data_YAD # _chem_comp.id YAD _chem_comp.name "(phenylmethyl) (2~{S})-2-[5-oxidanyl-6-oxidanylidene-4-(2-pyridin-4-ylethylcarbamoyl)-1~{H}-pyrimidin-2-yl]pyrrolidine-1-carboxylate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H25 N5 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-02-15 _chem_comp.pdbx_modified_date 2022-02-11 _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 463.486 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YAD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 7LP7 _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 YAD O15 O1 O 0 1 N N N -32.330 6.971 12.894 2.625 -1.732 1.038 O15 YAD 1 YAD O16 O2 O 0 1 N N N -30.622 7.369 14.303 1.020 -2.823 -0.038 O16 YAD 2 YAD C02 C1 C 0 1 N N N -29.147 4.616 17.641 2.707 3.007 1.105 C02 YAD 3 YAD C03 C2 C 0 1 N N N -30.138 4.034 16.707 1.713 2.284 0.465 C03 YAD 4 YAD C05 C3 C 0 1 N N N -31.462 6.173 16.822 3.280 0.820 -0.410 C05 YAD 5 YAD C07 C4 C 0 1 N N N -29.324 6.003 18.169 4.095 2.558 0.936 C07 YAD 6 YAD C09 C5 C 0 1 N N S -32.674 6.918 16.370 3.565 -0.395 -1.255 C09 YAD 7 YAD C10 C6 C 0 1 N N N -33.993 6.319 17.212 3.671 0.012 -2.740 C10 YAD 8 YAD C11 C7 C 0 1 N N N -34.462 5.310 16.530 2.982 -1.168 -3.474 C11 YAD 9 YAD C12 C8 C 0 1 N N N -34.005 5.544 15.030 1.855 -1.539 -2.478 C12 YAD 10 YAD C14 C9 C 0 1 N N N -31.950 7.001 14.018 2.054 -1.961 -0.010 C14 YAD 11 YAD C24 C10 C 0 1 N N N -29.959 2.622 16.169 0.296 2.691 0.592 C24 YAD 12 YAD C27 C11 C 0 1 N N N -30.443 0.935 14.367 -2.070 2.386 0.093 C27 YAD 13 YAD C28 C12 C 0 1 N N N -29.953 0.989 12.916 -2.950 1.423 -0.707 C28 YAD 14 YAD C29 C13 C 0 1 Y N N -30.574 2.094 12.056 -4.393 1.837 -0.577 C29 YAD 15 YAD C30 C14 C 0 1 Y N N -31.943 2.305 12.005 -4.960 2.727 -1.477 C30 YAD 16 YAD C31 C15 C 0 1 Y N N -32.463 3.309 11.196 -6.287 3.083 -1.327 C31 YAD 17 YAD C33 C16 C 0 1 Y N N -30.359 3.908 10.478 -6.507 1.735 0.527 C33 YAD 18 YAD C34 C17 C 0 1 Y N N -29.786 2.920 11.267 -5.188 1.333 0.441 C34 YAD 19 YAD N04 N1 N 0 1 N N N -31.281 4.802 16.299 2.047 1.210 -0.273 N04 YAD 20 YAD N06 N2 N 0 1 N N N -30.480 6.783 17.758 4.318 1.466 0.173 N06 YAD 21 YAD N13 N3 N 0 1 N N N -32.867 6.653 15.091 2.455 -1.353 -1.144 N13 YAD 22 YAD N26 N4 N 0 1 N N N -30.592 2.272 14.917 -0.667 1.983 -0.032 N26 YAD 23 YAD N32 N5 N 0 1 Y N N -31.671 4.076 10.464 -7.011 2.587 -0.344 N32 YAD 24 YAD O01 O3 O 0 1 N N N -28.054 3.826 18.003 2.409 4.096 1.857 O01 YAD 25 YAD O08 O4 O 0 1 N