data_6YB # _chem_comp.id 6YB _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-(2-carbamimidamidoethyl)amino]-2-azanyl-butanoic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 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 2016-07-22 _chem_comp.pdbx_modified_date 2017-08-11 _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 452.468 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6YB _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 5LKJ _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 6YB N1 N1 N 0 1 Y N N 50.574 42.021 126.715 -6.469 -0.498 1.643 N1 6YB 1 6YB C2 C1 C 0 1 Y N N 50.387 41.983 128.044 -6.026 -1.536 0.958 C2 6YB 2 6YB N3 N2 N 0 1 Y N N 50.245 40.807 128.704 -4.821 -1.572 0.429 N3 6YB 3 6YB C4 C2 C 0 1 Y N N 50.287 39.647 128.020 -3.990 -0.544 0.567 C4 6YB 4 6YB C6 C3 C 0 1 Y N N 50.628 40.877 125.993 -5.709 0.576 1.833 C6 6YB 5 6YB N10 N3 N 0 1 N N N 51.790 31.058 129.882 4.693 -2.760 0.865 N10 6YB 6 6YB C11 C4 C 0 1 N N N 52.338 32.202 130.714 3.889 -1.541 0.740 C11 6YB 7 6YB C10 C5 C 0 1 N N N 51.308 32.619 131.749 3.151 -1.553 -0.600 C10 6YB 8 6YB ND N4 N 0 1 N N N 51.349 34.042 132.133 2.346 -0.331 -0.726 ND 6YB 9 6YB "C5'" C6 C 0 1 N N N 51.235 34.943 130.920 1.443 -0.412 -1.883 "C5'" 6YB 10 6YB "C4'" C7 C 0 1 N N R 50.497 36.241 131.301 0.272 -1.338 -1.551 "C4'" 6YB 11 6YB "O4'" O1 O 0 1 N N N 51.059 37.331 130.549 -0.456 -0.822 -0.425 "O4'" 6YB 12 6YB "C1'" C8 C 0 1 N N R 49.978 37.990 129.827 -1.846 -1.152 -0.634 "C1'" 6YB 13 6YB N9 N5 N 0 1 Y N N 50.164 38.355 128.415 -2.710 -0.270 0.155 N9 6YB 14 6YB C5 C9 C 0 1 Y N N 50.483 39.651 126.639 -4.415 0.586 1.288 C5 6YB 15 6YB N6 N6 N 0 1 N N N 50.837 40.911 124.520 -6.183 1.659 2.553 N6 6YB 16 6YB N7 N7 N 0 1 Y N N 50.485 38.360 126.235 -3.391 1.473 1.278 N7 6YB 17 6YB C8 C10 C 0 1 Y N N 50.304 37.564 127.328 -2.390 0.973 0.614 C8 6YB 18 6YB "C2'" C11 C 0 1 N N R 48.812 37.012 129.825 -2.052 -0.909 -2.150 "C2'" 6YB 19 6YB "O2'" O2 O 0 1 N N N 47.528 37.677 129.861 -3.139 -1.690 -2.650 "O2'" 6YB 20 6YB "C3'" C12 C 0 1 N N S 49.025 36.209 131.038 -0.704 -1.396 -2.743 "C3'" 6YB 21 6YB "O3'" O3 O 0 1 N N N 48.377 36.800 132.111 -0.826 -2.734 -3.230 "O3'" 6YB 22 6YB CG C13 C 0 1 N N N 52.494 34.350 132.989 3.203 0.859 -0.810 CG 6YB 23 6YB CB C14 C 0 1 N N N 52.019 35.132 134.197 2.365 2.112 -0.550 CB 6YB 24 6YB CA C15 C 0 1 N N S 53.079 35.481 135.284 3.279 3.338 -0.510 CA 6YB 25 6YB C C16 C 0 1 N N N 52.986 34.552 136.461 2.441 4.585 -0.386 C 6YB 26 6YB O O4 O 0 1 N N N 53.957 33.803 136.754 2.285 5.104 0.694 O 6YB 27 6YB N N8 N 0 1 N N N 54.409 35.502 