data_KYK # _chem_comp.id KYK _chem_comp.name "N6-benzyl-(alpha,beta)-methylene-ADP" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H23 N5 O9 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-07-05 _chem_comp.pdbx_modified_date 2020-07-17 _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 515.351 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KYK _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 6S7F _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 KYK N1 N1 N 0 1 Y N N -13.142 23.579 -36.537 -5.229 1.737 -0.928 N1 KYK 1 KYK N3 N2 N 0 1 Y N N -14.563 21.641 -36.616 -3.170 2.779 -1.036 N3 KYK 2 KYK C4 C1 C 0 1 Y N N -14.478 21.647 -35.284 -2.552 1.703 -0.560 C4 KYK 3 KYK C5 C2 C 0 1 Y N N -13.767 22.541 -34.501 -3.312 0.564 -0.244 C5 KYK 4 KYK C6 C3 C 0 1 Y N N -13.067 23.564 -35.196 -4.701 0.616 -0.447 C6 KYK 5 KYK C8 C4 C 0 1 Y N N -14.755 21.226 -33.159 -1.240 0.102 0.200 C8 KYK 6 KYK C21 C5 C 0 1 N N N -12.133 24.674 -33.192 -6.948 -0.402 -0.373 C21 KYK 7 KYK C22 C6 C 0 1 Y N N -8.962 27.479 -32.451 -8.754 -4.108 0.745 C22 KYK 8 KYK C24 C7 C 0 1 Y N N -11.303 26.991 -32.629 -7.740 -2.714 -0.916 C24 KYK 9 KYK C26 C8 C 0 1 Y N N -9.694 25.265 -33.016 -8.021 -1.903 1.319 C26 KYK 10 KYK PB P1 P 0 1 N N N -17.141 19.671 -28.920 6.823 -2.622 -0.422 PB KYK 11 KYK O1B O1 O 0 1 N N N -18.317 20.536 -28.627 7.194 -3.661 -1.594 O1B KYK 12 KYK O2B O2 O 0 1 N N N -16.050 19.774 -27.841 6.324 -3.433 0.877 O2B KYK 13 KYK O3B O3 O 0 1 N N N -16.449 20.157 -30.208 8.018 -1.821 -0.075 O3B KYK 14 KYK PA P2 P 0 1 N N N -18.977 17.712 -30.337 5.072 -0.336 0.334 PA KYK 15 KYK O1A O4 O 0 1 N N N -20.272 18.455 -30.277 6.372 0.535 0.712 O1A KYK 16 KYK O2A O5 O 0 1 N N N -19.202 16.175 -30.457 4.614 -1.081 1.528 O2A KYK 17 KYK C3A C9 C 0 1 N N N -17.624 17.957 -29.167 5.493 -1.513 -0.993 C3A KYK 18 KYK "O5'" O6 O 0 1 N N N -18.310 18.160 -31.693 3.898 0.644 -0.170 "O5'" KYK 19 KYK "C5'" C10 C 0 1 N N N -17.082 17.572 -32.156 3.274 1.611 0.677 "C5'" KYK 20 KYK "C4'" C11 C 0 1 N N R -16.843 17.923 -33.595 2.206 2.369 -0.115 "C4'" KYK 21 KYK "O4'" O7 O 0 1 N N N -16.834 19.354 -33.764 1.133 1.478 -0.463 "O4'" KYK 22 KYK "C3'" C12 C 0 1 N N S -15.483 17.467 -34.087 1.609 3.493 0.754 "C3'" KYK 23 KYK "O3'" O8 O 0 1 N N N -15.556 16.078 -34.405 1.827 4.766 0.143 "O3'" KYK 24 KYK "C2'" C13 C 0 1 N N R -15.218 18.423 -35.254 0.097 3.167 0.810 "C2'" KYK 25 KYK "O2'" O9 O 0 1 N N N -15.802 17.964 -36.464 -0.688 4.355 0.689 "O2'" KYK 26 KYK "C1'" C14 C 0 1 N N R -15.961 