N N -28.527 6.469 18.919 5.017 3.152 1.468 O08 YAD 26 YAD O25 O5 O 0 1 N N N -29.309 1.833 16.765 -0.001 3.662 1.260 O25 YAD 27 YAD H2 H2 H 0 1 N N N -32.578 7.992 16.590 4.495 -0.862 -0.931 H2 YAD 28 YAD H3 H3 H 0 1 N N N -33.681 5.985 18.212 3.138 0.945 -2.924 H3 YAD 29 YAD H4 H4 H 0 1 N N N -34.763 7.098 17.309 4.715 0.101 -3.042 H4 YAD 30 YAD H5 H5 H 0 1 N N N -35.560 5.282 16.595 2.568 -0.846 -4.430 H5 YAD 31 YAD H6 H6 H 0 1 N N N -34.048 4.365 16.912 3.673 -2.000 -3.611 H6 YAD 32 YAD H7 H7 H 0 1 N N N -34.851 5.897 14.422 1.002 -0.874 -2.606 H7 YAD 33 YAD H8 H8 H 0 1 N N N -33.609 4.612 14.601 1.553 -2.577 -2.616 H8 YAD 34 YAD H9 H9 H 0 1 N N N -31.416 0.422 14.399 -2.194 3.398 -0.293 H9 YAD 35 YAD H10 H10 H 0 1 N N N -29.714 0.376 14.972 -2.363 2.359 1.143 H10 YAD 36 YAD H11 H11 H 0 1 N N N -30.182 0.022 12.444 -2.657 1.450 -1.756 H11 YAD 37 YAD H12 H12 H 0 1 N N N -28.864 1.141 12.931 -2.826 0.412 -0.320 H12 YAD 38 YAD H13 H13 H 0 1 N N N -32.606 1.689 12.594 -4.372 3.137 -2.285 H13 YAD 39 YAD H14 H14 H 0 1 N N N -33.531 3.466 11.164 -6.735 3.776 -2.024 H14 YAD 40 YAD H15 H15 H 0 1 N N N -29.730 4.543 9.872 -7.133 1.346 1.317 H15 YAD 41 YAD H16 H16 H 0 1 N N N -28.714 2.793 11.267 -4.781 0.635 1.157 H16 YAD 42 YAD H17 H17 H 0 1 N N N -30.613 7.714 18.099 5.224 1.141 0.045 H17 YAD 43 YAD H18 H18 H 0 1 N N N -31.135 2.954 14.427 -0.431 1.208 -0.565 H18 YAD 44 YAD H19 H19 H 0 1 N N N -28.183 2.941 17.683 3.180 4.524 2.253 H19 YAD 45 YAD C35 C35 C 0 1 N N N ? ? ? 0.641 -3.441 1.220 C35 YAD 46 YAD C36 C36 C 0 1 Y N N ? ? ? -0.526 -4.367 0.994 C36 YAD 47 YAD C37 C37 C 0 1 Y N N ? ? ? -0.304 -5.694 0.675 C37 YAD 48 YAD C38 C38 C 0 1 Y N N ? ? ? -1.374 -6.543 0.468 C38 YAD 49 YAD C39 C39 C 0 1 Y N N ? ? ? -2.667 -6.066 0.581 C39 YAD 50 YAD C40 C40 C 0 1 Y N N ? ? ? -2.889 -4.740 0.900 C40 YAD 51 YAD C41 C41 C 0 1 Y N N ? ? ? -1.818 -3.891 1.112 C41 YAD 52 YAD H1 H1 H 0 1 N N N ? ? ? 1.485 -4.008 1.614 H1 YAD 53 YAD H20 H20 H 0 1 N N N ? ? ? 0.359 -2.667 1.934 H20 YAD 54 YAD H21 H21 H 0 1 N N N ? ? ? 0.706 -6.066 0.588 H21 YAD 55 YAD H22 H22 H 0 1 N N N ? ? ? -1.201 -7.580 0.219 H22 YAD 56 YAD H23 H23 H 0 1 N N N ? ? ? -3.503 -6.730 0.418 H23 YAD 57 YAD H24 H24 H 0 1 N N N ? ? ? -3.899 -4.367 0.988 H24 YAD 58 YAD H25 H25 H 0 1 N N N ? ? ? -1.992 -2.855 1.362 H25 YAD 59 # # 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 YAD N32 C33 DOUB Y N 1 YAD N32 C31 SING Y N 2 YAD C33 C34 SING Y N 3 YAD C31 