data_6D4 # _chem_comp.id 6D4 _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl][2-(triazan-1-yl)ethyl]amino}-5'-deoxyadenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H28 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 2017-03-10 _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 440.458 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6D4 _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 5ISF _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 6D4 C16 C1 C 0 1 N N N 52.453 32.824 130.326 3.617 2.228 -0.923 C16 6D4 1 6D4 C15 C2 C 0 1 N N N 51.730 33.065 131.670 3.028 1.951 0.462 C15 6D4 2 6D4 C14 C3 C 0 1 N N N 53.560 34.689 136.234 3.747 -4.181 0.049 C14 6D4 3 6D4 N10 N1 N 0 1 N N N 52.354 29.889 131.694 3.851 5.041 -2.959 N10 6D4 4 6D4 C11 C4 C 0 1 N N N 52.593 34.924 132.981 3.642 -0.390 0.559 C11 6D4 5 6D4 C12 C5 C 0 1 N N N 51.924 35.220 134.380 3.125 -1.786 0.205 C12 6D4 6 6D4 C01 C6 C 0 1 Y N N 50.312 39.923 127.971 -3.968 0.125 -0.386 C01 6D4 7 6D4 C02 C7 C 0 1 Y N N 50.511 39.881 126.556 -4.332 -0.976 -1.180 C02 6D4 8 6D4 C03 C8 C 0 1 Y N N 50.693 41.079 125.938 -5.672 -1.087 -1.586 C03 6D4 9 6D4 N01 N2 N 0 1 Y N N 50.680 42.211 126.639 -6.530 -0.147 -1.202 N01 6D4 10 6D4 C04 C9 C 0 1 Y N N 50.483 42.136 127.980 -6.141 0.870 -0.455 C04 6D4 11 6D4 N02 N3 N 0 1 Y N N 50.289 41.011 128.726 -4.895 1.017 -0.055 N02 6D4 12 6D4 N03 N4 N 0 1 Y N N 50.165 38.650 128.241 -2.625 -0.015 -0.139 N03 6D4 13 6D4 C05 C10 C 0 1 Y N N 50.245 37.786 127.307 -2.213 -1.157 -0.757 C05 6D4 14 6D4 N04 N5 N 0 1 Y N N 50.463 38.426 126.110 -3.214 -1.717 -1.372 N04 6D4 15 6D4 N05 N6 N 0 1 N N N 50.904 41.111 124.483 -6.089 -2.149 -2.369 N05 6D4 16 6D4 C06 C11 C 0 1 N N R 49.958 38.248 129.590 -1.789 0.897 0.646 C06 6D4 17 6D4 C07 C12 C 0 1 N N R 48.910 37.231 129.811 -1.877 0.555 2.155 C07 6D4 18 6D4 C08 C13 C 0 1 N N S 49.341 36.462 130.983 -0.541 1.122 2.694 C08 6D4 19 6D4 C09 C14 C 0 1 N N R 50.791 36.629 131.129 0.360 1.215 1.447 C09 6D4 20 6D4 O01 O1 O 0 1 N N N 51.258 37.638 130.091 -0.393 0.700 0.337 O01 6D4 21 6D4 O02 O2 O 0 1 N N N 47.639 37.876 130.073 -2.991 1.213 2.763 O02 6D4 22 6D4 O03 O3 O 0 1 N N N 48.683 36.973 132.187 -0.740 2.416 3.265 O03 6D4 23 6D4 C10 C15 C 0 1 N N N 51.516 35.349 130.865 1.625 0.380 1.655 C10 6D4 24 6D4 N06 N7 N 0 1 N N N 51.548 34.492 132.041 2.530 0.570 0.514 N06 6D4 25 6D4 C13 C16 C 0 1 N N S 52.914 35.808 135.433 4.278 -2.789 0.277 C13 6D4 26 6D4 O04 O4 O 0 1 N N N 52.898 34.044 137.084 3.151 -4.845 1.052 O04 6D4 27 6D4 O05 O5 O 0 1 N N