data_SN3
#
_chem_comp.id SN3
_chem_comp.name
;(R)-3-((2S,3R)-1-((2S,3AR,5S,6S,7AS)-2-(2-(1-CARBAMIMIDOYL-2,5-DIHYDRO-1H-PYRROL-3-YL)ETHYLCARBAMOYL)-5,6-DIHYDROXYOCTA
HYDRO-1H-INDOL-1-YL)-3-CHLORO-4-METHYL-1-OXOPENTAN-2-YLAMINO)-2-METHOXY-3-OXOPROPYL HYDROGEN SULFATE
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C26 H43 Cl N6 O10 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms CHLORODYSINOSIN
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-03-29
_chem_comp.pdbx_modified_date 2020-06-17
_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 667.172
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SN3
_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 2GDE
_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
SN3 C1 C1 C 0 1 N N S N N N 20.655 -15.222 18.446 0.301 2.977 -2.658 C1 SN3 1
SN3 C2 C2 C 0 1 N N N N N N 21.176 -14.095 19.376 -0.705 3.402 -1.591 C2 SN3 2
SN3 C3 C3 C 0 1 N N R N N N 20.219 -13.557 20.437 -0.038 4.299 -0.547 C3 SN3 3
SN3 C4 C4 C 0 1 N N S N N N 19.184 -14.565 20.969 1.197 3.604 0.055 C4 SN3 4
SN3 C5 C5 C 0 1 N N N N N N 18.611 -15.545 19.914 2.143 3.068 -0.995 C5 SN3 5
SN3 C6 C6 C 0 1 N N S N N N 19.753 -16.255 19.181 1.413 2.163 -1.988 C6 SN3 6
SN3 O7 O7 O 0 1 N N N N N N 20.482 -17.049 20.139 2.331 1.696 -2.978 O7 SN3 7
SN3 N8 N8 N 0 1 N N N N N N 18.155 -13.668 21.558 0.671 2.559 0.938 N8 SN3 8
SN3 C9 C9 C 0 1 N N S N N N 18.190 -12.379 20.864 -0.674 2.971 1.378 C9 SN3 9
SN3 C10 C10 C 0 1 N N N N N N 19.318 -12.473 19.817 -0.985 4.320 0.692 C10 SN3 10
SN3 C11 C11 C 0 1 N N N N N N 16.878 -12.130 20.153 -1.689 1.938 0.962 C11 SN3 11
SN3 N12 N12 N 0 1 N N N N N N 16.365 -10.872 20.154 -2.998 2.140 1.212 N12 SN3 12
SN3 C13 C13 C 0 1 N N N N N N 15.098 -10.602 19.449 -3.973 1.089 0.908 C13 SN3 13
SN3 C14 C14 C 0 1 N N N N N N 14.281 -9.611 20.270 -5.357 1.520 1.398 C14 SN3 14
SN3 C15 C15 C 0 1 N N N N N N 13.558 -10.383 21.348 -6.359 0.439 1.084 C15 SN3 15
SN3 C16 C16 C 0 1 N N N N N N 12.961 -9.731 22.550 -7.078 0.285 -0.230 C16 SN3 16
SN3 N17 N17 N 0 1 N N N N N N 12.209 -10.755 23.271 -7.956 -0.888 -0.108 N17 SN3 17
SN3 C18 C18 C 0 1 N N N N N N 12.607 -12.034 22.670 -7.744 -1.398 1.254 C18 SN3 18
SN3 C19 C19 C 0 1 N N N N N N 13.388 -11.683 21.422 -6.726 -0.502 1.909 C19 SN3 19
SN3 C20 C20 C 0 1 N N N N N N 11.347 -10.539 24.238 -8.799 -1.400 -1.066 C20 SN3 20
SN3 N21 N21 N 0 1 N N N N N N 10.664 -11.592 24.821 -8.878 -0.830 -2.236 N21 SN3 21
SN3 N22 N22 N 0 1 N N N N N N 11.086 -9.263 24.653 -9.559 -2.512 -0.790 N22 SN3 22
SN3 O23 O23 O 0 1 N N N N N N 16.305 -13.056 19.582 -1.328 0.925 0.401 O23 SN3 23
SN3 C24 C24 C 0 1 N N N N N N 17.332 -13.971 22.580 1.305 1.422 1.287 C24 SN3 24
