data_6D6 # _chem_comp.id 6D6 _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H28 N8 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 2023-11-03 _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 424.455 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6D6 _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 5ISG _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.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 6D6 C1 C4 C 0 1 N N N Y N Y 52.620 31.191 129.501 -3.817 3.851 2.064 C1 6D6 1 6D6 C2 C5 C 0 1 N N N N N N 52.397 32.715 129.578 -3.534 2.403 1.659 C2 6D6 2 6D6 C3 C6 C 0 1 N N N N N N 51.508 33.036 130.784 -3.012 2.368 0.222 C3 6D6 3 6D6 C4 C8 C 0 1 N N N N N N 52.494 34.867 132.028 -3.798 0.139 -0.302 C4 6D6 4 6D6 C5 C10 C 0 1 N N S N N N 52.985 36.027 134.295 -4.599 -2.222 -0.465 C5 6D6 5 6D6 C6 C15 C 0 1 N N N N N N 51.281 35.266 129.952 -1.767 0.976 -1.320 C6 6D6 6 6D6 C7 C21 C 0 1 N N S N N N 49.157 36.673 130.184 0.412 1.766 -2.293 C7 6D6 7 6D6 C8 C24 C 0 1 Y N N N N N 50.255 37.895 126.388 2.018 -1.264 0.560 C8 6D6 8 6D6 C9 C26 C 0 1 Y N N N N N 50.472 39.941 125.622 4.157 -1.314 0.913 C9 6D6 9 6D6 N1 N2 N 0 1 N Y N Y N Y 53.525 30.883 128.447 -4.319 3.885 3.444 N1 6D6 10 6D6 N2 N7 N 0 1 N N N N N N 51.393 34.451 131.132 -2.618 0.995 -0.123 N2 6D6 11 6D6 C10 C9 C 0 1 N N N N N N 51.925 35.607 133.299 -3.374 -1.330 -0.253 C10 6D6 12 6D6 N3 N11 N 0 1 N N N N N N 54.048 36.746 133.627 -5.532 -2.049 0.656 N3 6D6 13 6D6 C11 C12 C 0 1 N N N N N N 53.605 34.824 135.071 -4.165 -3.663 -0.539 C11 6D6 14 6D6 O1 O13 O 0 1 N N N N N N 54.835 34.527 134.899 -4.278 -4.378 0.428 O1 6D6 15 6D6 O2 O14 O 0 1 N N N N N N 52.877 34.148 135.879 -3.653 -4.152 -1.679 O2 6D6 16 6D6 C12 C16 C 0 1 N N R N N N 50.629 36.673 130.335 -0.438 1.669 -1.011 C12 6D6 17 6D6 O3 O17 O 0 1 N N N N N N 51.158 37.700 129.434 0.309 0.892 -0.060 O3 6D6 18 6D6 C13 C18 C 0 1 N N R N N N 49.980 38.393 128.818 1.706 1.053 -0.390 C13 6D6 19 6D6 C14 C19 C 0 1 N N R N N N 48.839 37.396 128.952 1.719 1.015 -1.939 C14 6D6 20 6D6 O4 O20 O 0 1 N N N N N N 47.579 38.063 129.029 2.859 1.703 -2.457 O4 6D6 21 6D6 O5 O22 O 0 1 N N N N N N 48.596 37.355 131.331 0.690 3.132 -2.607 O5 6D6 22 6D6 N4 N23 N 0 1 Y N N N N N 50.139 38.729 127.425 2.496 -0.052 0.160 N4 6D6 23 6D6 N5 N25 N 0 1 Y N N N N N 50.439 38.623 125.271 2.994 -2.003 1.002 N5 6D6 24 6D6 C15 C27 C 0 1 Y N N N N N 50.643 41.140 124.897 5.498 -1.594 1.227 C15 6D6 25 6D6 N6 N28 N 0 1 N N N N N N 50.828 41.074 123.484 5.859 -2.816 1.767 N6 6D6 26 6D6 N7 N29 N 0 1 Y N N N N N 50.627 42.313 