data_3YN # _chem_comp.id 3YN _chem_comp.name ;[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,4R,6R)-4-hydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl dihydrogen diphosphate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H24 N2 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms TDP-4-keto-D-olivose _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-12-10 _chem_comp.pdbx_modified_date 2020-06-17 _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 530.314 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3YN _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 4RVH _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 3YN O4P O4P O 0 1 N N N -22.952 4.353 14.350 -3.814 -2.328 -0.529 O4P 3YN 1 3YN P2 P2 P 0 1 N N N -22.968 4.729 12.940 -3.227 -1.019 0.202 P2 3YN 2 3YN O3P O3P O 0 1 N N N -22.790 6.146 12.594 -3.563 -1.067 1.643 O3P 3YN 3 3YN O1 O1 O 0 1 N N N -24.348 4.242 12.387 -3.875 0.300 -0.456 O1 3YN 4 3YN C1 C1 C 0 1 N N R -24.595 4.048 11.010 -5.268 0.608 -0.371 C1 3YN 5 3YN C2 C2 C 0 1 N N N -26.038 4.410 10.732 -5.691 1.397 -1.613 C2 3YN 6 3YN C3 C3 C 0 1 N N R -26.990 3.466 11.455 -7.194 1.691 -1.531 C3 3YN 7 3YN O3 O3 O 0 1 N N N -28.320 3.663 11.024 -7.933 0.474 -1.653 O3 3YN 8 3YN C4 C4 C 0 1 N N N -26.608 2.045 11.221 -7.473 2.327 -0.184 C4 3YN 9 3YN O4 O4 O 0 1 N N N -27.431 1.203 11.025 -8.134 3.333 -0.094 O4 3YN 10 3YN C5 C5 C 0 1 N N R -25.152 1.744 11.327 -6.896 1.657 1.045 C5 3YN 11 3YN O5 O5 O 0 1 N N N -24.413 2.694 10.605 -5.511 1.386 0.801 O5 3YN 12 3YN C6 C6 C 0 1 N N N -24.862 0.381 10.780 -7.640 0.348 1.316 C6 3YN 13 3YN OPP OPP O 0 1 N N N -22.002 3.800 12.106 -1.628 -0.977 0.025 OPP 3YN 14 3YN P P P 0 1 N N N -20.454 3.536 12.198 -0.407 -1.786 0.693 P 3YN 15 3YN O1P O1P O 0 1 N N N -20.118 2.997 10.900 -0.734 -3.229 0.731 O1P 3YN 16 3YN O2P O2P O 0 1 N N N -20.178 2.705 13.341 -0.164 -1.251 2.192 O2P 3YN 17 3YN "O5'" "O5'" O 0 1 N N N -19.742 4.912 12.406 0.928 -1.561 -0.179 "O5'" 3YN 18 3YN "C5'" "C5'" C 0 1 N N N -18.358 4.991 12.643 2.159 -2.232 0.095 "C5'" 3YN 19 3YN "C4'" "C4'" C 0 1 N N R -17.895 6.423 12.589 3.217 -1.791 -0.919 "C4'" 3YN 20 3YN "O4'" "O4'" O 0 1 N N N -16.564 6.448 13.052 3.543 -0.396 -0.740 "O4'" 3YN 21 3YN "C3'" "C3'" C 0 1 N N S -17.864 6.951 11.184 4.562 -2.513 -0.653 "C3'" 3YN 22 3YN "O3'" "O3'" O 0 1 N N N -18.289 8.287 11.227 4.600 -3.780 -1.313 "O3'" 3YN 23 3YN "C2'" "C2'" C 0 1 N N N -16.419 6.943 10.781 5.585 -1.534 -1.278 "C2'" 3YN 24 3YN "C1'" "C1'" C 0 1 N N R -15.671 6.946 12.091 4.837 -0.188 -1.330 "C1'" 3YN 25 3YN N11 N11 N 0 1 N N N -14.442 6.182 12.067 5.575 0.822 -0.568 N11 3YN 26 3YN C21 C21 C 0 1 N N N -13.233 6.839 12.306 5.719 0.680 0.762 C21 3YN 27 3YN O21 O21 O 0 1 N N N -13.208 8.034 12.526 5.233 -0.287 1.318 O21 3YN 28 3YN N31 N31 N 0 1 N N N -12.088 6.227 12.302 6.392 1.593 1.487 N31 3YN 29 3YN C41 C41 C 0 1 N N N -12.038 4.942 12.076 6.937 2.670 0.886 C41 3YN 30 3YN O41 O41 O 0 1 N N N -10.960 4.376 12.075 7.547 3.496 1.541 O41 3YN 31 3YN C51 C51 C 0 1 N N N -13.268 4.202 11.830 6.793 2.832 -0.513 C51 3YN 32 3YN C5A C5A C 0 1 N N N -13.180 2.743 11.563 7.398 4.023 -1.210 C5A 3YN 33 3YN C61 C61 C 0 1 N N N -14.464 4.878 11.840 6.118 1.898 -1.217 C61 3YN 34 3YN H1 H1 H 0 1 N N N -22.820 5.128 14.883 -3.631 -2.363 -1.478 H1 3YN 35 3YN H2 H2 H 0 1 N N N -23.946 4.707 10.414 -5.841 -0.318 -0.317 H2 3YN 36 3YN H3 H3 H 0 1 N N N -26.223 5.439 11.075 -5.137 2.335 -1.656 H3 3YN 37 3YN H4 H4 H 0 1 N N N -26.222 4.346 9.649 -5.483 0.808 -2.507 H4 3YN 38 3YN H5 H5 H 0 1 N N N -26.919 3.672 12.533 -7.480 2.377 -2.328 H5 3YN 39 3YN H6 H6 H 0 1 N N N -28.704 2.827 10.789 -8.892 0.589 -1.610 H6 3YN 40 3YN H7 H7 H 0 1 N N N -24.861 1.768 12.388 -6.995 2.320 1.905 H7 3YN 41 3YN H8 H8 H 0 1 N N N -25.438 -0.370 11.341 -7.531 -0.316 0.458 H8 3YN 42 3YN H9 H9 H 0 1 N N N -25.147 0.344 9.718 -7.222 -0.131 2.201 H9 3YN 43 3YN H10 H10 H 0 1 N N N -23.787 0.168 10.878 -8.697 0.558 1.481 H10 3YN 44 3YN H11 H11 H 0 1 N N N -19.796 1.885 13.052 0.055 -0.311 2.244 H11 3YN 45 3YN H12 H12 H 0 1 N N N -18.137 4.576 13.637 2.494 -1.980 1.102 H12 3YN 46 3YN H13 H13 H 0 1 N N N -17.826 4.409 11.876 2.011 -3.309 0.021 H13 3YN 47 3YN H14 H14 H 0 1 N N N -18.548 7.052 13.213 2.873 -1.977 -1.936 H14 3YN 48 3YN H15 H15 H 0 1 N N N -18.471 6.330 10.509 4.737 -2.629 0.417 H15 3YN 49 3YN H16 H16 H 0 1 N N N -19.204 8.321 11.481 5.422 -4.271 -1.177 H16 3YN 50 3YN H17 H17 H 0 1 N N N -16.181 6.041 10.198 6.471 -1.454 -0.649 H17 3YN 51 3YN H18 H18 H 0 1 N N N -16.174 7.837 10.189 5.858 -1.858 -2.283 H18 3YN 52 3YN H19 H19 H 0 1 N N N -15.427 7.991 12.334 4.725 0.134 -2.365 H19 3YN 53 3YN H20 H20 H 0 1 N N N -11.246 6.739 12.472 6.486 1.475 2.445 H20 3YN 54 3YN H21 H21 H 0 1 N N N -12.128 2.425 11.606 6.671 4.835 -1.237 H21 3YN 55 3YN H22 H22 H 0 1 N N N -13.760 2.196 12.321 8.286 4.348 -0.669 H22 3YN 56 3YN H23 H23 H 0 1 N N N -13.587 2.528 10.564 7.672 3.748 -2.228 H23 3YN 57 3YN H24 H24 H 0 1 N N N -15.396 4.360 11.668 5.998 2.004 -2.285 H24 3YN 58 # # 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 3YN O5 C1 SING N N 1 3YN O5 C5 SING N N 2 3YN C2 C1 SING N N 3 3YN C2 C3 SING N N 4 3YN C6 C5 SING N N 5 3YN "C2'" "C3'" SING N N 6 3YN "C2'" "C1'" SING N N 7 3YN O1P P DOUB N N 8 3YN C1 O1 SING N N 9 3YN O3 C3 SING N N 10 3YN O4 C4 DOUB N N 11 3YN "C3'" "O3'" SING N N 12 3YN "C3'" "C4'" SING N N 13 3YN C4 C5 SING N N 14 3YN C4 C3 SING N N 15 3YN C5A C51 SING N N 16 3YN C51 C61 DOUB N N 17 3YN C51 C41 SING N N 18 3YN C61 N11 SING N N 19 3YN N11 "C1'" SING N N 20 3YN N11 C21 SING N N 21 3YN O41 C41 DOUB N N 22 3YN C41 N31 SING N N 23 3YN "C1'" "O4'" SING N N 24 3YN OPP P SING N N 25 3YN OPP P2 SING N N 26 3YN P "O5'" SING N N 27 3YN P O2P SING N N 28 3YN N31 C21 SING N N 29 3YN C21 O21 DOUB N N 30 3YN O1 P2 SING N N 31 3YN "O5'" "C5'" SING N N 32 3YN "C4'" "C5'" SING N N 33 3YN "C4'" "O4'" SING N N 34 3YN O3P P2 DOUB N N 35 3YN P2 O4P SING N N 36 3YN O4P H1 SING N N 37 3YN C1 H2 SING N N 38 3YN C2 H3 SING N N 39 3YN C2 H4 SING N N 40 3YN C3 H5 SING N N 41 3YN O3 H6 SING N N 42 3YN C5 H7 SING N N 43 3YN C6 H8 SING N N 44 3YN C6 H9 SING N N 45 3YN C6 H10 SING N N 46 3YN O2P H11 SING N N 47 3YN "C5'" H12 SING N N 48 3YN "C5'" H13 SING N N 49 3YN "C4'" H14 SING N N 50 3YN "C3'" H15 SING N N 51 3YN "O3'" H16 SING N N 52 3YN "C2'" H17 SING N N 53 3YN "C2'" H18 SING N N 54 3YN "C1'" H19 SING N N 55 3YN N31 H20 SING N N 56 3YN C5A H21 SING N N 57 3YN C5A H22 SING N N 58 3YN C5A H23 SING N N 59 3YN C61 H24 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 3YN SMILES ACDLabs 12.01 "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(=O)C(O)C3)C)O)O)C" 3YN InChI InChI 1.03 "InChI=1S/C16H24N2O14P2/c1-7-5-18(16(23)17-15(7)22)12-3-9(19)11(30-12)6-28-33(24,25)32-34(26,27)31-13-4-10(20)14(21)8(2)29-13/h5,8-13,19-20H,3-4,6H2,1-2H3,(H,24,25)(H,26,27)(H,17,22,23)/t8-,9+,10-,11-,12-,13-/m1/s1" 3YN InChIKey InChI 1.03 AONILRCSLAIOQE-LREJFELKSA-N 3YN SMILES_CANONICAL CACTVS 3.385 "C[C@H]1O[C@@H](C[C@@H](O)C1=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O" 3YN SMILES CACTVS 3.385 "C[CH]1O[CH](C[CH](O)C1=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O" 3YN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1C(=O)[C@@H](C[C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O" 3YN SMILES "OpenEye OEToolkits" 1.7.6 "CC1C(=O)C(CC(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O" # # 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 3YN "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,4R,6R)-4-hydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" 3YN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,4R,6R)-6-methyl-4-oxidanyl-5-oxidanylidene-oxan-2-yl] 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 3YN "Create component" 2014-12-10 RCSB 3YN "Initial release" 2015-01-28 RCSB 3YN "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3YN _pdbx_chem_comp_synonyms.name TDP-4-keto-D-olivose _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##