SN3 O25 O25 O 0 1 N N N N N N 16.560 -13.112 22.946 0.834 0.703 2.142 O25 SN3 25
SN3 C26 C26 C 0 1 N N S N N N 17.366 -15.327 23.271 2.599 1.044 0.613 C26 SN3 26
SN3 C27 C27 C 0 1 N N R N N N 17.745 -15.115 24.750 3.745 1.857 1.218 C27 SN3 27
SN3 C28 C28 C 0 1 N N N N N N 17.741 -16.408 25.571 5.024 1.612 0.414 C28 SN3 28
SN3 C29 C29 C 0 1 N N N N N N 18.658 -17.501 24.992 4.845 2.154 -1.006 C29 SN3 29
SN3 C30 C30 C 0 1 N N N N N N 18.158 -16.049 26.995 6.195 2.329 1.089 C30 SN3 30
SN3 CL31 CL31 CL 0 0 N N N N N N 19.334 -14.269 24.819 3.330 3.611 1.169 CL31 SN3 31
SN3 N32 N32 N 0 1 N N N N N N 16.043 -15.948 23.241 2.854 -0.384 0.812 N32 SN3 32
SN3 C33 C33 C 0 1 N N N N N N 15.769 -17.033 22.477 3.624 -1.060 -0.064 C33 SN3 33
SN3 C34 C34 C 0 1 N N R N N N 14.389 -17.615 22.522 3.887 -2.530 0.142 C34 SN3 34
SN3 O35 O35 O 0 1 N N N N N N 13.451 -16.603 22.925 4.815 -2.990 -0.843 O35 SN3 35
SN3 C36 C36 C 0 1 N N N N N N 12.928 -15.839 21.824 5.637 -4.073 -0.405 C36 SN3 36
SN3 C37 C37 C 0 1 N N N N N N 14.411 -18.827 23.471 2.575 -3.306 0.008 C37 SN3 37
SN3 O38 O38 O 0 1 N N N N N N 14.486 -18.467 24.862 2.803 -4.682 0.317 O38 SN3 38
SN3 S39 S39 S 0 1 N N N N N N 15.053 -19.563 25.796 1.559 -5.553 0.215 S39 SN3 39
SN3 O40 O40 O 0 1 N N N N N N 15.221 -19.010 27.092 1.277 -5.766 -1.265 O40 SN3 40
SN3 O41 O41 O 0 1 N N N N N N 13.975 -20.620 26.032 1.914 -6.824 0.742 O41 SN3 41
SN3 O42 O42 O 0 1 N N N N N N 16.113 -20.172 25.054 0.482 -4.776 0.721 O42 SN3 42
SN3 O43 O43 O 0 1 N N N N N N 16.601 -17.548 21.750 4.105 -0.485 -1.017 O43 SN3 43
SN3 O46 O46 O 0 1 N N N N N N 19.994 -14.632 17.310 -0.354 2.173 -3.642 O46 SN3 44
SN3 H1 H1 H 0 1 N N N N N N 21.521 -15.804 18.097 0.729 3.861 -3.131 H1 SN3 45
SN3 H21 H21 H 0 1 N N N N N N 22.049 -14.499 19.909 -1.521 3.947 -2.065 H21 SN3 46
SN3 H22 H22 H 0 1 N N N N N N 21.446 -13.247 18.730 -1.104 2.515 -1.100 H22 SN3 47
SN3 H3 H3 H 0 1 N N N N N N 20.894 -13.232 21.242 0.189 5.292 -0.936 H3 SN3 48
SN3 H4 H4 H 0 1 N N N N N N 19.626 -15.275 21.684 1.734 4.325 0.671 H4 SN3 49
SN3 H51 H51 H 0 1 N N N N N N 17.982 -16.294 20.418 2.588 3.904 -1.535 H51 SN3 50
SN3 H52 H52 H 0 1 N N N N N N 18.007 -14.983 19.187 2.933 2.498 -0.507 H52 SN3 51
SN3 H6 H6 H 0 1 N N N N N N 19.359 -16.925 18.403 0.979 1.314 -1.460 H6 SN3 52
SN3 HO7 HO7 H 0 1 N N N N N N 19.890 -17.662 20.559 1.930 1.128 -3.650 HO7 SN3 53
SN3 H9 H9 H 0 1 N N N N N N 18.359 -11.559 21.577 -0.689 3.094 2.461 H9 SN3 54
SN3 H101 H101 H 0 0 N N N N N N 19.846 -11.517 19.686 -0.742 5.154 1.350 H101 SN3 55
SN3 H102 H102 H 0 0 N N N N N N 18.942 -12.761 18.824 -2.029 4.364 0.380 H102 SN3 56
SN3 HN12 HN12 H 0 0 N N N N N N 16.843 -10.134 20.630 -3.295 2.980 1.594 HN12 SN3 57