125.549 6.411 -0.657 0.994 N7 6D6 27 6D6 C16 C30 C 0 1 Y N N N N N 50.453 42.351 126.877 6.076 0.512 0.479 C16 6D6 28 6D6 N8 N31 N 0 1 Y N N N N N 50.290 41.219 127.608 4.833 0.821 0.177 N8 6D6 29 6D6 C17 C32 C 0 1 Y N N N N N 50.294 40.011 126.974 3.852 -0.056 0.367 C17 6D6 30 6D6 H1 H1 H 0 1 N N N Y N Y 51.658 30.691 129.313 -2.898 4.433 1.997 H1 6D6 31 6D6 H2 H33 H 0 1 N N N Y N Y 53.037 30.836 130.455 -4.565 4.276 1.395 H2 6D6 32 6D6 H3 H2 H 0 1 N N N N N N 53.366 33.223 129.690 -2.786 1.979 2.329 H3 6D6 33 6D6 H4 H34 H 0 1 N N N N N N 51.906 33.062 128.657 -4.454 1.821 1.726 H4 6D6 34 6D6 H5 H3 H 0 1 N N N N N N 50.498 32.659 130.568 -3.795 2.703 -0.458 H5 6D6 35 6D6 H6 H4 H 0 1 N N N N N N 51.919 32.506 131.656 -2.148 3.027 0.133 H6 6D6 36 6D6 H7 H5 H 0 1 N N N N N N 53.055 33.977 132.349 -4.516 0.337 0.494 H7 6D6 37 6D6 H8 H6 H 0 1 N N N N N N 53.166 35.547 131.484 -4.258 0.352 -1.267 H8 6D6 38 6D6 H9 H7 H 0 1 N N N N N N 52.514 36.691 135.035 -5.094 -1.944 -1.396 H9 6D6 39 6D6 H10 H8 H 0 1 N N N N N N 50.645 34.756 129.214 -1.578 -0.056 -1.615 H10 6D6 40 6D6 H11 H9 H 0 1 N N N N N N 52.281 35.430 129.524 -2.270 1.501 -2.132 H11 6D6 41 6D6 H12 H10 H 0 1 N N N N N N 48.783 35.640 130.128 -0.096 1.280 -3.126 H12 6D6 42 6D6 H13 H11 H 0 1 N N N N N N 50.209 36.817 126.438 0.981 -1.566 0.521 H13 6D6 43 6D6 H14 HE*1 H 0 1 N Y N Y N Y 53.664 29.894 128.404 -3.671 3.439 4.076 H14 6D6 44 6D6 H15 HE*2 H 0 1 N Y N Y N Y 53.147 31.204 127.579 -4.514 4.832 3.735 H15 6D6 45 6D6 H18 H19 H 0 1 N N N N N N 51.390 36.508 132.964 -2.643 -1.524 -1.037 H18 6D6 46 6D6 H19 H20 H 0 1 N N N N N N 51.222 34.930 133.807 -2.931 -1.548 0.719 H19 6D6 47 6D6 H20 H21 H 0 1 N N N N N N 54.740 37.017 134.296 -5.096 -2.300 1.531 H20 6D6 48 6D6 H21 H22 H 0 1 N N N N N N 54.466 36.156 132.936 -5.888 -1.105 0.688 H21 6D6 49 6D6 H23 H15 H 0 1 N N N N N N 53.398 33.458 136.274 -3.388 -5.082 -1.678 H23 6D6 50 6D6 H24 H25 H 0 1 N N N N N N 50.898 36.908 131.375 -0.624 2.667 -0.614 H24 6D6 51 6D6 H25 H26 H 0 1 N N N N N N 49.741 39.294 129.401 2.078 2.010 -0.026 H25 6D6 52 6D6 H26 H27 H 0 1 N N N N N N 48.859 36.706 128.095 1.688 -0.012 -2.303 H26 6D6 53 6D6 H27 H28 H 0 1 N N N N N N 46.884 37.420 129.112 2.911 1.706 -3.422 H27 6D6 54 6D6 H28 H29 H 0 1 N N N N N N 48.811 36.874 132.122 1.223 3.252 -3.405 H28 6D6 55 6D6 H29 H31 H 0 1 N N N N N N 50.933 41.998 123.118 6.787 -2.997 1.980 H29 6D6 56 6D6 H30 H30 H 0 1 N N N N N N 51.648 40.539 123.280 5.182 -3.491 1.933 H30 6D6 57 6D6 H31 H32 H 0 1 N N N N N N 50.442 43.307 127.379 6.850 1.245 0.306 H31 6D6 