data_QPY # _chem_comp.id QPY _chem_comp.name "benzyl (2S)-2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)pyrrolidine-1-carboxylate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H25 N9 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-12-06 _chem_comp.pdbx_modified_date 2020-12-04 _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 519.513 _chem_comp.one_letter_code ? _chem_comp.three_letter_code QPY _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 6V56 _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 QPY C15 C1 C 0 1 N N N 37.595 13.465 15.159 3.035 -2.976 1.035 C15 QPY 1 QPY C17 C2 C 0 1 Y N N 39.757 14.685 14.177 3.086 -5.398 0.407 C17 QPY 2 QPY C1 C3 C 0 1 N N N 39.353 15.137 18.240 3.538 3.932 0.901 C1 QPY 3 QPY C10 C4 C 0 1 Y N N 41.679 14.413 10.682 -6.312 1.515 -1.860 C10 QPY 4 QPY C11 C5 C 0 1 Y N N 41.450 12.084 10.754 -7.374 0.130 -0.351 C11 QPY 5 QPY C12 C6 C 0 1 N N N 39.523 12.829 17.530 3.391 2.054 -0.495 C12 QPY 6 QPY C13 C7 C 0 1 N N S 38.924 11.431 17.380 4.065 1.109 -1.456 C13 QPY 7 QPY C14 C8 C 0 1 N N N 38.898 11.480 14.727 3.525 -0.994 -0.202 C14 QPY 8 QPY C16 C9 C 0 1 Y N N 38.262 14.673 14.494 2.357 -4.308 0.847 C16 QPY 9 QPY C18 C10 C 0 1 Y N N 40.309 15.745 13.620 2.463 -6.619 0.229 C18 QPY 10 QPY C19 C11 C 0 1 Y N N 39.462 16.977 13.310 1.112 -6.751 0.491 C19 QPY 11 QPY C2 C12 C 0 1 N N N 40.678 15.374 17.689 2.120 3.734 1.228 C2 QPY 12 QPY C20 C13 C 0 1 Y N N 38.179 16.973 13.603 0.384 -5.662 0.932 C20 QPY 13 QPY C21 C14 C 0 1 Y N N 37.538 15.743 14.241 1.008 -4.442 1.115 C21 QPY 14 QPY C22 C15 C 0 1 N N N 40.313 9.889 16.229 2.878 -0.625 -2.600 C22 QPY 15 QPY C23 C16 C 0 1 N N N 40.262 9.462 17.711 3.612 0.227 -3.665 C23 QPY 16 QPY C24 C17 C 0 1 N N N 39.470 10.510 18.437 3.812 1.567 -2.908 C24 QPY 17 QPY C3 C18 C 0 1 N N N 41.368 14.328 17.071 1.463 2.669 0.633 C3 QPY 18 QPY C4 C19 C 0 1 N N N 42.755 14.497 16.454 0.034 2.418 0.922 C4 QPY 19 QPY C5 C20 C 0 1 N N N 44.708 13.458 15.260 -2.015 1.131 0.626 C5 QPY 20 QPY C6 C21 C 0 1 N N N 44.671 13.814 13.772 -2.485 -0.097 -0.156 C6 QPY 21 QPY C7 C22 C 0 1 Y N N 43.890 11.588 13.276 -4.395 -1.201 1.069 C7 QPY 22 QPY C8 C23 C 0 1 Y N N 42.393 12.046 11.712 -6.118 -0.301 0.106 C8 QPY 23 QPY C9 C24 C 0 1 Y N N 42.972 13.213 12.145 -4.970 0.240 -0.498 C9 QPY 24 QPY N1 N1 N 0 1 N N N 38.786 13.895 18.157 4.115 3.068 0.037 N1 QPY 25 QPY N2 N2 N 0 1 N N N 43.394 13.334 15.859 -0.600 1.380 0.340 N2 QPY 26 QPY N3 N3 N 0 1 Y N N 43.809 12.879 13.063 -3.900 -0.345 0.130 N3 QPY 27 QPY N4 N4 N 0 1 Y N N 42.999 10.901 12.475 -5.696 -1.176 1.051 N4 QPY 28 QPY N5 N5 N 0 1 Y N N 42.637 14.389 11.654 -5.114 1.141 -1.465 N5 QPY 29 QPY N6 N6 N 0 1 Y N N 41.099 13.255 10.246 -7.418 1.031 -1.327 N6 QPY 30 QPY N7 N7 N 0 1 N N N 40.832 10.856 10.289 -8.539 -0.368 0.206 N7 QPY 31 QPY N8 N8 N 0 1 N N N 40.779 13.063 16.989 2.136 1.865 -0.210 N8 QPY 32 QPY N9 N9 N 0 1 N N N 39.318 10.978 16.039 3.493 -0.238 -1.317 N9 QPY 33 QPY O1 O1 O 0 1 N N N 38.652 16.174 18.860 4.173 4.850 1.390 O1 QPY 34 QPY O2 O2 O 0 1 N N N 41.249 16.647 17.784 1.474 4.566 2.083 O2 QPY 35 QPY O3 O3 O 0 1 N N N 43.326 15.534 16.495 -0.570 3.147 1.684 O3 QPY 36 QPY O4 O4 O 0 1 N N N 37.740 12.248 14.477 2.963 -2.217 -0.201 O4 QPY 37 QPY O5 O5 O 0 1 N N N 39.583 11.208 13.800 4.062 -0.572 0.803 O5 QPY 38 QPY H1 H1 H 0 1 N N N 36.520 13.678 15.249 2.534 -2.423 1.830 H1 QPY 39 QPY H2 H2 H 0 1 N N N 38.031 13.346 16.162 4.079 -3.133 1.304 H2 QPY 40 QPY H3 H3 H 0 1 N N N 40.363 13.822 14.410 4.140 -5.294 0.198 H3 QPY 41 QPY H4 H4 H 0 1 N N N 41.376 15.357 10.253 -6.393 2.250 -2.648 H4 QPY 42 QPY H5 H5 H 0 1 N N N 37.828 11.488 17.460 5.137 1.081 -1.258 H5 QPY 43 QPY H6 H6 H 0 1 N N N 41.363 15.742 13.383 3.032 -7.470 -0.114 H6 QPY 44 QPY H7 H7 H 0 1 N N N 39.913 17.846 12.853 0.625 -7.704 0.348 H7 QPY 45 QPY H8 H8 H 0 1 N N N 37.577 17.844 13.391 -0.671 -5.765 1.137 H8 QPY 46 QPY H9 H9 H 0 1 N N N 36.486 15.751 14.486 0.439 -3.591 1.459 H9 QPY 47 QPY H10 H10 H 0 1 N N N 40.061 9.034 15.584 1.813 -0.392 -2.595 H10 QPY 48 QPY H11 H11 H 0 1 N N N 41.320 10.253 15.978 3.032 -1.687 -2.792 H11 QPY 49 QPY H12 H12 H 0 1 N N N 39.771 8.482 17.806 4.570 -0.219 -3.930 H12 QPY 50 QPY H13 H13 H 0 1 N N N 41.280 9.403 18.123 2.990 0.368 -4.549 H13 QPY 51 QPY H14 H14 H 0 1 N N N 40.119 11.066 19.130 2.914 2.181 -2.967 H14 QPY 52 QPY H15 H15 H 0 1 N N N 38.647 10.045 18.999 4.675 2.105 -3.299 H15 QPY 53 QPY H16 H16 H 0 1 N N N 45.235 12.499 15.375 -2.603 1.999 0.329 H16 QPY 54 QPY H17 H17 H 0 1 N N N 45.260 14.246 15.793 -2.144 0.953 1.694 H17 QPY 55 QPY H18 H18 H 0 1 N N N 45.689 13.759 13.358 -2.356 0.081 -1.224 H18 QPY 56 QPY H19 H19 H 0 1 N N N 44.280 14.835 13.650 -1.896 -0.965 0.141 H19 QPY 57 QPY H20 H20 H 0 1 N N N 44.563 11.124 13.982 -3.796 -1.811 1.728 H20 QPY 58 QPY H21 H21 H 0 1 N N N 37.872 13.730 18.527 5.048 3.174 -0.203 H21 QPY 59 QPY H22 H22 H 0 1 N N N 42.927 12.450 15.863 -0.118 0.797 -0.268 H22 QPY 60 QPY H23 H23 H 0 1 N N N 40.159 11.068 9.580 -8.494 -1.023 0.920 H23 QPY 61 QPY H24 H24 H 0 1 N N N 41.534 10.252 9.912 -9.401 -0.062 -0.118 H24 QPY 62 QPY H25 H25 H 0 1 N N N 42.109 16.640 17.380 2.030 5.273 2.438 H25 QPY 63 # # 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 QPY N6 C10 DOUB Y N 1 QPY N6 C11 SING Y N 2 QPY N7 C11 SING N N 3 QPY C10 N5 SING Y N 4 QPY C11 C8 DOUB Y N 5 QPY N5 C9 DOUB Y N 6 QPY C8 C9 SING Y N 7 QPY C8 N4 SING Y N 8 QPY C9 N3 SING Y N 9 QPY N4 C7 DOUB Y N 10 QPY N3 