SN3 H131 H131 H 0 0 N N N N N N 15.309 -10.176 18.457 -4.004 0.924 -0.169 H131 SN3 58
SN3 H132 H132 H 0 0 N N N N N N 14.533 -11.538 19.329 -3.680 0.166 1.408 H132 SN3 59
SN3 H141 H141 H 0 0 N N N N N N 14.946 -8.862 20.726 -5.325 1.685 2.475 H141 SN3 60
SN3 H142 H142 H 0 0 N N N N N N 13.554 -9.097 19.624 -5.649 2.443 0.897 H142 SN3 61
SN3 H161 H161 H 0 0 N N N N N N 13.754 -9.319 23.192 -7.674 1.174 -0.433 H161 SN3 62
SN3 H162 H162 H 0 0 N N N N N N 12.292 -8.912 22.245 -6.357 0.126 -1.031 H162 SN3 63
SN3 H181 H181 H 0 0 N N N N N N 13.230 -12.613 23.367 -8.680 -1.370 1.811 H181 SN3 64
SN3 H182 H182 H 0 0 N N N N N N 11.722 -12.636 22.417 -7.363 -2.418 1.213 H182 SN3 65
SN3 H192 H192 H 0 0 N N N N N N 13.752 -12.397 20.698 -6.355 -0.620 2.917 H192 SN3 66
SN3 HN21 HN21 H 0 0 N N N N N N 10.020 -11.280 25.520 -9.473 -1.191 -2.911 HN21 SN3 67
SN3 H221 H221 H 0 0 N N N N N N 10.408 -9.099 25.370 -9.500 -2.935 0.081 H221 SN3 68
SN3 H222 H222 H 0 0 N N N N N N 11.573 -8.493 24.240 -10.154 -2.873 -1.465 H222 SN3 69
SN3 H26 H26 H 0 1 N N N N N N 18.093 -15.971 22.754 2.528 1.255 -0.454 H26 SN3 70
SN3 H27 H27 H 0 1 N N N N N N 16.972 -14.490 25.220 3.902 1.550 2.252 H27 SN3 71
SN3 H28 H28 H 0 1 N N N N N N 16.729 -16.837 25.547 5.227 0.542 0.372 H28 SN3 72
SN3 H291 H291 H 0 0 N N N N N N 18.607 -18.397 25.627 4.010 1.643 -1.486 H291 SN3 73
SN3 H292 H292 H 0 0 N N N N N N 18.328 -17.755 23.974 4.641 3.224 -0.964 H292 SN3 74
SN3 H293 H293 H 0 0 N N N N N N 19.694 -17.132 24.961 5.756 1.979 -1.578 H293 SN3 75
SN3 H301 H301 H 0 0 N N N N N N 18.166 -16.957 27.615 6.379 1.883 2.067 H301 SN3 76
SN3 H302 H302 H 0 0 N N N N N N 19.165 -15.606 26.981 7.088 2.228 0.471 H302 SN3 77
SN3 H303 H303 H 0 0 N N N N N N 17.444 -15.325 27.415 5.955 3.385 1.210 H303 SN3 78
SN3 HN32 HN32 H 0 0 N N N N N N 15.314 -15.558 23.804 2.470 -0.844 1.575 HN32 SN3 79
SN3 H34 H34 H 0 1 N N N N N N 14.065 -17.964 21.530 4.303 -2.689 1.136 H34 SN3 80
SN3 H361 H361 H 0 0 N N N N N N 12.220 -15.087 22.202 6.218 -3.761 0.463 H361 SN3 81
SN3 H362 H362 H 0 0 N N N N N N 13.755 -15.335 21.302 5.008 -4.921 -0.135 H362 SN3 82
SN3 H363 H363 H 0 0 N N N N N N 12.409 -16.511 21.125 6.314 -4.364 -1.208 H363 SN3 83
SN3 H371 H371 H 0 0 N N N N N N 13.485 -19.401 23.315 1.838 -2.895 0.698 H371 SN3 84
SN3 H372 H372 H 0 0 N N N N N N 15.294 -19.437 23.227 2.204 -3.219 -1.013 H372 SN3 85
SN3 HO40 HO40 H 0 0 N N N N N N 14.635 -19.445 27.701 0.498 -6.311 -1.443 HO40 SN3 86
SN3 HO46 HO46 H 0 0 N N N N N N 19.673 -15.319 16.738 0.228 1.868 -4.352 HO46 SN3 87
#
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
SN3 C1 C2 SING N N 1
SN3 C1 C6 SING N N 2
SN3 C1 O46 SING N N 3
SN3 C1 H1 SING N N 4
SN3 C2 C3 SING N N 5
SN3 C2 H21 SING N N 6
SN3 C2 H22 SING N N 7
