data_6D5
# 
_chem_comp.id                                    6D5 
_chem_comp.name                                  "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azidopropyl)amino]-2-azanyl-butanoic acid" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H26 N10 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2016-03-16 
_chem_comp.pdbx_modified_date                    2018-02-27 
_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                        450.452 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     6D5 
_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        5ISA 
_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 
6D5 C1  C1  C 0  1 Y N N 50.315 42.517 127.396 5.972  1.639  0.799  C1  6D5 1  
6D5 C2  C2  C 0  1 Y N N 50.123 40.165 127.406 4.022  0.468  0.467  C2  6D5 2  
6D5 C3  C3  C 0  1 Y N N 50.321 40.143 126.057 4.547  -0.597 1.218  C3  6D5 3  
6D5 C4  C4  C 0  1 Y N N 50.520 41.328 125.366 5.838  -0.457 1.755  C4  6D5 4  
6D5 C5  C5  C 0  1 Y N N 50.061 38.070 126.738 2.556  -1.175 0.583  C5  6D5 5  
6D5 C6  C6  C 0  1 N N N 51.186 33.351 130.893 -3.107 1.492  -0.818 C6  6D5 6  
6D5 C7  C7  C 0  1 N N N 52.483 32.699 130.422 -3.835 1.773  0.498  C7  6D5 7  
6D5 C8  C8  C 0  1 N N N 52.176 31.426 129.648 -4.543 3.127  0.409  C8  6D5 8  
6D5 N1  N1  N 0  1 N N N 53.999 36.691 134.065 -4.695 -3.032 0.963  N1  6D5 9  
6D5 C9  C9  C 0  1 N N S 52.913 36.012 134.736 -3.693 -3.322 -0.072 C9  6D5 10 
6D5 C10 C10 C 0  1 N N N 53.484 34.912 135.608 -2.970 -4.598 0.273  C10 6D5 11 
6D5 O1  O1  O 0  1 N N N 54.616 34.561 135.162 -2.893 -4.957 1.424  O1  6D5 12 
6D5 C11 C11 C 0  1 N N N 51.842 35.493 133.778 -2.688 -2.171 -0.146 C11 6D5 13 
6D5 C12 C12 C 0  1 N N N 52.413 34.831 132.508 -3.398 -0.905 -0.630 C12 6D5 14 
6D5 N2  N2  N 0  1 N N N 51.314 34.700 131.498 -2.427 0.192  -0.733 N2  6D5 15 
6D5 C13 C13 C 0  1 N N N 51.462 35.673 130.367 -1.527 -0.007 -1.877 C13 6D5 16 
6D5 C14 C14 C 0  1 N N R 50.636 36.951 130.612 -0.262 0.833  -1.684 C14 6D5 17 
6D5 O2  O2  O 0  1 N N N 50.950 37.864 129.614 0.476  0.371  -0.532 O2  6D5 18 
6D5 C15 C15 C 0  1 N N S 49.153 36.748 130.614 0.701  0.636  -2.876 C15 6D5 19 
6D5 O3  O3  O 0  1 N N N 48.596 37.257 131.769 0.567  1.709  -3.810 O3  6D5 20 
6D5 C16 C16 C 0  1 N N R 48.639 37.467 129.443 2.104  0.651  -2.230 C16 6D5 21 
6D5 O4  O4  O 0  1 N N N 47.393 38.057 129.693 2.881  1.734  -2.746 O4  6D5 22 
6D5 C17 C17 C 0  1 N N R 49.727 38.452 129.198 1.823  0.855  -0.725 C17 6D5 23 
6D5 O5  O5  O 0  1 N N N 52.690 34.646 136.553 -2.411 -5.337 -0.699 O5  6D5 24 
6D5 N3  N3  N 0  1 Y N N 50.514 42.500 126.042 6.505  0.667  1.516  N3  6D5 25 
6D5 N4  N4  N 0  1 Y N N 50.124 41.345 128.077 4.763  1.556  0.285  N4  6D5 26 
6D5 N5  N5  N 0  1 N N N 50.736 41.270 123.939 6.406  -1.471 2.507  N5  6D5 27 
