data_KYB # _chem_comp.id KYB _chem_comp.name "1-[5-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azanylpropyl)amino]pentyl]guanidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H34 N10 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-07-04 _chem_comp.pdbx_modified_date 2020-02-28 _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 450.538 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KYB _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 6S70 _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 KYB C13 C1 C 0 1 Y N N 16.252 23.819 12.366 5.576 -1.422 0.235 C13 KYB 1 KYB C15 C2 C 0 1 Y N N 15.180 24.976 13.830 3.584 -1.209 -0.595 C15 KYB 2 KYB C17 C3 C 0 1 N N R 14.427 28.749 13.617 0.797 1.826 -0.226 C17 KYB 3 KYB C18 C4 C 0 1 N N N 14.804 29.241 15.026 -0.468 1.525 -1.032 C18 KYB 4 KYB C20 C5 C 0 1 N N N 14.115 31.554 14.624 -1.001 -0.573 0.054 C20 KYB 5 KYB C21 C6 C 0 1 N N N 15.338 32.511 14.906 -0.853 -1.296 -1.286 C21 KYB 6 KYB C22 C7 C 0 1 N N N 15.460 33.661 13.844 -0.531 -2.771 -1.036 C22 KYB 7 KYB C28 C8 C 0 1 N N N 12.766 31.027 20.473 -7.618 -0.050 0.093 C28 KYB 8 KYB N32 N1 N 0 1 N N N 12.259 29.734 23.132 -10.312 -0.326 -0.454 N32 KYB 9 KYB C02 C9 C 0 1 N N S 12.908 28.096 13.504 1.771 2.691 -1.057 C02 KYB 10 KYB C03 C10 C 0 1 N N R 13.028 26.813 13.192 3.169 2.152 -0.678 C03 KYB 11 KYB C05 C11 C 0 1 N N R 14.437 26.727 12.553 2.874 1.026 0.338 C05 KYB 12 KYB C07 C12 C 0 1 Y N N 15.727 24.893 11.755 5.064 -0.195 0.688 C07 KYB 13 KYB C09 C13 C 0 1 Y N N 16.654 24.194 9.765 7.020 0.179 1.834 C09 KYB 14 KYB C11 C14 C 0 1 Y N N 17.004 22.894 11.582 6.868 -1.794 0.646 C11 KYB 15 KYB C24 C15 C 0 1 N N N 14.376 30.754 16.913 -2.779 0.852 -0.767 C24 KYB 16 KYB C25 C16 C 0 1 N N N 14.096 29.747 18.037 -3.808 0.466 0.298 C25 KYB 17 KYB C26 C17 C 0 1 N N N 14.923 30.142 19.379 -5.198 0.401 -0.337 C26 KYB 18 KYB C27 C18 C 0 1 N N N 14.087 30.196 20.679 -6.227 0.015 0.728 C27 KYB 19 KYB C30 C19 C 0 1 N N N 12.061 31.056 22.830 -9.930 -0.540 0.774 C30 KYB 20 KYB N06 N2 N 0 1 Y N N 15.049 25.594 12.705 3.807 -0.088 0.149 N06 KYB 21 KYB N08 N3 N 0 1 Y N N 15.936 25.070 10.455 5.813 0.566 1.478 N08 KYB 22 KYB N10 N4 N 0 1 Y N N 17.178 23.124 10.339 7.543 -0.967 1.437 N10 KYB 23 KYB N12 N5 N 0 1 N N N 17.576 21.713 12.184 7.423 -2.994 0.236 N12 KYB 24 KYB N14 N6 N 0 1 Y N N 15.919 23.887 13.629 4.624 -1.990 -0.543 N14 KYB 25 KYB N19 N7 N 0 1 N N N 14.011 30.360 15.527 -1.431 0.812 -0.183 N19 KYB 26 KYB N23 N8 N 0 1 N N N 16.930 33.837 13.487 -0.389 -3.466 -2.322 N23 KYB 27 KYB N29 N9 N 0 1 N N N 12.278 31.660 21.675 -8.603 -0.419 1.113 N29 KYB 28 KYB N31 N10 N 0 1 N N N 11.611 31.868 23.807 -10.855 -0.887 1.731 N31 KYB 29 KYB O01 O1 O 0 1 N N N 12.265 29.013 12.532 