N 54.773 34.410 136.039 3.857 -4.700 -1.037 O05 6D4 28 6D4 N07 N8 N 0 1 N N N 53.963 36.578 134.819 5.271 -2.469 -0.757 N07 6D4 29 6D4 N08 N9 N 0 1 N N N 52.996 31.698 130.188 3.998 3.644 -1.018 N08 6D4 30 6D4 N09 N10 N 0 1 N N N 52.678 30.790 130.935 4.563 3.945 -2.323 N09 6D4 31 6D4 H23 H1 H 0 1 N N N 53.235 33.590 130.222 4.498 1.604 -1.074 H23 6D4 32 6D4 H24 H2 H 0 1 N N N 51.714 32.943 129.520 2.874 2.000 -1.686 H24 6D4 33 6D4 H22 H3 H 0 1 N N N 50.735 32.599 131.610 3.800 2.087 1.219 H22 6D4 34 6D4 H21 H4 H 0 1 N N N 52.316 32.579 132.464 2.207 2.641 0.652 H21 6D4 35 6D4 H25 H5 H 0 1 N N N 52.586 29.007 131.283 4.243 5.250 -3.865 H25 6D4 36 6D4 H1 H6 H 0 1 N N N 52.842 29.992 132.561 2.865 4.839 -3.030 H1 6D4 37 6D4 H14 H7 H 0 1 N N N 53.344 34.128 133.091 4.069 -0.404 1.561 H14 6D4 38 6D4 H13 H8 H 0 1 N N N 53.078 35.836 132.602 4.407 -0.093 -0.158 H13 6D4 39 6D4 H15 H9 H 0 1 N N N 51.107 35.941 134.229 2.347 -2.075 0.912 H15 6D4 40 6D4 H16 H10 H 0 1 N N N 51.514 34.279 134.776 2.714 -1.776 -0.804 H16 6D4 41 6D4 H01 H11 H 0 1 N N N 50.480 43.073 128.517 -6.871 1.611 -0.166 H01 6D4 42 6D4 H02 H12 H 0 1 N N N 50.155 36.717 127.436 -1.202 -1.538 -0.745 H02 6D4 43 6D4 H03 H13 H 0 1 N N N 51.020 42.058 124.183 -5.454 -2.828 -2.644 H03 6D4 44 6D4 H04 H14 H 0 1 N N N 51.724 40.586 124.254 -7.018 -2.214 -2.644 H04 6D4 45 6D4 H26 H15 H 0 1 N N N 49.732 39.130 130.206 -2.082 1.932 0.469 H26 6D4 46 6D4 H05 H16 H 0 1 N N N 48.833 36.573 128.933 -1.933 -0.522 2.308 H05 6D4 47 6D4 H06 H17 H 0 1 N N N 49.098 35.398 130.844 -0.107 0.442 3.428 H06 6D4 48 6D4 H07 H18 H 0 1 N N N 51.034 36.997 132.137 0.629 2.255 1.262 H07 6D4 49 6D4 H08 H19 H 0 1 N N N 46.971 37.215 130.214 -3.088 1.030 3.707 H08 6D4 50 6D4 H09 H20 H 0 1 N N N 48.967 36.470 132.941 -1.346 2.425 4.019 H09 6D4 51 6D4 H10 H21 H 0 1 N N N 51.008 34.814 130.049 2.123 0.697 2.571 H10 6D4 52 6D4 H11 H22 H 0 1 N N N 52.549 35.580 130.565 1.355 -0.674 1.734 H11 6D4 53 6D4 H17 H24 H 0 1 N N N 52.341 36.446 136.122 4.746 -2.735 1.260 H17 6D4 54 6D4 H2 H25 H 0 1 N N N 53.454 33.388 137.487 2.827 -5.735 0.858 H2 6D4 55 6D4 H20 H26 H 0 1 N N N 54.573 36.935 135.527 4.861 -2.512 -1.678 H20 6D4 56 6D4 H19 H27 H 0 1 N N N 54.483 35.995 134.195 5.689 -1.566 -0.590 H19 6D4 57 6D4 H3 H29 H 0 1 N N N 52.801 31.392 129.256 3.212 4.244 -0.817 H3 6D4 58 6D4 H4 H30 H 0 1 N N N 52.138 30.373 130.204 4.567 3.126 -2.913 H4 6D4 59 # 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 6D4 N05 C03 SING N N 1 6D4 C03 C02 DOUB Y N 2 6D4 C03 N01 SING Y N 3 6D4 N04 C02 