6D5 N6  N6  N 0  1 Y N N 50.288 38.864 125.641 3.602  -1.567 1.250  N6  6D5 28 
6D5 N7  N7  N 0  1 Y N N 49.942 38.876 127.828 2.766  0.075  0.080  N7  6D5 29 
6D5 N8  N8  N 0  1 N N N 52.146 30.263 130.527 -5.241 3.396  1.669  N8  6D5 30 
6D5 N9  N9  N 1  1 N N N 51.791 29.046 129.987 -4.976 4.305  2.274  N9  6D5 31 
6D5 N10 N10 N -1 1 N N N 51.458 27.794 129.536 -4.711 5.214  2.880  N10 6D5 32 
6D5 H1  H1  H 0  1 N N N 50.309 43.457 127.928 6.547  2.538  0.632  H1  6D5 33 
6D5 H2  H2  H 0  1 N N N 49.989 36.992 126.736 1.654  -1.753 0.447  H2  6D5 34 
6D5 H4  H3  H 0  1 N N N 50.517 33.435 130.024 -3.828 1.472  -1.635 H4  6D5 35 
6D5 H3  H4  H 0  1 N N N 50.730 32.688 131.643 -2.372 2.275  -1.001 H3  6D5 36 
6D5 H5  H5  H 0  1 N N N 53.105 32.453 131.295 -4.570 0.990  0.681  H5  6D5 37 
6D5 H6  H6  H 0  1 N N N 53.027 33.399 129.770 -3.114 1.793  1.315  H6  6D5 38 
6D5 H8  H7  H 0  1 N N N 51.196 31.531 129.160 -3.808 3.910  0.226  H8  6D5 39 
6D5 H7  H8  H 0  1 N N N 52.952 31.276 128.883 -5.264 3.106  -0.408 H7  6D5 40 
6D5 H9  H9  H 0  1 N N N 54.665 37.006 134.742 -5.407 -3.747 0.987  H9  6D5 41 
6D5 H11 H10 H 0  1 N N N 54.444 36.061 133.429 -4.260 -2.923 1.867  H11 6D5 42 
6D5 H12 H12 H 0  1 N N N 52.423 36.734 135.405 -4.189 -3.434 -1.036 H12 6D5 43 
6D5 H14 H13 H 0  1 N N N 51.209 36.340 133.473 -2.264 -1.994 0.843  H14 6D5 44 
6D5 H13 H14 H 0  1 N N N 51.230 34.751 134.311 -1.891 -2.429 -0.842 H13 6D5 45 
6D5 H15 H15 H 0  1 N N N 52.808 33.835 132.756 -3.843 -1.089 -1.607 H15 6D5 46 
6D5 H16 H16 H 0  1 N N N 53.221 35.454 132.097 -4.179 -0.632 0.080  H16 6D5 47 
6D5 H19 H18 H 0  1 N N N 51.117 35.197 129.438 -1.257 -1.060 -1.947 H19 6D5 48 
6D5 H18 H19 H 0  1 N N N 52.523 35.946 130.267 -2.031 0.301  -2.793 H18 6D5 49 
6D5 H20 H20 H 0  1 N N N 50.929 37.356 131.592 -0.520 1.886  -1.574 H20 6D5 50 
6D5 H21 H21 H 0  1 N N N 48.935 35.675 130.513 0.513  -0.320 -3.365 H21 6D5 51 
6D5 H22 H22 H 0  1 N N N 48.936 36.784 132.520 1.150  1.636  -4.578 H22 6D5 52 
6D5 H23 H23 H 0  1 N N N 48.574 36.778 128.588 2.614  -0.298 -2.401 H23 6D5 53 
6D5 H24 H24 H 0  1 N N N 46.745 37.378 129.841 3.036  1.688  -3.699 H24 6D5 54 
6D5 H25 H25 H 0  1 N N N 49.529 39.341 129.814 1.887  1.912  -0.467 H25 6D5 55 
6D5 H26 H26 H 0  1 N N N 53.065 33.966 137.101 -1.958 -6.147 -0.429 H26 6D5 56 
6D5 H27 H27 H 0  1 N N N 50.869 42.195 123.584 7.301  -1.365 2.867  H27 6D5 57 
6D5 H28 H28 H 0  1 N N N 51.548 40.719 123.747 5.909  -2.287 2.675  H28 6D5 58 
# 
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 
6D5 N5  C4  SING N N 1  
6D5 C4  N3  DOUB Y N 2  
6D5 C4  C3  SING Y N 3  
6D5 N6  C3  SING Y N 4  
6D5 N6  C5  DOUB Y N 5  
6D5 N3  C1  SING Y N 6  
6D5 C3  C2  DOUB Y N 7  
6D5 C5  N7  SING Y N 8  
6D5 C1  N4  DOUB Y N 9  
6D5 C2  N7  SING Y N 10 
6D5 C2  N4  SING Y N 11 
6D5 N7  C17 SING N N 12 
6D5 C17 C16 SING N N 13 
