data_1YF # _chem_comp.id 1YF _chem_comp.name ; [(2R,3R,4S,5S,6R)-4-formamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H27 N3 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-08-05 _chem_comp.pdbx_modified_date 2013-08-21 _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 575.355 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1YF _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 4LY3 _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 1YF O1F O1F O 0 1 N N N -1.141 11.591 49.726 4.414 -2.272 -3.209 O1F 1YF 1 1YF C1F C1F C 0 1 N N N -2.218 11.621 50.449 5.341 -2.976 -2.869 C1F 1YF 2 1YF N3Q N3Q N 0 1 N N N -2.906 12.764 51.085 5.817 -2.903 -1.610 N3Q 1YF 3 1YF C3Q C3Q C 0 1 N N S -4.258 12.764 51.696 5.214 -1.972 -0.653 C3Q 1YF 4 1YF C2Q C2Q C 0 1 N N R -5.335 13.237 50.709 5.856 -0.590 -0.808 C2Q 1YF 5 1YF O2Q O2Q O 0 1 N N N -5.400 12.240 49.667 5.576 -0.077 -2.112 O2Q 1YF 6 1YF C4Q C4Q C 0 1 N N S -4.289 13.683 52.907 5.454 -2.477 0.773 C4Q 1YF 7 1YF O4Q O4Q O 0 1 N N N -3.350 13.127 53.836 4.798 -3.734 0.952 O4Q 1YF 8 1YF C5Q C5Q C 0 1 N N R -5.673 13.816 53.536 4.891 -1.459 1.768 C5Q 1YF 9 1YF C6Q C6Q C 0 1 N N N -5.621 14.760 54.736 5.180 -1.928 3.196 C6Q 1YF 10 1YF O5Q O5Q O 0 1 N N N -6.647 14.272 52.582 5.507 -0.189 1.549 O5Q 1YF 11 1YF C1Q C1Q C 0 1 N N R -6.679 13.484 51.387 5.277 0.355 0.248 C1Q 1YF 12 1YF O3B O3B O 0 1 N N N -7.272 12.208 51.692 3.872 0.503 0.036 O3B 1YF 13 1YF PB PB P 0 1 N N N -8.887 12.119 51.827 3.064 1.843 0.416 PB 1YF 14 1YF O2B O2B O 0 1 N N N -9.524 13.251 51.082 3.292 2.168 1.842 O2B 1YF 15 1YF O1B O1B O 0 1 N N N -9.068 10.662 51.426 3.581 3.060 -0.502 O1B 1YF 16 1YF O3A O3A O 0 1 N N N -8.869 12.371 53.411 1.491 1.611 0.164 O3A 1YF 17 1YF PA PA P 0 1 N N N -9.859 12.254 54.660 0.159 2.396 0.612 PA 1YF 18 1YF O1A O1A O 0 1 N N N -10.431 13.631 54.903 0.352 3.850 0.413 O1A 1YF 19 1YF O2A O2A O 0 1 N N N -9.068 11.652 55.788 -0.140 2.102 2.167 O2A 1YF 20 1YF "O5'" "O5'" O 0 1 N N N -11.063 11.360 54.161 -1.086 1.893 -0.278 "O5'" 1YF 21 1YF "C5'" "C5'" C 0 1 N N N -10.874 9.955 54.122 -2.388 2.474 -0.192 "C5'" 1YF 22 1YF "C4'" "C4'" C 0 1 N N R -12.041 9.384 53.326 -3.328 1.764 -1.169 "C4'" 1YF 23 1YF "O4'" "O4'" O 0 1 N N N -13.236 9.765 53.976 -3.540 0.394 -0.765 "O4'" 1YF 24 1YF "C3'" "C3'" C 0 1 N N S -12.193 9.944 51.922 -4.748 2.382 -1.107 "C3'" 1YF 25 1YF "O3'" "O3'" O 0 1 N N N -11.332 9.315 50.985 -4.852 3.509 -1.980 "O3'" 1YF 26 1YF "C2'" "C2'" C 0 1 N N N -13.656 9.628 51.688 -5.633 1.213 -1.605 "C2'" 1YF 27 1YF "C1'" "C1'" C 0 1 N N R -14.273 9.872 53.045 -4.766 -0.040 -1.378 "C1'" 1YF 28 1YF N1 N1 N 0 1 N N N -14.899 11.173 53.262 -5.463 -0.975 -0.491 N1 1YF 29 1YF C2 C2 C 0 1 N N N -16.205 11.291 52.951 -5.717 -0.622 0.782 C2 1YF 30 1YF O2 O2 O 0 1 N N N -16.945 10.265 52.399 -5.364 0.471 1.183 O2 1YF 31 1YF C6 C6 C 0 1 N N N -14.208 12.171 53.847 -5.855 -2.196 -0.967 C6 1YF 32 1YF C5 C5 C 0 1 N N N -14.811 13.413 54.043 -6.498 -3.057 -0.150 C5 1YF 33 1YF C5M C5M C 0 1 N N N -14.088 14.603 54.666 -6.937 -4.407 -0.656 C5M 1YF 34 1YF C4 C4 C 0 1 N N N -16.158 13.518 53.736 -6.754 -2.675 1.189 C4 1YF 35 1YF N3 N3 N 0 1 N N N -16.814 12.481 53.172 -6.356 -1.461 1.618 N3 1YF 36 1YF O4 O4 O 0 1 N N N -16.828 14.680 53.963 -7.333 -3.435 1.945 O4 1YF 37 1YF H2 H2 H 0 1 N N N -2.685 10.661 50.611 5.782 -3.665 -3.574 H2 1YF 38 1YF H3 H3 H 0 1 N N N -4.507 11.743 52.022 4.142 -1.901 -0.839 H3 1YF 39 1YF H4 H4 H 0 1 N N N -4.996 14.188 50.273 6.935 -0.672 -0.671 H4 1YF 40 1YF H5 H5 H 0 1 N N N -4.539 12.128 49.281 5.950 0.799 -2.279 H5 1YF 41 1YF H6 H6 H 0 1 N N N -3.952 14.682 52.595 6.524 -2.597 0.942 H6 1YF 42 1YF H7 H7 H 0 1 N N N -3.325 13.663 54.620 4.908 -4.113 1.834 H7 1YF 43 1YF H8 H8 H 0 1 N N N -5.972 12.823 53.903 3.814 -1.370 1.626 H8 1YF 44 1YF H9 H9 H 0 1 N N N -4.872 14.398 55.456 6.257 -2.017 3.338 H9 1YF 45 1YF H10 H10 H 0 1 N N N -5.345 15.769 54.397 4.778 -1.203 3.904 H10 1YF 46 1YF H11 H11 H 0 1 N N N -6.608 14.793 55.220 4.710 -2.897 3.362 H11 1YF 47 1YF H12 H12 H 0 1 N N N -7.322 13.994 50.655 5.761 1.328 0.170 H12 1YF 48 1YF H13 H13 H 0 1 N N N -9.628 10.611 50.660 3.463 2.915 -1.450 H13 1YF 49 1YF H14 H14 H 0 1 N N N -9.046 12.258 56.519 -0.278 1.166 2.371 H14 1YF 50 1YF H15 H15 H 0 1 N N N -10.872 9.543 55.142 -2.769 2.365 0.823 H15 1YF 51 1YF H16 H16 H 0 1 N N N -9.922 9.713 53.627 -2.332 3.532 -0.447 H16 1YF 52 1YF H17 H17 H 0 1 N N N -11.950 8.289 53.277 -2.931 1.808 -2.183 H17 1YF 53 1YF H18 H18 H 0 1 N N N -12.042 11.034 51.936 -5.008 2.659 -0.085 H18 1YF 54 1YF H19 H19 H 0 1 N N N -10.431 9.546 51.177 -5.722 3.930 -1.977 H19 1YF 55 1YF H20 H20 H 0 1 N N N -14.089 10.297 50.930 -6.550 1.153 -1.019 H20 1YF 56 1YF H21 H21 H 0 1 N N N -13.790 8.582 51.374 -5.862 1.332 -2.664 H21 1YF 57 1YF H22 H22 H 0 1 N N N -15.019 9.085 53.229 -4.555 -0.522 -2.333 H22 1YF 58 1YF H23 H23 H 0 1 N N N -13.188 12.009 54.164 -5.651 -2.470 -1.992 H23 1YF 59 1YF H24 H24 H 0 1 N N N -13.034 14.342 54.840 -6.141 -5.134 -0.491 H24 1YF 60 1YF H25 H25 H 0 1 N N N -14.144 15.464 53.984 -7.833 -4.722 -0.121 H25 1YF 61 1YF H26 H26 H 0 1 N N N -14.565 14.862 55.623 -7.154 -4.342 -1.722 H26 1YF 62 1YF H27 H27 H 0 1 N N N -17.773 12.594 52.911 -6.531 -1.190 2.533 H27 1YF 63 1YF H1 H1 H 0 1 N N N -2.407 13.630 51.106 6.558 -3.466 -1.338 H1 1YF 64 # # 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 1YF O2Q C2Q SING N N 1 1YF O1F C1F DOUB N N 2 1YF C1F N3Q SING N N 3 1YF C2Q C1Q SING N N 4 1YF C2Q C3Q SING N N 5 1YF "O3'" "C3'" SING N N 6 1YF O2B PB DOUB N N 7 1YF N3Q C3Q SING N N 8 1YF C1Q O3B SING N N 9 1YF C1Q O5Q SING N N 10 1YF O1B PB