C7 SING Y N 11 QPY N3 C6 SING N N 12 QPY C19 C20 DOUB Y N 13 QPY C19 C18 SING Y N 14 QPY C20 C21 SING Y N 15 QPY C18 C17 DOUB Y N 16 QPY C6 C5 SING N N 17 QPY O5 C14 DOUB N N 18 QPY C17 C16 SING Y N 19 QPY C21 C16 DOUB Y N 20 QPY O4 C14 SING N N 21 QPY O4 C15 SING N N 22 QPY C16 C15 SING N N 23 QPY C14 N9 SING N N 24 QPY C5 N2 SING N N 25 QPY N2 C4 SING N N 26 QPY N9 C22 SING N N 27 QPY N9 C13 SING N N 28 QPY C22 C23 SING N N 29 QPY C4 O3 DOUB N N 30 QPY C4 C3 SING N N 31 QPY N8 C3 SING N N 32 QPY N8 C12 DOUB N N 33 QPY C3 C2 DOUB N N 34 QPY C13 C12 SING N N 35 QPY C13 C24 SING N N 36 QPY C12 N1 SING N N 37 QPY C2 O2 SING N N 38 QPY C2 C1 SING N N 39 QPY C23 C24 SING N N 40 QPY N1 C1 SING N N 41 QPY C1 O1 DOUB N N 42 QPY C15 H1 SING N N 43 QPY C15 H2 SING N N 44 QPY C17 H3 SING N N 45 QPY C10 H4 SING N N 46 QPY C13 H5 SING N N 47 QPY C18 H6 SING N N 48 QPY C19 H7 SING N N 49 QPY C20 H8 SING N N 50 QPY C21 H9 SING N N 51 QPY C22 H10 SING N N 52 QPY C22 H11 SING N N 53 QPY C23 H12 SING N N 54 QPY C23 H13 SING N N 55 QPY C24 H14 SING N N 56 QPY C24 H15 SING N N 57 QPY C5 H16 SING N N 58 QPY C5 H17 SING N N 59 QPY C6 H18 SING N N 60 QPY C6 H19 SING N N 61 QPY C7 H20 SING N N 62 QPY N1 H21 SING N N 63 QPY N2 H22 SING N N 64 QPY N7 H23 SING N N 65 QPY N7 H24 SING N N 66 QPY O2 H25 SING N N 67 # # 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 QPY SMILES ACDLabs 12.01 "C(c1ccccc1)OC(N5C(C=4NC(=O)C(O)=C(C(=O)NCCn3cnc2c(ncnc23)N)N=4)CCC5)=O" QPY InChI InChI 1.03 "InChI=1S/C24H25N9O5/c25-19-17-21(28-12-27-19)32(13-29-17)10-8-26-22(35)16-18(34)23(36)31-20(30-16)15-7-4-9-33(15)24(37)38-11-14-5-2-1-3-6-14/h1-3,5-6,12-13,15,34H,4,7-11H2,(H,26,35)(H2,25,27,28)(H,30,31,36)/t15-/m0/s1" QPY InChIKey InChI 1.03 GEKIERMMQOYZBF-HNNXBMFYSA-N QPY SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(CCNC(=O)C3=C(O)C(=O)NC(=N3)[C@@H]4CCCN4C(=O)OCc5ccccc5)cnc12" QPY SMILES CACTVS 3.385 "Nc1ncnc2n(CCNC(=O)C3=C(O)C(=O)NC(=N3)[CH]4CCCN4C(=O)OCc5ccccc5)cnc12" QPY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)COC(=O)N2CCC[C@H]2C3=NC(=C(C(=O)N3)O)C(=O)NCCn4cnc5c4ncnc5N" QPY SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)COC(=O)N2CCCC2C3=NC(=C(C(=O)N3)O)C(=O)NCCn4cnc5c4ncnc5N" # # 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 QPY "SYSTEMATIC NAME" ACDLabs 12.01 "benzyl (2S)-2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)pyrrolidine-1-carboxylate" QPY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(phenylmethyl) (2~{S})-2-[4-[2-(6-aminopurin-9-yl)ethylcarbamoyl]-5-oxidanyl-6-oxidanylidene-1~{H}-pyrimidin-2-yl]pyrrolidine-1-carboxylate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site QPY "Create component" 2019-12-06 RCSB QPY "Initial release" 2020-12-09 RCSB ##