SN3 C3 C4 SING N N 8
SN3 C3 C10 SING N N 9
SN3 C3 H3 SING N N 10
SN3 C4 C5 SING N N 11
SN3 C4 N8 SING N N 12
SN3 C4 H4 SING N N 13
SN3 C5 C6 SING N N 14
SN3 C5 H51 SING N N 15
SN3 C5 H52 SING N N 16
SN3 C6 O7 SING N N 17
SN3 C6 H6 SING N N 18
SN3 O7 HO7 SING N N 19
SN3 N8 C9 SING N N 20
SN3 N8 C24 SING N N 21
SN3 C9 C10 SING N N 22
SN3 C9 C11 SING N N 23
SN3 C9 H9 SING N N 24
SN3 C10 H101 SING N N 25
SN3 C10 H102 SING N N 26
SN3 C11 N12 SING N N 27
SN3 C11 O23 DOUB N N 28
SN3 N12 C13 SING N N 29
SN3 N12 HN12 SING N N 30
SN3 C13 C14 SING N N 31
SN3 C13 H131 SING N N 32
SN3 C13 H132 SING N N 33
SN3 C14 C15 SING N N 34
SN3 C14 H141 SING N N 35
SN3 C14 H142 SING N N 36
SN3 C15 C16 SING N N 37
SN3 C15 C19 DOUB N N 38
SN3 C16 N17 SING N N 39
SN3 C16 H161 SING N N 40
SN3 C16 H162 SING N N 41
SN3 N17 C18 SING N N 42
SN3 N17 C20 SING N N 43
SN3 C18 C19 SING N N 44
SN3 C18 H181 SING N N 45
SN3 C18 H182 SING N N 46
SN3 C19 H192 SING N N 47
SN3 C20 N21 DOUB N N 48
SN3 C20 N22 SING N N 49
SN3 N21 HN21 SING N N 50
SN3 N22 H221 SING N N 51
SN3 N22 H222 SING N N 52
SN3 C24 O25 DOUB N N 53
SN3 C24 C26 SING N N 54
SN3 C26 C27 SING N N 55
SN3 C26 N32 SING N N 56
SN3 C26 H26 SING N N 57
SN3 C27 C28 SING N N 58
SN3 C27 CL31 SING N N 59
SN3 C27 H27 SING N N 60
SN3 C28 C29 SING N N 61
SN3 C28 C30 SING N N 62
SN3 C28 H28 SING N N 63
SN3 C29 H291 SING N N 64
SN3 C29 H292 SING N N 65
SN3 C29 H293 SING N N 66
SN3 C30 H301 SING N N 67
SN3 C30 H302 SING N N 68
SN3 C30 H303 SING N N 69
SN3 N32 C33 SING N N 70
SN3 N32 HN32 SING N N 71
SN3 C33 C34 SING N N 72
SN3 C33 O43 DOUB N N 73
SN3 C34 O35 SING N N 74
SN3 C34 C37 SING N N 75
SN3 C34 H34 SING N N 76
SN3 O35 C36 SING N N 77
SN3 C36 H361 SING N N 78
SN3 C36 H362 SING N N 79
SN3 C36 H363 SING N N 80
SN3 C37 O38 SING N N 81
SN3 C37 H371 SING N N 82
SN3 C37 H372 SING N N 83
SN3 O38 S39 SING N N 84
SN3 S39 O40 SING N N 85
SN3 S39 O41 DOUB N N 86
SN3 S39 O42 DOUB N N 87
SN3 O40 HO40 SING N N 88
SN3 O46 HO46 SING N N 89
#
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
SN3 SMILES ACDLabs 12.01 O=S(=O)(O)OCC(OC)C(=O)NC(C(=O)N2C(C(=O)NCCC1=CCN(C(=[N@H])N)C1)CC3CC(O)C(O)CC23)C(Cl)C(C)C
SN3 SMILES_CANONICAL CACTVS 3.370 CO[C@H](CO[S](O)(=O)=O)C(=O)N[C@H]([C@H](Cl)C(C)C)C(=O)N1[C@H]2C[C@H](O)[C@@H](O)C[C@H]2C[C@H]1C(=O)NCCC3=CCN(C3)C(N)=N
SN3 SMILES CACTVS 3.370 CO[CH](CO[S](O)(=O)=O)C(=O)N[CH]([CH](Cl)C(C)C)C(=O)N1[CH]2C[CH](O)[CH](O)C[CH]2C[CH]1C(=O)NCCC3=CCN(C3)C(N)=N
SN3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "[H]/N=C(\N)/N1CC=C(C1)CCNC(=O)[C@@H]2C[C@@H]3C[C@@H]([C@H](C[C@@H]3N2C(=O)[C@@H]([C@@H](C(C)C)Cl)NC(=O)[C@@H](COS(=O)(=O)O)OC)O)O"
SN3 SMILES "OpenEye OEToolkits" 1.7.0 CC(C)C(C(C(=O)N1C2CC(C(CC2CC1C(=O)NCCC3=CCN(C3)C(=N)N)O)O)NC(=O)C(COS(=O)(=O)O)OC)Cl