C30 DOUB Y N 4 YAD C34 C29 DOUB Y N 5 YAD C30 C29 SING Y N 6 YAD C29 C28 SING N N 7 YAD O15 C14 DOUB N N 8 YAD C28 C27 SING N N 9 YAD C14 O16 SING N N 10 YAD C14 N13 SING N N 11 YAD C27 N26 SING N N 12 YAD N26 C24 SING N N 13 YAD C12 N13 SING N N 14 YAD C12 C11 SING N N 15 YAD N13 C09 SING N N 16 YAD C24 C03 SING N N 17 YAD C24 O25 DOUB N N 18 YAD N04 C03 SING N N 19 YAD N04 C05 DOUB N N 20 YAD C09 C05 SING N N 21 YAD C09 C10 SING N N 22 YAD C11 C10 SING N N 23 YAD C03 C02 DOUB N N 24 YAD C05 N06 SING N N 25 YAD C02 O01 SING N N 26 YAD C02 C07 SING N N 27 YAD N06 C07 SING N N 28 YAD C07 O08 DOUB N N 29 YAD C09 H2 SING N N 30 YAD C10 H3 SING N N 31 YAD C10 H4 SING N N 32 YAD C11 H5 SING N N 33 YAD C11 H6 SING N N 34 YAD C12 H7 SING N N 35 YAD C12 H8 SING N N 36 YAD C27 H9 SING N N 37 YAD C27 H10 SING N N 38 YAD C28 H11 SING N N 39 YAD C28 H12 SING N N 40 YAD C30 H13 SING N N 41 YAD C31 H14 SING N N 42 YAD C33 H15 SING N N 43 YAD C34 H16 SING N N 44 YAD N06 H17 SING N N 45 YAD N26 H18 SING N N 46 YAD O01 H19 SING N N 47 YAD O16 C35 SING N N 48 YAD C35 C36 SING N N 49 YAD C36 C37 SING Y N 50 YAD C37 C38 DOUB Y N 51 YAD C38 C39 SING Y N 52 YAD C39 C40 DOUB Y N 53 YAD C40 C41 SING Y N 54 YAD C41 C36 DOUB Y N 55 YAD C35 H1 SING N N 56 YAD C35 H20 SING N N 57 YAD C37 H21 SING N N 58 YAD C38 H22 SING N N 59 YAD C39 H23 SING N N 60 YAD C40 H24 SING N N 61 YAD C41 H25 SING N N 62 # # 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 YAD InChI InChI 1.03 "InChI=1S/C24H25N5O5/c30-20-19(22(31)26-13-10-16-8-11-25-12-9-16)27-21(28-23(20)32)18-7-4-14-29(18)24(33)34-15-17-5-2-1-3-6-17/h1-3,5-6,8-9,11-12,18,30H,4,7,10,13-15H2,(H,26,31)(H,27,28,32)/t18-/m0/s1" YAD InChIKey InChI 1.03 PLCSROHBVUGSBJ-SFHVURJKSA-N YAD SMILES_CANONICAL CACTVS 3.385 "OC1=C(N=C(NC1=O)[C@@H]2CCCN2C(=O)OCc3ccccc3)C(=O)NCCc4ccncc4" YAD SMILES CACTVS 3.385 "OC1=C(N=C(NC1=O)[CH]2CCCN2C(=O)OCc3ccccc3)C(=O)NCCc4ccncc4" YAD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)COC(=O)N2CCC[C@H]2C3=NC(=C(C(=O)N3)O)C(=O)NCCc4ccncc4" YAD SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)COC(=O)N2CCCC2C3=NC(=C(C(=O)N3)O)C(=O)NCCc4ccncc4" # _pdbx_chem_comp_identifier.comp_id YAD _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 "(phenylmethyl) (2~{S})-2-[5-oxidanyl-6-oxidanylidene-4-(2-pyridin-4-ylethylcarbamoyl)-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 YAD "Create component" 2021-02-15 RCSB YAD "Initial release" 2022-02-16 RCSB ##