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 6D6 N6 C15 SING N N 1 6D6 C15 N7 DOUB Y N 2 6D6 C15 C9 SING Y N 3 6D6 N5 C9 SING Y N 4 6D6 N5 C8 DOUB Y N 5 6D6 N7 C16 SING Y N 6 6D6 C9 C17 DOUB Y N 7 6D6 C8 N4 SING Y N 8 6D6 C16 N8 DOUB Y N 9 6D6 C17 N4 SING Y N 10 6D6 C17 N8 SING Y N 11 6D6 N4 C13 SING N N 12 6D6 N1 C1 SING N N 13 6D6 C13 C14 SING N N 14 6D6 C13 O3 SING N N 15 6D6 C14 O4 SING N N 16 6D6 C14 C7 SING N N 17 6D6 O3 C12 SING N N 18 6D6 C1 C2 SING N N 19 6D6 C2 C3 SING N N 20 6D6 C6 C12 SING N N 21 6D6 C6 N2 SING N N 22 6D6 C7 C12 SING N N 23 6D6 C7 O5 SING N N 24 6D6 C3 N2 SING N N 25 6D6 N2 C4 SING N N 26 6D6 C4 C10 SING N N 27 6D6 C10 C5 SING N N 28 6D6 N3 C5 SING N N 29 6D6 C5 C11 SING N N 30 6D6 O1 C11 DOUB N N 31 6D6 C11 O2 SING N N 32 6D6 C1 H1 SING N N 33 6D6 C1 H2 SING N N 34 6D6 C2 H3 SING N N 35 6D6 C2 H4 SING N N 36 6D6 C3 H5 SING N N 37 6D6 C3 H6 SING N N 38 6D6 C4 H7 SING N N 39 6D6 C4 H8 SING N N 40 6D6 C5 H9 SING N N 41 6D6 C6 H10 SING N N 42 6D6 C6 H11 SING N N 43 6D6 C7 H12 SING N N 44 6D6 C8 H13 SING N N 45 6D6 N1 H14 SING N N 46 6D6 N1 H15 SING N N 47 6D6 C10 H18 SING N N 48 6D6 C10 H19 SING N N 49 6D6 N3 H20 SING N N 50 6D6 N3 H21 SING N N 51 6D6 O2 H23 SING N N 52 6D6 C12 H24 SING N N 53 6D6 C13 H25 SING N N 54 6D6 C14 H26 SING N N 55 6D6 O4 H27 SING N N 56 6D6 O5 H28 SING N N 57 6D6 N6 H29 SING N N 58 6D6 N6 H30 SING N N 59 6D6 C16 H31 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 6D6 SMILES ACDLabs 12.01 "C(CCN(CCC(C(O)=O)N)CC1C(O)C(C(O1)n2cnc3c2ncnc3N)O)N" 6D6 InChI InChI 1.03 "InChI=1S/C17H28N8O5/c18-3-1-4-24(5-2-9(19)17(28)29)6-10-12(26)13(27)16(30-10)25-8-23-11-14(20)21-7-22-15(11)25/h7-10,12-13,16,26-27H,1-6,18-19H2,(H,28,29)(H2,20,21,22)/t9-,10+,12+,13+,16+/m0/s1" 6D6 InChIKey InChI 1.03 NHAKJKNYYCYZBR-UOYPZJKHSA-N 6D6 SMILES_CANONICAL CACTVS 3.385 "NCCCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" 6D6 SMILES CACTVS 3.385 "NCCCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" 6D6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CCCN)CC[C@@H](C(=O)O)N)O)O)N" 6D6 SMILES "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCN)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 6D6 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine" 6D6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "(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-azanylpropyl)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 6D6 "Create component" 2016-03-16 EBI 6D6 "Initial release" 2017-03-15 RCSB 6D6 "Modify leaving atom flag" 2021-08-26 PDBE 6D6 "Modify backbone" 2023-11-03 PDBE #