1.648 4.068 -0.699 O01 KYB 30 KYB O04 O2 O 0 1 N N N 12.061 26.403 12.213 3.955 3.181 -0.074 O04 KYB 31 KYB O16 O3 O 0 1 N N N 15.243 27.810 13.339 1.522 0.607 0.045 O16 KYB 32 KYB H1 H1 H 0 1 N N N 14.761 25.289 14.775 2.678 -1.418 -1.145 H1 KYB 33 KYB H2 H2 H 0 1 N N N 14.481 29.594 12.914 0.542 2.331 0.705 H2 KYB 34 KYB H3 H3 H 0 1 N N N 14.684 28.399 15.724 -0.910 2.460 -1.377 H3 KYB 35 KYB H4 H4 H 0 1 N N N 15.859 29.553 15.007 -0.213 0.905 -1.891 H4 KYB 36 KYB H5 H5 H 0 1 N N N 13.192 32.142 14.731 -1.745 -1.085 0.664 H5 KYB 37 KYB H6 H6 H 0 1 N N N 14.200 31.191 13.589 -0.043 -0.571 0.574 H6 KYB 38 KYB H7 H7 H 0 1 N N N 16.263 31.916 14.889 -1.785 -1.218 -1.846 H7 KYB 39 KYB H8 H8 H 0 1 N N N 15.211 32.962 15.901 -0.045 -0.840 -1.858 H8 KYB 40 KYB H9 H9 H 0 1 N N N 15.066 34.598 14.265 0.401 -2.850 -0.476 H9 KYB 41 KYB H10 H10 H 0 1 N N N 14.889 33.395 12.942 -1.339 -3.227 -0.464 H10 KYB 42 KYB H11 H11 H 0 1 N N N 12.962 31.809 19.725 -7.873 0.925 -0.323 H11 KYB 43 KYB H12 H12 H 0 1 N N N 11.986 30.349 20.098 -7.620 -0.796 -0.701 H12 KYB 44 KYB H13 H13 H 0 1 N N N 12.034 29.530 24.085 -11.248 -0.412 -0.693 H13 KYB 45 KYB H14 H14 H 0 1 N N N 12.431 28.225 14.487 1.587 2.556 -2.123 H14 KYB 46 KYB H15 H15 H 0 1 N N N 12.991 26.158 14.075 3.675 1.752 -1.556 H15 KYB 47 KYB H16 H16 H 0 1 N N N 14.369 27.035 11.499 2.941 1.407 1.357 H16 KYB 48 KYB H17 H17 H 0 1 N N N 16.815 24.358 8.710 7.604 0.821 2.477 H17 KYB 49 KYB H18 H18 H 0 1 N N N 15.456 30.964 16.921 -2.835 0.149 -1.598 H18 KYB 50 KYB H19 H19 H 0 1 N N N 13.821 31.674 17.150 -2.989 1.859 -1.127 H19 KYB 51 KYB H20 H20 H 0 1 N N N 13.019 29.747 18.263 -3.552 -0.508 0.714 H20 KYB 52 KYB H21 H21 H 0 1 N N N 14.401 28.743 17.707 -3.806 1.212 1.092 H21 KYB 53 KYB H22 H22 H 0 1 N N N 15.720 29.397 19.518 -5.454 1.375 -0.753 H22 KYB 54 KYB H23 H23 H 0 1 N N N 15.372 31.134 19.222 -5.200 -0.345 -1.131 H23 KYB 55 KYB H24 H24 H 0 1 N N N 13.823 29.171 20.978 -6.225 0.762 1.522 H24 KYB 56 KYB H25 H25 H 0 1 N N N 14.687 30.667 21.472 -5.972 -0.959 1.144 H25 KYB 57 KYB H26 H26 H 0 1 N N N 18.072 21.191 11.490 6.920 -3.589 -0.341 H26 KYB 58 KYB H27 H27 H 0 1 N N N 18.206 21.982 12.912 8.315 -3.239 0.527 H27 KYB 59 KYB H29 H29 H 0 1 N N N 17.024 34.567 12.810 -0.176 -4.443 -2.184 H29 KYB 60 KYB H30 H30 H 0 1 N N N 17.446 34.076 14.309 -1.217 -3.353 -2.888 H30 KYB 61 KYB H32 H32 H 0 1 N N N 12.088 32.641 21.630 -8.319 -0.578 2.026 H32 KYB 62 KYB H33 H33 H 0 1 N N N 11.432 31.501 24.720 -11.791 -0.972 1.492 H33 KYB 63 KYB H34 H34 H 0 1 N N N 11.456 32.838 23.619 -10.571 -1.046 2.645 H34 KYB 64 KYB H35 H35 H 0 1 N N N 12.249 29.893 12.889 2.237 4.657 -1.190 H35 KYB 65 KYB H36 H36 H 0 1 N N N 11.190 26.450 12.589 4.119 3.940 -0.650 H36 KYB 66 # # 