data_K3B # _chem_comp.id K3B _chem_comp.name "(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[3-(6-azanyl-9~{H}-purin-8-yl)prop-2-ynoxymethyl]oxolane-3,4-diol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H18 N10 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-04-16 _chem_comp.pdbx_modified_date 2020-02-14 _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 438.400 _chem_comp.one_letter_code ? _chem_comp.three_letter_code K3B _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 6RG6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 K3B C2 C1 C 0 1 Y N N 20.076 6.098 8.761 6.636 -1.879 1.828 C2 K3B 1 K3B C4 C2 C 0 1 Y N N 17.839 6.526 8.298 5.010 -1.101 0.402 C4 K3B 2 K3B C5 C3 C 0 1 Y N N 17.707 5.307 7.646 5.321 -2.133 -0.499 C5 K3B 3 K3B C6 C4 C 0 1 Y N N 18.797 4.457 7.548 6.335 -3.039 -0.145 C6 K3B 4 K3B N9 N1 N 0 1 Y N N 16.653 7.125 8.243 3.995 -0.384 -0.180 N9 K3B 5 K3B "C1'" C5 C 0 1 N N R 16.290 8.438 8.790 3.332 0.795 0.384 "C1'" K3B 6 K3B "C2'" C6 C 0 1 N N R 16.306 9.638 7.841 4.090 2.080 -0.016 "C2'" K3B 7 K3B "C3'" C7 C 0 1 N N S 15.446 10.675 8.608 2.970 3.118 -0.253 "C3'" K3B 8 K3B "C4'" C8 C 0 1 N N R 14.901 9.874 9.804 1.668 2.336 0.031 "C4'" K3B 9 K3B "C5'" C9 C 0 1 N N N 13.545 10.274 10.339 0.565 2.767 -0.938 "C5'" K3B 10 K3B C8 C10 C 0 1 Y N N 15.814 6.324 7.584 3.717 -0.969 -1.379 C8 K3B 11 K3B CAP C11 C 0 1 N N N 14.147 10.903 12.668 -1.759 2.456 -1.433 CAP K3B 12 K3B CAQ C12 C 0 1 N N N 15.609 11.005 12.680 -2.963 1.738 -0.983 CAQ K3B 13 K3B CAR C13 C 0 1 N N N 16.817 11.121 12.676 -3.923 1.166 -0.623 CAR K3B 14 K3B CAS C14 C 0 1 Y N N 18.235 11.280 12.659 -5.094 0.467 -0.185 CAS K3B 15 K3B CAU C15 C 0 1 Y N N 20.338 10.899 12.942 -6.764 -0.240 1.080 CAU K3B 16 K3B CAW C16 C 0 1 Y N N 22.648 11.113 12.931 -8.647 -1.398 1.708 CAW K3B 17 K3B CAY C17 C 0 1 Y N N 21.304 12.877 11.988 -7.867 -1.762 -0.433 CAY K3B 18 K3B CAZ C18 C 0 1 Y N N 20.184 12.128 12.317 -6.823 -0.851 -0.185 CAZ K3B 19 K3B N1 N2 N 0 1 Y N N 20.008 4.858 8.114 6.960 -2.868 1.015 N1 K3B 20 K3B N3 N3 N 0 1 Y N N 19.015 6.887 8.835 5.686 -1.013 1.543 N3 K3B 21 K3B N6 N4 N 0 1 N N N 18.689 3.286 6.926 6.686 -4.076 -0.992 N6 K3B 22 K3B N7 N5 N 0 1 Y N N 16.453 5.214 7.219 4.496 -1.995 -1.564 N7 K3B 23 K3B NAT N6 N 0 1 Y N N 19.120 10.406 13.138 -5.669 0.587 1.056 NAT K3B 24 K3B NAV N7 N 0 1 Y N N 21.559 10.426 13.232 -7.689 -0.539 1.986 NAV K3B 25 K3B NAX N8 N 0 1 Y N N 22.563 12.362 12.300 -8.743 -2.000 0.536 NAX K3B 26 K3B NBA N9 N 0 1 Y N N 18.882 12.332 12.158 -5.784 -0.381 -0.910 NBA K3B 27 K3B NBB N10 N 0 1 N N N 21.181 14.058 11.389 -7.975 -2.398 -1.658 NBB K3B 28 K3B "O2'" O1 O 0 1 N N N 17.623 10.063 7.565 4.949 2.505 1.044 "O2'" K3B 29 K3B "O3'" O2 O 0 1 N N N 16.278 11.733 9.078 3.103 4.215 0.653 "O3'" K3B 30 K3B "O4'" O3 O 0 1 N N N 15.053 8.493 9.441 2.014 0.951 -0.186 "O4'" K3B 31 K3B "O5'" O4 O 0 1 N N N 13.409 10.054 11.744 -0.659 2.120 -0.586 "O5'" K3B 32 K3B H1 H1 H 0 1 N N N 21.007 6.416 9.206 7.167 -1.779 2.763 H1 K3B 33 K3B H2 H2 H 0 1 N N N 17.053 8.665 9.550 3.269 0.711 1.469 H2 K3B 34 K3B H3 H3 H 0 1 N N N 15.784 9.366 6.912 4.661 1.919 -0.930 H3 K3B 35 K3B H4 H4 H 0 1 N N N 14.623 11.038 7.975 2.988 3.471 -1.284 H4 K3B 36 K3B H5 H5 H 0 1 N N N 15.609 10.060 10.625 1.348 2.492 1.061 H5 K3B 37 K3B H6 H6 H 0 1 N N N 13.390 11.344 10.136 0.434 3.848 -0.882 H6 K3B 38 K3B H7 H7 H 0 1 N N N 