SN3 InChI InChI 1.03 InChI=1S/C26H43ClN6O10S/c1-13(2)21(27)22(31-24(37)20(42-3)12-43-44(39,40)41)25(38)33-16-10-19(35)18(34)9-15(16)8-17(33)23(36)30-6-4-14-5-7-32(11-14)26(28)29/h5,13,15-22,34-35H,4,6-12H2,1-3H3,(H3,28,29)(H,30,36)(H,31,37)(H,39,40,41)/t15-,16+,17+,18+,19+,20-,21-,22-/m1/s1
SN3 InChIKey InChI 1.03 BVKDJAALSHFQTE-WNZJUFNWSA-N
#
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
SN3 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-3-({(2S,3R)-1-[(2S,3aR,5S,6S,7aS)-2-{[2-(1-carbamimidoyl-2,5-dihydro-1H-pyrrol-3-yl)ethyl]carbamoyl}-5,6-dihydroxyoctahydro-1H-indol-1-yl]-3-chloro-4-methyl-1-oxopentan-2-yl}amino)-2-methoxy-3-oxopropyl hydrogen sulfate (non-preferred name)"
SN3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R)-3-[[(2S,3R)-1-[(2S,3aR,5S,6S,7aS)-2-[2-(1-carbamimidoyl-2,5-dihydropyrrol-3-yl)ethylcarbamoyl]-5,6-dihydroxy-2,3,3a,4,5,6,7,7a-octahydroindol-1-yl]-3-chloro-4-methyl-1-oxo-pentan-2-yl]amino]-2-methoxy-3-oxo-propyl] hydrogen sulfate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SN3 'Create component' 2006-03-29 RCSB
SN3 'Other modification' 2010-10-11 RCSB
SN3 'Modify descriptor' 2011-06-04 RCSB
SN3 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SN3
_pdbx_chem_comp_synonyms.name CHLORODYSINOSIN
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id SN3
_pdbe_chem_comp_synonyms.name CHLORODYSINOSIN
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
SN3 C1 C 4.299 1.989 1
SN3 C2 C 5.598 2.739 2
SN3 C3 C 6.897 1.989 3
SN3 C4 C 6.897 0.489 4
SN3 C5 C 5.598 -0.261 5
SN3 C6 C 4.299 0.489 6
SN3 O7 O 3.000 -0.261 7
SN3 N8 N 8.316 0.032 8
SN3 C9 C 9.192 1.239 9
SN3 C10 C 8.316 2.446 10
SN3 C11 C 10.692 1.239 11
SN3 N12 N 11.442 2.538 12
SN3 C13 C 12.942 2.538 13
SN3 C14 C 13.692 3.837 14
SN3 C15 C 15.192 3.837 15
SN3 C16 C 16.074 5.051 16
SN3 N17 N 17.500 4.587 17
SN3 C18 C 17.500 3.087 18
SN3 C19 C 16.074 2.624 19
SN3 C20 C 18.714 5.469 20
SN3 N21 N 20.084 4.859 21
SN3 N22 N 18.557 6.961 22
SN3 O23 O 11.442 -0.060 23
SN3 C24 C 8.783 -1.394 24
SN3 O25 O 10.250 -1.703 25
SN3 C26 C 8.223 -2.785 26
SN3 C27 C 6.738 -2.997 27
SN3 C28 C 6.178 -4.389 28
SN3 C29 C 4.693 -4.600 29
SN3 C30 C 7.104 -5.569 30
SN3 CL31 Cl 5.812 -1.817 31
SN3 N32 N 9.149 -3.966 32
SN3 C33 C 10.633 -3.755 33
SN3 C34 C 11.559 -4.935 34
SN3 O35 O 10.999 -6.327 35
SN3 C36 C 11.925 -7.507 36
SN3 C37 C 13.044 -4.724 37
SN3 O38 O 13.970 -5.904 38
SN3 S39 S 15.455 -5.693 39
SN3 O40 O 16.940 -5.481 40
SN3 O41 O 15.666 -7.178 41
SN3 O42 O 15.243 -4.208 42
SN3 O43 O 11.193 -2.363 43
SN3 O46 O 3.000 2.739 44
SN3 HN21 H 21.298 5.740 45
#
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
SN3 C1 C2 SINGLE NONE 1
SN3 C1 C6 SINGLE NONE 2