134.762 4.181 3.238 0.645 N 6YB 28 6YB C12 C17 C 0 1 N N N 52.012 29.678 130.271 5.448 -2.972 1.994 C12 6YB 29 6YB N12 N9 N 0 1 N N N 52.768 29.364 131.455 6.163 -4.056 2.105 N12 6YB 30 6YB N11 N10 N 0 1 N N N 51.524 28.709 129.540 5.450 -2.041 3.005 N11 6YB 31 6YB OXT O5 O 0 1 N N N 51.913 34.532 137.173 1.868 5.119 -1.476 OXT 6YB 32 6YB H21 H1 H 0 1 N N N 50.349 42.909 128.599 -6.676 -2.388 0.827 H21 6YB 33 6YB H103 H2 H 0 0 N N N 51.268 31.258 129.053 4.692 -3.417 0.152 H103 6YB 34 6YB H112 H3 H 0 0 N N N 53.257 31.877 131.223 3.165 -1.498 1.553 H112 6YB 35 6YB H111 H4 H 0 0 N N N 52.564 33.056 130.058 4.542 -0.669 0.788 H111 6YB 36 6YB H102 H5 H 0 0 N N N 50.309 32.404 131.341 3.875 -1.596 -1.414 H102 6YB 37 6YB H101 H6 H 0 0 N N N 51.472 32.017 132.655 2.499 -2.425 -0.648 H101 6YB 38 6YB "H5'2" H8 H 0 0 N N N 50.674 34.422 130.130 1.065 0.583 -2.118 "H5'2" 6YB 39 6YB "H5'1" H9 H 0 0 N N N 52.242 35.190 130.553 1.987 -0.806 -2.741 "H5'1" 6YB 40 6YB "H4'1" H10 H 0 0 N N N 50.657 36.420 132.375 0.642 -2.338 -1.327 "H4'1" 6YB 41 6YB "H1'1" H11 H 0 0 N N N 49.671 38.886 130.386 -2.035 -2.196 -0.383 "H1'1" 6YB 42 6YB H62 H12 H 0 1 N N N 50.919 41.860 124.216 -5.618 2.437 2.686 H62 6YB 43 6YB H61 H13 H 0 1 N N N 51.674 40.414 124.291 -7.078 1.641 2.924 H61 6YB 44 6YB H81 H14 H 0 1 N N N 50.277 36.484 127.325 -1.445 1.469 0.451 H81 6YB 45 6YB "H2'1" H15 H 0 0 N N N 48.882 36.369 128.935 -2.209 0.150 -2.357 "H2'1" 6YB 46 6YB "H2'2" H16 H 0 0 N N N 46.834 37.028 129.858 -3.307 -1.572 -3.595 "H2'2" 6YB 47 6YB "H3'1" H17 H 0 0 N N N 48.691 35.173 130.878 -0.373 -0.729 -3.539 "H3'1" 6YB 48 6YB "H3'2" H18 H 0 0 N N N 48.517 36.278 132.892 -1.472 -2.836 -3.942 "H3'2" 6YB 49 6YB HG3 H19 H 0 1 N N N 52.968 33.414 133.320 3.994 0.790 -0.063 HG3 6YB 50 6YB HG2 H20 H 0 1 N N N 53.223 34.951 132.426 3.646 0.918 -1.804 HG2 6YB 51 6YB HB3 H21 H 0 1 N N N 51.596 36.079 133.832 1.632 2.231 -1.348 HB3 6YB 52 6YB HB2 H22 H 0 1 N N N 51.229 34.541 134.684 1.848 2.012 0.405 HB2 6YB 53 6YB HA H23 H 0 1 N N N 52.837 36.491 135.646 3.866 3.384 -1.427 HA 6YB 54 6YB H H24 H 0 1 N N N 55.051 35.730 135.494 3.661 3.194 1.508 H 6YB 55 6YB H2 H25 H 0 1 N N N 54.635 34.602 134.389 4.798 2.445 0.554 H2 6YB 56 6YB H121 H27 H 0 0 N N N 53.087 30.187 131.925 6.162 -4.714 1.392 H121 6YB 57 6YB H113 H28 H 0 0 N N N 51.677 27.757 129.805 4.918 -1.234 2.922 H113 6YB 58 6YB H4 H29 H 0 1 N N N 50.998 28.920 128.716 5.983 -2.190 3.802 H4 6YB 59 6YB H5 H30 H 0 1 N N N 52.012 33.903 137.878 1.340 5.919 -1.347 H5 6YB 60 # 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 6YB N6 C6 SING N N 1 6YB C6 