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 #