SING N N 11 1YF "C2'" "C3'" SING N N 12 1YF "C2'" "C1'" SING N N 13 1YF O3B PB SING N N 14 1YF C3Q C4Q SING N N 15 1YF PB O3A SING N N 16 1YF "C3'" "C4'" SING N N 17 1YF O2 C2 DOUB N N 18 1YF O5Q C5Q SING N N 19 1YF C4Q C5Q SING N N 20 1YF C4Q O4Q SING N N 21 1YF C2 N3 SING N N 22 1YF C2 N1 SING N N 23 1YF "C1'" N1 SING N N 24 1YF "C1'" "O4'" SING N N 25 1YF N3 C4 SING N N 26 1YF N1 C6 SING N N 27 1YF "C4'" "O4'" SING N N 28 1YF "C4'" "C5'" SING N N 29 1YF O3A PA SING N N 30 1YF C5Q C6Q SING N N 31 1YF C4 O4 DOUB N N 32 1YF C4 C5 SING N N 33 1YF C6 C5 DOUB N N 34 1YF C5 C5M SING N N 35 1YF "C5'" "O5'" SING N N 36 1YF "O5'" PA SING N N 37 1YF PA O1A DOUB N N 38 1YF PA O2A SING N N 39 1YF C1F H2 SING N N 40 1YF C3Q H3 SING N N 41 1YF C2Q H4 SING N N 42 1YF O2Q H5 SING N N 43 1YF C4Q H6 SING N N 44 1YF O4Q H7 SING N N 45 1YF C5Q H8 SING N N 46 1YF C6Q H9 SING N N 47 1YF C6Q H10 SING N N 48 1YF C6Q H11 SING N N 49 1YF C1Q H12 SING N N 50 1YF O1B H13 SING N N 51 1YF O2A H14 SING N N 52 1YF "C5'" H15 SING N N 53 1YF "C5'" H16 SING N N 54 1YF "C4'" H17 SING N N 55 1YF "C3'" H18 SING N N 56 1YF "O3'" H19 SING N N 57 1YF "C2'" H20 SING N N 58 1YF "C2'" H21 SING N N 59 1YF "C1'" H22 SING N N 60 1YF C6 H23 SING N N 61 1YF C5M H24 SING N N 62 1YF C5M H25 SING N N 63 1YF C5M H26 SING N N 64 1YF N3 H27 SING N N 65 1YF N3Q H1 SING N N 66 # # 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 1YF SMILES ACDLabs 12.01 "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(NC=O)C3O)C)O)O)C" 1YF InChI InChI 1.03 "InChI=1S/C17H27N3O15P2/c1-7-4-20(17(26)19-15(7)25)11-3-9(22)10(33-11)5-31-36(27,28)35-37(29,30)34-16-14(24)12(18-6-21)13(23)8(2)32-16/h4,6,8-14,16,22-24H,3,5H2,1-2H3,(H,18,21)(H,27,28)(H,29,30)(H,19,25,26)/t8-,9+,10-,11-,12+,13-,14-,16-/m1/s1" 1YF InChIKey InChI 1.03 XDTNOGIJZRWAPO-ADAYKIPUSA-N 1YF SMILES_CANONICAL CACTVS 3.385 "C[C@H]1O[C@H](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)[C@H](O)[C@@H](NC=O)[C@@H]1O" 1YF SMILES CACTVS 3.385 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](NC=O)[CH]1O" 1YF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1[C@H]([C@@H]([C@H]([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)NC=O)O" 1YF SMILES "OpenEye OEToolkits" 1.7.6 "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)NC=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 1YF "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4S,5S,6R)-4-(formylamino)-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 1YF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4S,5S,6R)-4-formamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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 1YF "Create component" 2013-08-05 RCSB 1YF "Initial release" 2013-08-14 RCSB 1YF "Other modification" 2013-08-16 RCSB 1YF "Modify name" 2013-08-21 RCSB ##