data_YHK # _chem_comp.id YHK _chem_comp.name "5'-O-[(R)-(cyclopropyloxy)(hydroxy)phosphoryl]adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H18 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-03 _chem_comp.pdbx_modified_date 2023-02-10 _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 387.285 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YHK _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 8G0T _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 YHK C1 C1 C 0 1 N N S -15.133 24.564 8.210 -0.268 2.586 0.526 C1 YHK 1 YHK C10 C2 C 0 1 N N N -13.554 23.808 6.338 1.886 1.275 0.648 C10 YHK 2 YHK C11 C3 C 0 1 N N N -12.966 22.299 3.413 6.206 -1.552 -0.454 C11 YHK 3 YHK C12 C4 C 0 1 N N N -14.428 21.971 3.492 7.217 -1.168 -1.536 C12 YHK 4 YHK C13 C5 C 0 1 N N N -13.521 21.116 2.671 6.685 -2.600 -1.460 C13 YHK 5 YHK C2 C6 C 0 1 N N R -15.973 25.837 8.303 -1.719 2.086 0.343 C2 YHK 6 YHK C3 C7 C 0 1 N N R -16.129 26.177 6.824 -1.563 0.748 -0.413 C3 YHK 7 YHK C4 C8 C 0 1 Y N N -17.019 24.457 5.184 -2.356 -1.171 1.021 C4 YHK 8 YHK C5 C9 C 0 1 Y N N -19.116 24.782 5.317 -4.404 -1.409 0.348 C5 YHK 9 YHK C6 C10 C 0 1 Y N N -18.532 25.678 6.193 -3.845 -0.347 -0.381 C6 YHK 10 YHK C7 C11 C 0 1 Y N N -20.488 26.494 6.793 -5.842 -0.077 -1.485 C7 YHK 11 YHK C8 C12 C 0 1 Y N N -20.520 24.796 5.220 -5.741 -1.758 0.093 C8 YHK 12 YHK C9 C13 C 0 1 N N R -14.141 24.965 7.108 0.593 1.490 -0.141 C9 YHK 13 YHK N1 N1 N 0 1 Y N N -17.179 25.462 6.102 -2.552 -0.223 0.061 N1 YHK 14 YHK N2 N2 N 0 1 Y N N -18.148 24.015 4.685 -3.444 -1.865 1.189 N2 YHK 15 YHK N3 N3 N 0 1 Y N N -19.173 26.571 6.965 -4.594 0.285 -1.279 N3 YHK 16 YHK N4 N4 N 0 1 Y N N -21.190 25.686 5.990 -6.411 -1.069 -0.824 N4 YHK 17 YHK N5 N5 N 0 1 N N N -21.217 23.991 4.420 -6.346 -2.796 0.780 N5 YHK 18 YHK O1 O1 O 0 1 N N N -14.414 24.248 9.392 -0.083 3.839 -0.135 O1 YHK 19 YHK O2 O2 O 0 1 N N N -14.881 25.835 6.221 -0.226 0.301 -0.099 O2 YHK 20 YHK O3 O3 O 0 1 N N N -15.290 26.867 8.986 -2.474 3.016 -0.436 O3 YHK 21 YHK O4 O4 O 0 1 N N N -12.477 24.286 5.508 2.719 0.345 -0.047 O4 YHK 22 YHK O5 O5 O 0 1 N N N -10.570 22.847 6.229 3.981 -0.930 1.875 O5 YHK 23 YHK O6 O6 O 0 1 N N N -12.202 21.974 4.540 4.870 -1.063 -0.596 O6 YHK 24 YHK O7 O7 O 0 1 N N N -10.617 23.830 3.904 5.004 1.077 0.736 O7 YHK 25 YHK P1 P1 P 0 1 N N N -11.360 23.243 5.041 4.162 -0.117 0.497 P1 YHK 26 YHK H1 H1 H 0 1 N N N -15.755 23.722 7.871 -0.025 2.674 1.585 H1 YHK 27 YHK H2 H2 H 0 1 N N N -14.332 23.355 5.706 2.410 2.225 0.752 H2 YHK 28 YHK H3 H3 H 0 1 N N N -13.169 23.055 7.042 1.648 0.882 1.636 H3 YHK 29 YHK H4 H4 H 0 1 N N N -12.684 23.176 2.811 6.570 -1.632 0.570 H4 YHK 30 YHK H5 H5 H 0 1 N N N -15.164 22.622 2.999 6.864 -0.543 -2.356 H5 YHK 31 YHK H6 H6 H 0 1 N N N -14.853 21.580 4.428 8.247 -0.996 -1.224 H6 YHK 32 YHK H7 H7 H 0 1 N N N -13.589 21.138 1.573 7.365 -3.371 -1.098 H7 YHK 33 YHK H8 H8 H 0 1 N N N -13.278 20.096 3.003 5.981 -2.918 -2.230 H8 YHK 34 YHK H9 H9 H 0 1 N N N -16.953 25.619 8.753 -2.193 1.927 1.312 H9 YHK 35 YHK H10 H10 H 0 1 N N N -16.300 27.260 6.733 -1.669 0.904 -1.486 H10 YHK 36 YHK H11 H11 H 0 1 N N N -16.054 24.066 4.898 -1.434 -1.325 1.561 H11 YHK 37 YHK H12 H12 H 0 1 N N N -21.074 27.181 7.385 -6.424 0.458 -2.222 H12 YHK 38 YHK H13 H13 H 0 1 N N N -13.319 25.530 7.573 0.819 1.761 -1.173 H13 YHK 39 YHK H14 H14 H 0 1 N N N -22.193 24.184 4.521 -5.846 -3.293 1.447 H14 YHK 40 YHK H15 H15 H 0 1 N N N -20.943 24.146 3.471 -7.269 -3.027 0.595 H15 YHK 41 YHK H16 H16 H 0 1 N N N -15.023 23.999 10.077 -0.645 4.549 0.205 H16 YHK 42 YHK H17 H17 H 0 1 N N N -15.204 26.636 9.903 -2.552 3.893 -0.035 H17 YHK 43 YHK H18 H18 H 0 1 N N N -9.652 23.039 6.078 3.439 -1.727 1.793 H18 YHK 44 # 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 YHK C13 C11 SING N N 1 YHK C13 C12 SING N N 2 YHK C11 C12 SING N N 3 YHK C11 O6 SING N N 4 YHK O7 P1 DOUB N N 5 YHK N5 C8 SING N N 6 YHK O6 P1 SING N N 7 YHK N2 C4 DOUB Y N 8 YHK N2 C5 SING Y N 9 YHK P1 O4 SING N N 10 YHK P1 O5 SING N N 11 YHK C4 N1 SING Y N 12 YHK C8 C5 SING Y N 13 YHK C8 N4 DOUB Y N 14 YHK C5 C6 DOUB Y N 15 YHK O4 C10 SING N N 16 YHK N4 C7 SING Y N 17 YHK N1 C6 SING Y N 18 YHK N1 C3 SING N N 19 YHK C6 N3 SING Y N 20 YHK O2 C3 SING N N 21 YHK O2 C9 SING N N 22 YHK C10 C9 SING N N 23 YHK C7 N3 DOUB Y N 24 YHK C3 C2 SING N N 25 YHK C9 C1 SING N N 26 YHK C1 C2 SING N N 27 YHK C1 O1 SING N N 28 YHK C2 O3 SING N N 29 YHK C1 H1 SING N N 30 YHK C10 H2 SING N N 31 YHK C10 H3 SING N N 32 YHK C11 H4 SING N N 33 YHK C12 H5 SING N N 34 YHK C12 H6 SING N N 35 YHK C13 H7 SING N N 36 YHK C13 H8 SING N N 37 YHK C2 H9 SING N N 38 YHK C3 H10 SING N N 39 YHK C4 H11 SING N N 40 YHK C7 H12 SING N N 41 YHK C9 H13 SING N N 42 YHK N5 H14 SING N N 43 YHK N5 H15 SING N N 44 YHK O1 H16 SING N N 45 YHK O3 H17 SING N N 46 YHK O5 H18 SING N N 47 # 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 YHK SMILES ACDLabs 12.01 "O=P(O)(OC1CC1)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1O" YHK InChI InChI 1.06 "InChI=1S/C13H18N5O7P/c14-11-8-12(16-4-15-11)18(5-17-8)13-10(20)9(19)7(24-13)3-23-26(21,22)25-6-1-2-6/h4-7,9-10,13,19-20H,1-3H2,(H,21,22)(H2,14,15,16)/t7-,9-,10-,13-/m1/s1" YHK InChIKey InChI 1.06 FJCZQSQASCNEEZ-QYVSTXNMSA-N YHK SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC4CC4)[C@@H](O)[C@H]3O" YHK SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)OC4CC4)[CH](O)[CH]3O" YHK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OC4CC4)O)O)N" YHK SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4CC4)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 YHK "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-(cyclopropyloxy)(hydroxy)phosphoryl]adenosine" YHK "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl cyclopropyl hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YHK "Create component" 2023-02-03 RCSB YHK "Initial release" 2023-02-15 RCSB #