SN3 C1 O46 SINGLE BEGINWEDGE 3
SN3 C2 C3 SINGLE NONE 4
SN3 C3 C4 SINGLE NONE 5
SN3 C3 C10 SINGLE NONE 6
SN3 C4 C5 SINGLE NONE 7
SN3 C4 N8 SINGLE NONE 8
SN3 C5 C6 SINGLE NONE 9
SN3 C6 O7 SINGLE BEGINDASH 10
SN3 N8 C9 SINGLE NONE 11
SN3 N8 C24 SINGLE NONE 12
SN3 C9 C10 SINGLE NONE 13
SN3 C9 C11 SINGLE BEGINWEDGE 14
SN3 C11 N12 SINGLE NONE 15
SN3 C11 O23 DOUBLE NONE 16
SN3 N12 C13 SINGLE NONE 17
SN3 C13 C14 SINGLE NONE 18
SN3 C14 C15 SINGLE NONE 19
SN3 C15 C16 SINGLE NONE 20
SN3 C15 C19 DOUBLE NONE 21
SN3 C16 N17 SINGLE NONE 22
SN3 N17 C18 SINGLE NONE 23
SN3 N17 C20 SINGLE ENDUPRIGHT 24
SN3 C18 C19 SINGLE NONE 25
SN3 C20 N21 DOUBLE NONE 26
SN3 C20 N22 SINGLE ENDUPRIGHT 27
SN3 C24 O25 DOUBLE NONE 28
SN3 C24 C26 SINGLE NONE 29
SN3 C26 C27 SINGLE NONE 30
SN3 C26 N32 SINGLE BEGINDASH 31
SN3 C27 C28 SINGLE NONE 32
SN3 C27 CL31 SINGLE BEGINWEDGE 33
SN3 C28 C29 SINGLE NONE 34
SN3 C28 C30 SINGLE NONE 35
SN3 N32 C33 SINGLE NONE 36
SN3 C33 C34 SINGLE NONE 37
SN3 C33 O43 DOUBLE NONE 38
SN3 C34 O35 SINGLE NONE 39
SN3 C34 C37 SINGLE BEGINWEDGE 40
SN3 O35 C36 SINGLE NONE 41
SN3 C37 O38 SINGLE NONE 42
SN3 O38 S39 SINGLE NONE 43
SN3 S39 O40 SINGLE NONE 44
SN3 S39 O41 DOUBLE NONE 45
SN3 S39 O42 DOUBLE NONE 46
#
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
SN3 MurckoScaffold S1 scaffold 'O=C(NCCC1=CCNC1)[C@@H]1C[C@@H]2CCCC[C@@H]2N1' InChI=1S/C15H25N3O/c19-15(17-8-6-11-5-7-16-10-11)14-9-12-3-1-2-4-13(12)18-14/h5,12-14,16,18H,1-4,6-10H2,(H,17,19)/t12-,13-,14-/m0/s1 GJRSZDJQYGZYAL-IHRRRGAJSA-N
SN3 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
SN3 cyclohexane F2 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
SN3 peptide F3 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
SN3 3-pyrroline F4 fragment C1=CCNC1 InChI=1S/C4H7N/c1-2-4-5-3-1/h1-2,5H,3-4H2 JVQIKJMSUIMUDI-UHFFFAOYSA-N
SN3 Z2856434901 F5 fragment CNCCC1CCCCC1 InChI=1S/C9H19N/c1-10-8-7-9-5-3-2-4-6-9/h9-10H,2-8H2,1H3 KCYFTGSOYOWCJF-UHFFFAOYSA-N
SN3 Z32016974 F6 fragment CNC(=O)CCC1CCCCC1 InChI=1S/C10H19NO/c1-11-10(12)8-7-9-5-3-2-4-6-9/h9H,2-8H2,1H3,(H,11,12) NKQAGLASNCWFIR-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
SN3 C1 S1 1
SN3 C2 S1 1
SN3 C3 S1 1
SN3 C4 S1 1
SN3 C5 S1 1
SN3 C6 S1 1
SN3 N8 S1 1
SN3 C9 S1 1
SN3 C10 S1 1
SN3 C11 S1 1
SN3 N12 S1 1
SN3 C13 S1 1
SN3 C14 S1 1
SN3 C15 S1 1
SN3 C16 S1 1
SN3 N17 S1 1
SN3 C18 S1 1
SN3 C19 S1 1
SN3 O23 S1 1
SN3 N8 F1 1
SN3 C24 F1 1
SN3 O25 F1 1
SN3 C26 F1 1
SN3 N12 F1 2
SN3 C11 F1 2
SN3 O23 F1 2
SN3 C9 F1 2
SN3 N32 F1 3
SN3 C33 F1 3
SN3 O43 F1 3
SN3 C34 F1 3
SN3 C1 F2 1
SN3 C2 F2 1
SN3 C3 F2 1
SN3 C4 F2 1
SN3 C5 F2 1
SN3 C6 F2 1
SN3 O23 F3 1
SN3 C11 F3 1
SN3 C9 F3 1
SN3 N8 F3 1
SN3 O25 F3 2
SN3 C24 F3 2
SN3 C26 F3 2
SN3 N32 F3 2
SN3 C16 F4 1
SN3 N17 F4 1