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 KYB C09 N10 DOUB Y N 1 KYB C09 N08 SING Y N 2 KYB N10 C11 SING Y N 3 KYB N08 C07 DOUB Y N 4 KYB C11 N12 SING N N 5 KYB C11 C13 DOUB Y N 6 KYB C07 C13 SING Y N 7 KYB C07 N06 SING Y N 8 KYB O04 C03 SING N N 9 KYB C13 N14 SING Y N 10 KYB O01 C02 SING N N 11 KYB C05 N06 SING N N 12 KYB C05 C03 SING N N 13 KYB C05 O16 SING N N 14 KYB N06 C15 SING Y N 15 KYB C03 C02 SING N N 16 KYB O16 C17 SING N N 17 KYB N23 C22 SING N N 18 KYB C02 C17 SING N N 19 KYB C17 C18 SING N N 20 KYB N14 C15 DOUB Y N 21 KYB C22 C21 SING N N 22 KYB C20 C21 SING N N 23 KYB C20 N19 SING N N 24 KYB C18 N19 SING N N 25 KYB N19 C24 SING N N 26 KYB C24 C25 SING N N 27 KYB C25 C26 SING N N 28 KYB C26 C27 SING N N 29 KYB C28 C27 SING N N 30 KYB C28 N29 SING N N 31 KYB N29 C30 SING N N 32 KYB C30 N32 DOUB N N 33 KYB C30 N31 SING N N 34 KYB C15 H1 SING N N 35 KYB C17 H2 SING N N 36 KYB C18 H3 SING N N 37 KYB C18 H4 SING N N 38 KYB C20 H5 SING N N 39 KYB C20 H6 SING N N 40 KYB C21 H7 SING N N 41 KYB C21 H8 SING N N 42 KYB C22 H9 SING N N 43 KYB C22 H10 SING N N 44 KYB C28 H11 SING N N 45 KYB C28 H12 SING N N 46 KYB N32 H13 SING N N 47 KYB C02 H14 SING N N 48 KYB C03 H15 SING N N 49 KYB C05 H16 SING N N 50 KYB C09 H17 SING N N 51 KYB C24 H18 SING N N 52 KYB C24 H19 SING N N 53 KYB C25 H20 SING N N 54 KYB C25 H21 SING N N 55 KYB C26 H22 SING N N 56 KYB C26 H23 SING N N 57 KYB C27 H24 SING N N 58 KYB C27 H25 SING N N 59 KYB N12 H26 SING N N 60 KYB N12 H27 SING N N 61 KYB N23 H29 SING N N 62 KYB N23 H30 SING N N 63 KYB N29 H32 SING N N 64 KYB N31 H33 SING N N 65 KYB N31 H34 SING N N 66 KYB O01 H35 SING N N 67 KYB O04 H36 SING N N 68 # # 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 KYB InChI InChI 1.03 "InChI=1S/C19H34N10O3/c20-5-4-8-28(7-3-1-2-6-24-19(22)23)9-12-14(30)15(31)18(32-12)29-11-27-13-16(21)25-10-26-17(13)29/h10-12,14-15,18,30-31H,1-9,20H2,(H2,21,25,26)(H4,22,23,24)/t12-,14-,15-,18-/m1/s1" KYB InChIKey InChI 1.03 DDMCCWMSVOANNB-SCFUHWHPSA-N KYB SMILES_CANONICAL CACTVS 3.385 "NCCCN(CCCCCNC(N)=N)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" KYB SMILES CACTVS 3.385 "NCCCN(CCCCCNC(N)=N)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" KYB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NCCCCCN(CCCN)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" KYB SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCCCNC(=N)N)CCCN)O)O)N" # _pdbx_chem_comp_identifier.comp_id KYB _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "1-[5-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azanylpropyl)amino]pentyl]guanidine" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site KYB "Create component" 2019-07-04 EBI KYB "Initial release" 2020-03-04 RCSB ##