SING Y N 4 6D4 N04 C05 DOUB Y N 5 6D4 C02 C01 SING Y N 6 6D4 N01 C04 DOUB Y N 7 6D4 C05 N03 SING Y N 8 6D4 C01 N03 SING Y N 9 6D4 C01 N02 DOUB Y N 10 6D4 C04 N02 SING Y N 11 6D4 N03 C06 SING N N 12 6D4 C06 C07 SING N N 13 6D4 C06 O01 SING N N 14 6D4 C07 O02 SING N N 15 6D4 C07 C08 SING N N 16 6D4 O01 C09 SING N N 17 6D4 N08 C16 SING N N 18 6D4 N08 N09 SING N N 19 6D4 C16 C15 SING N N 20 6D4 C10 C09 SING N N 21 6D4 C10 N06 SING N N 22 6D4 N09 N10 SING N N 23 6D4 C08 C09 SING N N 24 6D4 C08 O03 SING N N 25 6D4 C15 N06 SING N N 26 6D4 N06 C11 SING N N 27 6D4 C11 C12 SING N N 28 6D4 C12 C13 SING N N 29 6D4 N07 C13 SING N N 30 6D4 C13 C14 SING N N 31 6D4 O05 C14 DOUB N N 32 6D4 C14 O04 SING N N 33 6D4 C16 H23 SING N N 34 6D4 C16 H24 SING N N 35 6D4 C15 H22 SING N N 36 6D4 C15 H21 SING N N 37 6D4 N10 H25 SING N N 38 6D4 N10 H1 SING N N 39 6D4 C11 H14 SING N N 40 6D4 C11 H13 SING N N 41 6D4 C12 H15 SING N N 42 6D4 C12 H16 SING N N 43 6D4 C04 H01 SING N N 44 6D4 C05 H02 SING N N 45 6D4 N05 H03 SING N N 46 6D4 N05 H04 SING N N 47 6D4 C06 H26 SING N N 48 6D4 C07 H05 SING N N 49 6D4 C08 H06 SING N N 50 6D4 C09 H07 SING N N 51 6D4 O02 H08 SING N N 52 6D4 O03 H09 SING N N 53 6D4 C10 H10 SING N N 54 6D4 C10 H11 SING N N 55 6D4 C13 H17 SING N N 56 6D4 O04 H2 SING N N 57 6D4 N07 H20 SING N N 58 6D4 N07 H19 SING N N 59 6D4 N08 H3 SING N N 60 6D4 N09 H4 SING N N 61 # 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 6D4 SMILES ACDLabs 12.01 "C(CN(CCC(C(O)=O)N)CC3C(C(C(n2c1ncnc(c1nc2)N)O3)O)O)NNN" 6D4 InChI InChI 1.03 "InChI=1S/C16H28N10O5/c17-8(16(29)30)1-3-25(4-2-23-24-19)5-9-11(27)12(28)15(31-9)26-7-22-10-13(18)20-6-21-14(10)26/h6-9,11-12,15,23-24,27-28H,1-5,17,19H2,(H,29,30)(H2,18,20,21)/t8-,9+,11+,12+,15+/m0/s1" 6D4 InChIKey InChI 1.03 VMVULOLZRIEVIA-OPYVMVOTSA-N 6D4 SMILES_CANONICAL CACTVS 3.385 "NNNCCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" 6D4 SMILES CACTVS 3.385 "NNNCCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" 6D4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CC[C@@H](C(=O)O)N)CCNNN)O)O)N" 6D4 SMILES "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCC(C(=O)O)N)CCNNN)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 6D4 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(3S)-3-amino-3-carboxypropyl][2-(triazan-1-yl)ethyl]amino}-5'-deoxyadenosine" 6D4 "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-[2-(2-azanylhydrazinyl)ethyl]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 6D4 "Create component" 2016-03-16 EBI 6D4 "Initial release" 2017-03-15 RCSB #