SN3 C18 F4 1
SN3 C19 F4 1
SN3 C15 F4 1
SN3 C24 F5 1
SN3 N8 F5 1
SN3 C9 F5 1
SN3 C10 F5 1
SN3 C3 F5 1
SN3 C2 F5 1
SN3 C1 F5 1
SN3 C6 F5 1
SN3 C5 F5 1
SN3 C4 F5 1
SN3 C13 F6 1
SN3 N12 F6 1
SN3 C11 F6 1
SN3 O23 F6 1
SN3 C9 F6 1
SN3 C10 F6 1
SN3 C3 F6 1
SN3 C2 F6 1
SN3 C1 F6 1
SN3 C6 F6 1
SN3 C5 F6 1
SN3 C4 F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SN3
_pdbe_chem_comp_rdkit_properties.exactmw 666.245
_pdbe_chem_comp_rdkit_properties.amw 667.182
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 16
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 19
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 11
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 44
_pdbe_chem_comp_rdkit_properties.NumAtoms 87
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 18
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.769
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_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 8
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 322.205
_pdbe_chem_comp_rdkit_properties.tpsa 244.910
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.688
_pdbe_chem_comp_rdkit_properties.CrippenMR 157.681
_pdbe_chem_comp_rdkit_properties.chi0v 22.124
_pdbe_chem_comp_rdkit_properties.chi1v 12.133
_pdbe_chem_comp_rdkit_properties.chi2v 5.096
_pdbe_chem_comp_rdkit_properties.chi3v 5.096
_pdbe_chem_comp_rdkit_properties.chi4v 3.044
_pdbe_chem_comp_rdkit_properties.chi0n 63.552
_pdbe_chem_comp_rdkit_properties.chi1n 31.383
_pdbe_chem_comp_rdkit_properties.chi2n 4.440
_pdbe_chem_comp_rdkit_properties.chi3n 4.440
_pdbe_chem_comp_rdkit_properties.chi4n 2.743
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.540
_pdbe_chem_comp_rdkit_properties.kappa1 9.079
_pdbe_chem_comp_rdkit_properties.kappa2 15.162
_pdbe_chem_comp_rdkit_properties.kappa3 9.016
_pdbe_chem_comp_rdkit_properties.Phi 3.129
#
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
SN3 UniChem PDBe SN3
SN3 UniChem ZINC ZINC000058638570
SN3 UniChem PubChem 49867663
#
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
SN3 C1 2.100 -3.408 -2.079 ETKDGv3 1
SN3 C2 2.691 -3.286 -0.669 ETKDGv3 2
SN3 C3 1.569 -3.090 0.382 ETKDGv3 3
SN3 C4 0.357 -2.296 -0.137 ETKDGv3 4
SN3 C5 0.760 -1.338 -1.273 ETKDGv3 5
SN3 C6 1.357 -2.102 -2.482 ETKDGv3 6
SN3 O7 0.363 -2.379 -3.437 ETKDGv3 7
SN3 N8 -0.132 -1.546 1.015 ETKDGv3 8
SN3 C9 0.844 -1.507 2.103 ETKDGv3 9
SN3 C10 2.040 -2.347 1.638 ETKDGv3 10
SN3 C11 1.257 -0.089 2.407 ETKDGv3 11
SN3 N12 1.858 0.226 3.671 ETKDGv3 12
SN3 C13 2.302 1.576 4.023 ETKDGv3 13
SN3 C14 3.798 1.756 3.742 ETKDGv3 14
SN3 C15 4.107 1.651 2.273 ETKDGv3 15
SN3 C16 3.804 2.711 1.269 ETKDGv3 16
SN3 N17 4.151 2.080 0.002 ETKDGv3 17