C5 DOUB Y N 2 6YB C6 N1 SING Y N 3 6YB N7 C5 SING Y N 4 6YB N7 C8 DOUB Y N 5 6YB C5 C4 SING Y N 6 6YB N1 C2 DOUB Y N 7 6YB C8 N9 SING Y N 8 6YB C4 N9 SING Y N 9 6YB C4 N3 DOUB Y N 10 6YB C2 N3 SING Y N 11 6YB N9 "C1'" SING N N 12 6YB N11 C12 SING N N 13 6YB "C2'" "C1'" SING N N 14 6YB "C2'" "O2'" SING N N 15 6YB "C2'" "C3'" SING N N 16 6YB "C1'" "O4'" SING N N 17 6YB N10 C12 SING N N 18 6YB N10 C11 SING N N 19 6YB C12 N12 DOUB N N 20 6YB "O4'" "C4'" SING N N 21 6YB C11 C10 SING N N 22 6YB "C5'" "C4'" SING N N 23 6YB "C5'" ND SING N N 24 6YB "C3'" "C4'" SING N N 25 6YB "C3'" "O3'" SING N N 26 6YB C10 ND SING N N 27 6YB ND CG SING N N 28 6YB CG CB SING N N 29 6YB CB CA SING N N 30 6YB N CA SING N N 31 6YB CA C SING N N 32 6YB C O DOUB N N 33 6YB C OXT SING N N 34 6YB C2 H21 SING N N 35 6YB N10 H103 SING N N 36 6YB C11 H112 SING N N 37 6YB C11 H111 SING N N 38 6YB C10 H102 SING N N 39 6YB C10 H101 SING N N 40 6YB "C5'" "H5'2" SING N N 41 6YB "C5'" "H5'1" SING N N 42 6YB "C4'" "H4'1" SING N N 43 6YB "C1'" "H1'1" SING N N 44 6YB N6 H62 SING N N 45 6YB N6 H61 SING N N 46 6YB C8 H81 SING N N 47 6YB "C2'" "H2'1" SING N N 48 6YB "O2'" "H2'2" SING N N 49 6YB "C3'" "H3'1" SING N N 50 6YB "O3'" "H3'2" SING N N 51 6YB CG HG3 SING N N 52 6YB CG HG2 SING N N 53 6YB CB HB3 SING N N 54 6YB CB HB2 SING N N 55 6YB CA HA SING N N 56 6YB N H SING N N 57 6YB N H2 SING N N 58 6YB N12 H121 SING N N 59 6YB N11 H113 SING N N 60 6YB N11 H4 SING N N 61 6YB OXT H5 SING N N 62 # 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 6YB InChI InChI 1.03 "InChI=1S/C17H28N10O5/c18-8(16(30)31)1-3-26(4-2-22-17(20)21)5-9-11(28)12(29)15(32-9)27-7-25-10-13(19)23-6-24-14(10)27/h6-9,11-12,15,28-29H,1-5,18H2,(H,30,31)(H2,19,23,24)(H4,20,21,22)/t8-,9+,11+,12+,15+/m0/s1" 6YB InChIKey InChI 1.03 JNOBHECZYPSIIL-OPYVMVOTSA-N 6YB SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCN(CCNC(N)=N)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O" 6YB SMILES CACTVS 3.385 "N[CH](CCN(CCNC(N)=N)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O" 6YB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "[H]/N=C(\N)/NCCN(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" 6YB SMILES "OpenEye OEToolkits" 2.0.5 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCC(C(=O)O)N)CCNC(=N)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 6YB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.5 "(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-carbamimidamidoethyl)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 6YB "Create component" 2016-07-22 EBI 6YB "Initial release" 2017-08-16 RCSB #