETKDGv3 53
SO5 N1 -9.055 3.033 -4.277 ETKDGv3 54
SO5 C2 -9.959 1.935 -3.996 ETKDGv3 55
SO5 N3 -9.854 1.257 -2.883 ETKDGv3 56
SO5 H1 11.947 2.226 -2.679 ETKDGv3 57
SO5 H2 12.181 4.621 -2.098 ETKDGv3 58
SO5 H3 11.510 4.321 -0.449 ETKDGv3 59
SO5 H4 10.472 4.090 -1.911 ETKDGv3 60
SO5 H5 9.837 -0.679 0.049 ETKDGv3 61
SO5 H6 9.358 -1.238 -1.590 ETKDGv3 62
SO5 H7 7.766 0.669 -1.819 ETKDGv3 63
SO5 H8 8.167 1.235 -0.162 ETKDGv3 64
SO5 H9 6.372 -0.961 -0.902 ETKDGv3 65
SO5 H10 6.492 -2.609 2.340 ETKDGv3 66
SO5 H11 5.573 -2.464 0.809 ETKDGv3 67
SO5 H12 4.234 -1.851 2.860 ETKDGv3 68
SO5 H13 5.379 -0.503 3.200 ETKDGv3 69
SO5 H14 4.377 -0.241 0.468 ETKDGv3 70
SO5 H15 2.946 1.629 0.144 ETKDGv3 71
SO5 H16 1.446 2.504 2.405 ETKDGv3 72
SO5 H17 0.973 1.981 -1.339 ETKDGv3 73
SO5 H18 -0.108 2.524 -0.003 ETKDGv3 74
SO5 H19 -0.579 1.129 -1.031 ETKDGv3 75
SO5 H20 0.584 -1.048 -0.878 ETKDGv3 76
SO5 H21 2.199 -0.308 -1.139 ETKDGv3 77
SO5 H22 1.896 -1.338 0.310 ETKDGv3 78
SO5 H23 -0.311 1.151 2.110 ETKDGv3 79
SO5 H24 0.562 -0.428 2.263 ETKDGv3 80
SO5 H25 -1.757 0.313 4.000 ETKDGv3 81
SO5 H26 -5.151 -1.819 4.792 ETKDGv3 82
SO5 H27 -5.988 -0.913 1.137 ETKDGv3 83
SO5 H28 -6.787 -0.883 2.767 ETKDGv3 84
SO5 H29 -8.551 -2.423 1.916 ETKDGv3 85
SO5 H30 -9.869 -0.609 -0.650 ETKDGv3 86
SO5 H31 -6.885 -0.971 -1.284 ETKDGv3 87
SO5 H32 -8.264 -1.113 -3.000 ETKDGv3 88
SO5 H33 -6.801 -3.018 -0.255 ETKDGv3 89
SO5 H34 -6.387 -5.414 -0.515 ETKDGv3 90
SO5 H35 -7.495 -5.937 1.866 ETKDGv3 91
SO5 H36 -6.692 1.446 0.489 ETKDGv3 92
SO5 H37 -6.479 4.722 -3.056 ETKDGv3 93
SO5 H38 -7.314 4.972 -4.630 ETKDGv3 94
SO5 H39 -10.719 1.667 -4.718 ETKDGv3 95
SO5 H40 13.939 0.428 -1.988 ETKDGv3 96
#