6D5 C17 O2  SING N N 14 
6D5 C16 O4  SING N N 15 
6D5 C16 C15 SING N N 16 
6D5 N10 N9  DOUB N N 17 
6D5 O2  C14 SING N N 18 
6D5 C8  C7  SING N N 19 
6D5 C8  N8  SING N N 20 
6D5 N9  N8  DOUB N N 21 
6D5 C13 C14 SING N N 22 
6D5 C13 N2  SING N N 23 
6D5 C7  C6  SING N N 24 
6D5 C14 C15 SING N N 25 
6D5 C15 O3  SING N N 26 
6D5 C6  N2  SING N N 27 
6D5 N2  C12 SING N N 28 
6D5 C12 C11 SING N N 29 
6D5 C11 C9  SING N N 30 
6D5 N1  C9  SING N N 31 
6D5 C9  C10 SING N N 32 
6D5 O1  C10 DOUB N N 33 
6D5 C10 O5  SING N N 34 
6D5 C1  H1  SING N N 35 
6D5 C5  H2  SING N N 36 
6D5 C6  H4  SING N N 37 
6D5 C6  H3  SING N N 38 
6D5 C7  H5  SING N N 39 
6D5 C7  H6  SING N N 40 
6D5 C8  H8  SING N N 41 
6D5 C8  H7  SING N N 42 
6D5 N1  H9  SING N N 43 
6D5 N1  H11 SING N N 44 
6D5 C9  H12 SING N N 45 
6D5 C11 H14 SING N N 46 
6D5 C11 H13 SING N N 47 
6D5 C12 H15 SING N N 48 
6D5 C12 H16 SING N N 49 
6D5 C13 H19 SING N N 50 
6D5 C13 H18 SING N N 51 
6D5 C14 H20 SING N N 52 
6D5 C15 H21 SING N N 53 
6D5 O3  H22 SING N N 54 
6D5 C16 H23 SING N N 55 
6D5 O4  H24 SING N N 56 
6D5 C17 H25 SING N N 57 
6D5 O5  H26 SING N N 58 
6D5 N5  H27 SING N N 59 
6D5 N5  H28 SING N N 60 
# 
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 
6D5 InChI            InChI                1.03  "InChI=1S/C17H26N10O5/c18-9(17(30)31)2-5-26(4-1-3-24-25-20)6-10-12(28)13(29)16(32-10)27-8-23-11-14(19)21-7-22-15(11)27/h7-10,12-13,16,28-29H,1-6,18H2,(H,30,31)(H2,19,21,22)/t9-,10+,12+,13+,16+/m0/s1" 
6D5 InChIKey         InChI                1.03  HOYYGMYIDDINNM-UOYPZJKHSA-N                                                                                                                                                                             
6D5 SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCN(CCCN=[N+]=[N-])C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O"                                                                                                                     
6D5 SMILES           CACTVS               3.385 "N[CH](CCN(CCCN=[N+]=[N-])C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O"                                                                                                                            
6D5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CCCN=[N+]=[N-])CC[C@@H](C(=O)O)N)O)O)N"                                                                                                              
6D5 SMILES           "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCN=[N+]=[N-])CCC(C(=O)O)N)O)O)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 
6D5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azidopropyl)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 
6D5 "Create component"   2016-03-16 EBI  
6D5 "Initial release"    2017-03-15 RCSB 
6D5 "Other modification" 2018-02-27 EBI  
# 