19.694 -34.817 -0.085 2.254 -0.435 "C1'" KYK 27 KYK N9 N3 N 0 1 Y N N -15.111 20.801 -34.410 -1.250 1.382 -0.270 N9 KYK 28 KYK N7 N4 N 0 1 Y N N -13.947 22.260 -33.155 -2.450 -0.376 0.215 N7 KYK 29 KYK N6 N5 N 0 1 N N N -12.333 24.525 -34.617 -5.501 -0.475 -0.154 N6 KYK 30 KYK C2 C15 C 0 1 Y N N -13.857 22.638 -37.151 -4.474 2.783 -1.210 C2 KYK 31 KYK C23 C16 C 0 1 Y N N -10.279 27.892 -32.391 -8.326 -3.912 -0.555 C23 KYK 32 KYK C25 C17 C 0 1 Y N N -11.024 25.663 -32.934 -7.582 -1.711 0.023 C25 KYK 33 KYK C27 C18 C 0 1 Y N N -8.670 26.163 -32.758 -8.602 -3.103 1.682 C27 KYK 34 KYK H8 H1 H 0 1 N N N -15.108 20.752 -32.255 -0.357 -0.436 0.514 H8 KYK 35 KYK H3 H2 H 0 1 N N N -13.062 25.038 -32.729 -7.367 0.402 0.233 H3 KYK 36 KYK H1 H3 H 0 1 N N N -11.863 23.700 -32.757 -7.147 -0.206 -1.426 H1 KYK 37 KYK H21 H4 H 0 1 N N N -8.164 28.181 -32.259 -9.212 -5.045 1.027 H21 KYK 38 KYK H23 H5 H 0 1 N N N -12.329 27.323 -32.577 -7.405 -2.560 -1.931 H23 KYK 39 KYK H25 H6 H 0 1 N N N -9.457 24.246 -33.283 -7.897 -1.120 2.053 H25 KYK 40 KYK H4 H7 H 0 1 N N N -18.393 21.206 -29.297 7.896 -4.283 -1.360 H4 KYK 41 KYK H5 H8 H 0 1 N N N -15.248 20.102 -28.231 5.543 -3.980 0.722 H5 KYK 42 KYK H6 H9 H 0 1 N N N -20.994 17.839 -30.324 6.728 1.051 -0.025 H6 KYK 43 KYK H3A2 H10 H 0 0 N N N -17.934 17.545 -28.195 5.830 -0.964 -1.872 H3A2 KYK 44 KYK H3A1 H11 H 0 0 N N N -16.748 17.405 -29.537 4.613 -2.102 -1.248 H3A1 KYK 45 KYK "H5'2" H12 H 0 0 N N N -17.143 16.478 -32.055 2.809 1.107 1.524 "H5'2" KYK 46 KYK "H5'1" H13 H 0 0 N N N -16.247 17.950 -31.547 4.024 2.314 1.040 "H5'1" KYK 47 KYK "H4'" H14 H 0 1 N N N -17.627 17.469 -34.219 2.645 2.792 -1.018 "H4'" KYK 48 KYK "H3'" H15 H 0 1 N N N -14.735 17.644 -33.301 2.041 3.472 1.755 "H3'" KYK 49 KYK "HO3'" H16 H 0 0 N N N -15.723 15.580 -33.613 1.471 5.510 0.648 "HO3'" KYK 50 KYK "H2'" H17 H 0 1 N N N -14.141 18.620 -35.357 -0.152 2.630 1.725 "H2'" KYK 51 KYK "HO2'" H18 H 0 0 N N N -15.356 17.176 -36.753 -0.608 4.957 1.442 "HO2'" KYK 52 KYK "H1'" H19 H 0 1 N N N -16.562 20.026 -35.676 -0.181 2.854 -1.340 "H1'" KYK 53 KYK HN61 H20 H 0 0 N N N -11.417 24.431 -35.006 -5.103 -1.288 0.196 HN61 KYK 54 KYK H2 H21 H 0 1 N N N -13.866 22.689 -38.230 -4.944 3.674 -1.599 H2 KYK 55 KYK H22 H22 H 0 1 N N N -10.510 28.921 -32.158 -8.449 -4.696 -1.288 H22 KYK 56 KYK H26 H23 H 0 1 N N N -7.642 25.834 -32.797 -8.937 -3.257 2.697 H26 KYK 57 # # 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 KYK C2 N3 DOUB Y N 1 KYK C2 N1 SING Y N 2 KYK N3 C4 SING Y N 3 