12.776 9.687 9.817 0.845 2.487 -1.954 H7 K3B 39 K3B H8 H8 H 0 1 N N N 14.776 6.542 7.378 2.961 -0.632 -2.073 H8 K3B 40 K3B H9 H9 H 0 1 N N N 13.776 11.925 12.500 -1.528 2.170 -2.459 H9 K3B 41 K3B H10 H10 H 0 1 N N N 13.860 10.570 13.677 -1.939 3.530 -1.387 H10 K3B 42 K3B H11 H11 H 0 1 N N N 23.618 10.706 13.175 -9.383 -1.619 2.467 H11 K3B 43 K3B H12 H12 H 0 1 N N N 19.569 2.812 6.952 6.229 -4.184 -1.841 H12 K3B 44 K3B H13 H13 H 0 1 N N N 17.996 2.728 7.384 7.387 -4.695 -0.736 H13 K3B 45 K3B H14 H14 H 0 1 N N N 18.904 9.530 13.570 -5.358 1.152 1.781 H14 K3B 46 K3B H16 H16 H 0 1 N N N 22.088 14.448 11.231 -8.697 -3.026 -1.816 H16 K3B 47 K3B H17 H17 H 0 1 N N N 20.712 13.940 10.514 -7.329 -2.215 -2.358 H17 K3B 48 K3B H18 H18 H 0 1 N N N 18.085 9.378 7.096 5.404 3.340 0.871 H18 K3B 49 K3B H19 H19 H 0 1 N N N 15.749 12.367 9.548 3.931 4.704 0.559 H19 K3B 50 # # 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 K3B N6 C6 SING N N 1 K3B N7 C8 DOUB Y N 2 K3B N7 C5 SING Y N 3 K3B C6 C5 DOUB Y N 4 K3B C6 N1 SING Y N 5 K3B "O2'" "C2'" SING N N 6 K3B C8 N9 SING Y N 7 K3B C5 C4 SING Y N 8 K3B "C2'" "C3'" SING N N 9 K3B "C2'" "C1'" SING N N 10 K3B N1 C2 DOUB Y N 11 K3B N9 C4 SING Y N 12 K3B N9 "C1'" SING N N 13 K3B C4 N3 DOUB Y N 14 K3B "C3'" "O3'" SING N N 15 K3B "C3'" "C4'" SING N N 16 K3B C2 N3 SING Y N 17 K3B "C1'" "O4'" SING N N 18 K3B "O4'" "C4'" SING N N 19 K3B "C4'" "C5'" SING N N 20 K3B "C5'" "O5'" SING N N 21 K3B NBB CAY SING N N 22 K3B "O5'" CAP SING N N 23 K3B CAY NAX DOUB Y N 24 K3B CAY CAZ SING Y N 25 K3B NBA CAZ SING Y N 26 K3B NBA CAS DOUB Y N 27 K3B NAX CAW SING Y N 28 K3B CAZ CAU DOUB Y N 29 K3B CAS CAR SING N N 30 K3B CAS NAT SING Y N 31 K3B CAP CAQ SING N N 32 K3B CAR CAQ TRIP N N 33 K3B CAW NAV DOUB Y N 34 K3B CAU NAT SING Y N 35 K3B CAU NAV SING Y N 36 K3B C2 H1 SING N N 37 K3B "C1'" H2 SING N N 38 K3B "C2'" H3 SING N N 39 K3B "C3'" H4 SING N N 40 K3B "C4'" H5 SING N N 41 K3B "C5'" H6 SING N N 42 K3B "C5'" H7 SING N N 43 K3B C8 H8 SING N N 44 K3B CAP H9 SING N N 45 K3B CAP H10 SING N N 46 K3B CAW H11 SING N N 47 K3B N6 H12 SING N N 48 K3B N6 H13 SING N N 49 K3B NAT H14 SING N N 50 K3B NBB H16 SING N N 51 K3B NBB H17 SING N N 52 K3B "O2'" H18 SING N N 53 K3B "O3'" H19 SING N N 54 # # 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 K3B InChI InChI 1.03 "InChI=1S/C18H18N10O4/c19-14-10-16(23-5-21-14)27-9(26-10)2-1-3-31-4-8-12(29)13(30)18(32-8)28-7-25-11-15(20)22-6-24-17(11)28/h5-8,12-13,18,29-30H,3-4H2,(H2,20,22,24)(H3,19,21,23,26,27)/t8-,12-,13-,18-/m1/s1" K3B InChIKey InChI 1.03 BVXWUAMSMQSLCT-IKGPEZKQSA-N K3B SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](COCC#Cc4[nH]c5ncnc(N)c5n4)[C@@H](O)[C@H]3O" K3B SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](COCC#Cc4[nH]c5ncnc(N)c5n4)[CH](O)[CH]3O" K3B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)[nH]c(n2)C#CCOC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N" K3B SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)[nH]c(n2)C#CCOCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N" # _pdbx_chem_comp_identifier.comp_id K3B _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 "(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[3-(6-azanyl-9~{H}-purin-8-yl)prop-2-ynoxymethyl]oxolane-3,4-diol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site K3B "Create component" 2019-04-16 RCSB K3B "Initial release" 2020-02-19 RCSB ##