SN3 C18 4.656 0.730 0.211 ETKDGv3 18
SN3 C19 4.589 0.557 1.687 ETKDGv3 19
SN3 C20 3.960 2.695 -1.284 ETKDGv3 20
SN3 N21 3.506 3.907 -1.354 ETKDGv3 21
SN3 N22 4.265 1.979 -2.486 ETKDGv3 22
SN3 O23 1.120 0.806 1.529 ETKDGv3 23
SN3 C24 -1.486 -1.065 1.189 ETKDGv3 24
SN3 O25 -1.792 -0.470 2.258 ETKDGv3 25
SN3 C26 -2.576 -1.297 0.161 ETKDGv3 26
SN3 C27 -3.544 -2.422 0.628 ETKDGv3 27
SN3 C28 -4.659 -2.805 -0.393 ETKDGv3 28
SN3 C29 -5.791 -1.768 -0.468 ETKDGv3 29
SN3 C30 -4.123 -3.117 -1.799 ETKDGv3 30
SN3 CL31 -2.632 -3.907 1.061 ETKDGv3 31
SN3 N32 -3.309 -0.041 -0.024 ETKDGv3 32
SN3 C33 -3.072 0.853 -1.121 ETKDGv3 33
SN3 C34 -3.689 2.226 -1.112 ETKDGv3 34
SN3 O35 -3.641 2.774 -2.421 ETKDGv3 35
SN3 C36 -4.820 3.495 -2.706 ETKDGv3 36
SN3 C37 -2.923 3.133 -0.139 ETKDGv3 37
SN3 O38 -1.584 3.261 -0.558 ETKDGv3 38
SN3 S39 -0.783 4.290 0.523 ETKDGv3 39
SN3 O40 -0.916 3.718 2.099 ETKDGv3 40
SN3 O41 0.670 4.355 0.147 ETKDGv3 41
SN3 O42 -1.367 5.673 0.440 ETKDGv3 42
SN3 O43 -2.326 0.508 -2.077 ETKDGv3 43
SN3 O46 3.132 -3.678 -2.991 ETKDGv3 44
SN3 H1 1.386 -4.266 -2.069 ETKDGv3 45
SN3 H21 3.404 -2.432 -0.663 ETKDGv3 46
SN3 H22 3.268 -4.204 -0.422 ETKDGv3 47
SN3 H3 1.203 -4.096 0.694 ETKDGv3 48
SN3 H4 -0.410 -3.015 -0.496 ETKDGv3 49
SN3 H51 -0.107 -0.732 -1.600 ETKDGv3 50
SN3 H52 1.520 -0.623 -0.887 ETKDGv3 51
SN3 H6 2.092 -1.417 -2.962 ETKDGv3 52
SN3 HO7 -0.338 -2.922 -2.990 ETKDGv3 53
SN3 H9 0.397 -1.971 3.010 ETKDGv3 54
SN3 H101 2.911 -1.699 1.406 ETKDGv3 55
SN3 H102 2.349 -3.067 2.427 ETKDGv3 56
SN3 HN12 2.054 -0.549 4.344 ETKDGv3 57
SN3 H131 1.708 2.342 3.479 ETKDGv3 58
SN3 H132 2.124 1.738 5.107 ETKDGv3 59
SN3 H141 4.377 0.998 4.314 ETKDGv3 60
SN3 H142 4.115 2.758 4.100 ETKDGv3 61
SN3 H161 2.726 2.974 1.288 ETKDGv3 62
SN3 H162 4.436 3.607 1.444 ETKDGv3 63
SN3 H181 3.998 -0.012 -0.290 ETKDGv3 64
SN3 H182 5.705 0.645 -0.144 ETKDGv3 65
SN3 H192 4.855 -0.354 2.214 ETKDGv3 66
SN3 HN21 3.353 4.385 -2.270 ETKDGv3 67
SN3 H221 4.631 1.003 -2.459 ETKDGv3 68
SN3 H222 4.123 2.424 -3.420 ETKDGv3 69
SN3 H26 -2.123 -1.603 -0.798 ETKDGv3 70
SN3 H27 -4.034 -2.093 1.571 ETKDGv3 71
SN3 H28 -5.132 -3.739 -0.014 ETKDGv3 72
SN3 H291 -5.484 -0.867 -1.036 ETKDGv3 73
SN3 H292 -6.667 -2.210 -0.989 ETKDGv3 74
SN3 H293 -6.116 -1.467 0.550 ETKDGv3 75
SN3 H301 -3.781 -2.194 -2.312 ETKDGv3 76
SN3 H302 -4.926 -3.576 -2.415 ETKDGv3 77
SN3 H303 -3.278 -3.836 -1.747 ETKDGv3 78
SN3 HN32 -3.932 0.284 0.750 ETKDGv3 79
SN3 H34 -4.733 2.105 -0.731 ETKDGv3 80
SN3 H361 -5.696 2.812 -2.758 ETKDGv3 81
SN3 H362 -4.998 4.298 -1.957 ETKDGv3 82
SN3 H363 -4.709 3.978 -3.698 ETKDGv3 83
SN3 H371 -3.423 4.127 -0.117 ETKDGv3 84
SN3 H372 -2.976 2.688 0.880 ETKDGv3 85
SN3 HO40 -0.659 2.764 2.046 ETKDGv3 86
SN3 HO46 2.698 -3.986 -3.829 ETKDGv3 87
#