KYK N1 C6 DOUB Y N 4 KYK "O2'" "C2'" SING N N 5 KYK C4 C5 DOUB Y N 6 KYK C4 N9 SING Y N 7 KYK "C2'" "C1'" SING N N 8 KYK "C2'" "C3'" SING N N 9 KYK C6 N6 SING N N 10 KYK C6 C5 SING Y N 11 KYK "C1'" N9 SING N N 12 KYK "C1'" "O4'" SING N N 13 KYK N6 C21 SING N N 14 KYK C5 N7 SING Y N 15 KYK N9 C8 SING Y N 16 KYK "O3'" "C3'" SING N N 17 KYK "C3'" "C4'" SING N N 18 KYK "O4'" "C4'" SING N N 19 KYK "C4'" "C5'" SING N N 20 KYK C21 C25 SING N N 21 KYK C8 N7 DOUB Y N 22 KYK C26 C25 DOUB Y N 23 KYK C26 C27 SING Y N 24 KYK C25 C24 SING Y N 25 KYK C27 C22 DOUB Y N 26 KYK C24 C23 DOUB Y N 27 KYK C22 C23 SING Y N 28 KYK "C5'" "O5'" SING N N 29 KYK "O5'" PA SING N N 30 KYK O2A PA DOUB N N 31 KYK PA O1A SING N N 32 KYK PA C3A SING N N 33 KYK O3B PB DOUB N N 34 KYK C3A PB SING N N 35 KYK PB O1B SING N N 36 KYK PB O2B SING N N 37 KYK C8 H8 SING N N 38 KYK C21 H3 SING N N 39 KYK C21 H1 SING N N 40 KYK C22 H21 SING N N 41 KYK C24 H23 SING N N 42 KYK C26 H25 SING N N 43 KYK O1B H4 SING N N 44 KYK O2B H5 SING N N 45 KYK O1A H6 SING N N 46 KYK C3A H3A2 SING N N 47 KYK C3A H3A1 SING N N 48 KYK "C5'" "H5'2" SING N N 49 KYK "C5'" "H5'1" SING N N 50 KYK "C4'" "H4'" SING N N 51 KYK "C3'" "H3'" SING N N 52 KYK "O3'" "HO3'" SING N N 53 KYK "C2'" "H2'" SING N N 54 KYK "O2'" "HO2'" SING N N 55 KYK "C1'" "H1'" SING N N 56 KYK N6 HN61 SING N N 57 KYK C2 H2 SING N N 58 KYK C23 H22 SING N N 59 KYK C27 H26 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 KYK InChI InChI 1.03 "InChI=1S/C18H23N5O9P2/c24-14-12(7-31-34(29,30)10-33(26,27)28)32-18(15(14)25)23-9-22-13-16(20-8-21-17(13)23)19-6-11-4-2-1-3-5-11/h1-5,8-9,12,14-15,18,24-25H,6-7,10H2,(H,29,30)(H,19,20,21)(H2,26,27,28)/t12-,14-,15-,18-/m1/s1" KYK InChIKey InChI 1.03 DMBYYIJBPDWQFF-SCFUHWHPSA-N KYK SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)C[P](O)(O)=O)n2cnc3c(NCc4ccccc4)ncnc23" KYK SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)C[P](O)(O)=O)n2cnc3c(NCc4ccccc4)ncnc23" KYK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(CP(=O)(O)O)O)O)O" KYK SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNc2c3c(ncn2)n(cn3)C4C(C(C(O4)COP(=O)(CP(=O)(O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id KYK _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~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[6-[(phenylmethyl)amino]purin-9-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic 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 KYK "Create component" 2019-07-05 EBI KYK "Initial release" 2020-07-22 RCSB ##