data_Y6W # _chem_comp.id Y6W _chem_comp.name "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-{3-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]propyl}phosphonate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H29 N2 O13 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-02-04 _chem_comp.pdbx_modified_date 2016-03-04 _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 512.402 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y6W _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 ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 Y6W C1 C1 C 0 1 N N R 24.209 -25.322 6.251 -5.674 -0.885 -0.106 C1 Y6W 1 Y6W C2 C2 C 0 1 N N R 23.377 -26.595 6.158 -6.750 -0.555 -1.143 C2 Y6W 2 Y6W O2 O2 O 0 1 N N N 22.032 -26.261 5.788 -6.617 -1.432 -2.264 O2 Y6W 3 Y6W C3 C3 C 0 1 N N R 23.373 -27.302 7.502 -6.576 0.895 -1.605 C3 Y6W 4 Y6W O3 O3 O 0 1 N N N 22.679 -28.552 7.383 -7.620 1.234 -2.519 O3 Y6W 5 Y6W C4 C4 C 0 1 N N R 24.804 -27.557 7.941 -6.642 1.819 -0.386 C4 Y6W 6 Y6W O4 O4 O 0 1 N N N 25.437 -28.451 7.015 -7.932 1.719 0.220 O4 Y6W 7 Y6W C5 C5 C 0 1 N N R 25.561 -26.240 7.974 -5.570 1.398 0.623 C5 Y6W 8 Y6W O5 O5 O 0 1 N N N 25.552 -25.644 6.665 -5.771 0.031 0.987 O5 Y6W 9 Y6W C6 C6 C 0 1 N N N 27.006 -26.493 8.409 -5.668 2.278 1.870 C6 Y6W 10 Y6W O6 O6 O 0 1 N N N 27.764 -26.970 7.294 -4.596 1.964 2.761 O6 Y6W 11 Y6W "C1'" "C1'" C 0 1 N N R 28.158 -24.816 13.526 4.953 -0.442 -0.634 "C1'" Y6W 12 Y6W "C2'" "C2'" C 0 1 N N R 28.673 -25.821 12.509 5.523 -1.406 0.438 "C2'" Y6W 13 Y6W "O2'" "O2'" O 0 1 N N N 30.030 -26.167 12.822 6.832 -1.853 0.077 "O2'" Y6W 14 Y6W "C3'" "C3'" C 0 1 N N S 28.634 -25.066 11.190 4.509 -2.575 0.394 "C3'" Y6W 15 Y6W "O3'" "O3'" O 0 1 N N N 29.965 -24.938 10.671 5.006 -3.639 -0.420 "O3'" Y6W 16 Y6W "C4'" "C4'" C 0 1 N N R 28.101 -23.693 11.566 3.247 -1.957 -0.238 "C4'" Y6W 17 Y6W "O4'" "O4'" O 0 1 N N N 27.334 -23.932 12.754 3.523 -0.565 -0.476 "O4'" Y6W 18 Y6W "C5'" "C5'" C 0 1 N N N 27.179 -23.182 10.457 2.062 -2.097 0.720 "C5'" Y6W 19 Y6W "O5'" "O5'" O 0 1 N N N 26.277 -24.221 10.069 0.874 -1.627 0.080 "O5'" Y6W 20 Y6W CAK CAK C 0 1 N N N 23.553 -24.350 7.237 -4.291 -0.766 -0.749 CAK Y6W 21 Y6W CAL CAL C 0 1 N N N 24.599 -23.356 7.747 -3.223 -1.213 0.250 CAL Y6W 22 Y6W CAM CAM C 0 1 N N N 24.199 -22.863 9.139 -1.840 -1.094 -0.393 CAM Y6W 23 Y6W PAN PAN P 0 1 N N N 24.703 -24.076 10.375 -0.567 -1.628 0.798 PAN Y6W 24 Y6W OAO OAO O 0 1 N N N 24.550 -23.482 11.720 -0.544 -0.614 2.049 OAO Y6W 25 Y6W NAZ NAZ N 0 1 N N N 27.336 -25.483 14.561 5.385 0.933 -0.371 NAZ Y6W 26 Y6W CBA CBA C 0 1 N N N 27.921 -25.999 15.651 6.157 1.572 -1.269 CBA Y6W 27 Y6W CBB CBB C 0 1 N N N 25.950 -25.573 14.400 4.995 1.558 0.782 CBB Y6W 28 Y6W CBC CBC C 0 1 N N N 25.204 -26.203 15.385 5.392 2.826 1.023 CBC Y6W 29 Y6W CBD CBD C 0 1 N N N 25.861 -26.720 16.494 6.208 3.484 0.073 CBD Y6W 30 Y6W OBE OBE O 0 1 N N N 29.270 -25.905 15.797 6.488 1.000 -2.290 OBE Y6W 31 Y6W NBF NBF N 0 1 N N N 27.193 -26.608 16.601 6.567 2.836 -1.054 NBF Y6W 32 Y6W OBG OBG O 0 1 N N N 25.152 -27.343 17.474 6.580 4.628 0.268 OBG Y6W 33 Y6W OBH OBH O 0 1 N N N 24.055 -25.370 10.068 -0.880 -2.993 1.276 OBH Y6W 34 Y6W H1 H1 H 0 1 N N N 24.233 -24.847 5.259 -5.819 -1.902 0.258 H1 Y6W 35 Y6W H2 H2 H 0 1 N N N 23.824 -27.260 5.404 -7.736 -0.679 -0.697 H2 Y6W 36 Y6W HO2 HO2 H 0 1 N N N 21.513 -27.054 5.730 -7.269 -1.280 -2.962 HO2 Y6W 37 Y6W H3 H3 H 0 1 N N N 22.877 -26.660 8.245 -5.609 1.008 -2.096 H3 Y6W 38 Y6W HO3 HO3 H 0 1 N N N 22.676 -28.995 8.224 -7.572 2.141 -2.853 HO3 Y6W 39 Y6W H4 H4 H 0 1 N N N 24.799 -27.994 8.950 -6.463 2.848 -0.698 H4 Y6W 40 Y6W HO4 HO4 H 0 1 N N N 26.332 -28.610 7.290 -8.045 2.279 1.000 HO4 Y6W 41 Y6W H5 H5 H 0 1 N N N 25.082 -25.568 8.701 -4.583 1.513 0.174 H5 Y6W 42 Y6W H6 H6 H 0 1 N N N 27.447 -25.555 8.778 -5.604 3.327 1.581 H6 Y6W 43 Y6W H6A H6A H 0 1 N N N 27.021 -27.246 9.211 -6.621 2.096 2.369 H6A Y6W 44 Y6W HO6 HO6 H 0 1 N N N 28.661 -27.127 7.564 -4.596 2.485 3.576 HO6 Y6W 45 Y6W "H1'" "H1'" H 0 1 N N N 29.000 -24.279 13.986 5.258 -0.754 -1.632 "H1'" Y6W 46 Y6W "H2'" "H2'" H 0 1 N N N 28.020 -26.706 12.471 5.532 -0.935 1.420 "H2'" Y6W 47 Y6W "HO2'" "HO2'" H 0 0 N N N 30.352 -26.795 12.186 7.230 -2.459 0.716 "HO2'" Y6W 48 Y6W "H3'" "H3'" H 0 1 N N N 27.960 -25.563 10.477 4.295 -2.932 1.401 "H3'" Y6W 49 Y6W "HO3'" "HO3'" H 0 0 N N N 29.940 -24.466 9.847 5.832 -4.026 -0.100 "HO3'" Y6W 50 Y6W "H4'" "H4'" H 0 1 N N N 28.927 -22.987 11.741 3.024 -2.454 -1.182 "H4'" Y6W 51 Y6W "H5'" "H5'" H 0 1 N N N 26.606 -22.318 10.826 1.938 -3.145 0.992 "H5'" Y6W 52 Y6W "H5'A" "H5'A" H 0 0 N N N 27.783 -22.878 9.589 2.249 -1.508 1.617 "H5'A" Y6W 53 Y6W HAK HAK H 0 1 N N N 22.745 -23.803 6.730 -4.247 -1.398 -1.636 HAK Y6W 54 Y6W HAKA HAKA H 0 0 N N N 23.138 -24.913 8.086 -4.110 0.271 -1.033 HAKA Y6W 55 Y6W HAL HAL H 0 1 N N N 25.580 -23.851 7.801 -3.267 -0.581 1.137 HAL Y6W 56 Y6W HALA HALA H 0 0 N N N 24.658 -22.500 7.058 -3.403 -2.250 0.535 HALA Y6W 57 Y6W HAM HAM H 0 1 N N N 24.695 -21.903 9.344 -1.796 -1.727 -1.280 HAM Y6W 58 Y6W HAMA HAMA H 0 0 N N N 23.108 -22.729 9.181 -1.659 -0.057 -0.677 HAMA Y6W 59 Y6W HOAO HOAO H 0 0 N N N 24.013 -24.051 12.259 -0.345 0.301 1.809 HOAO Y6W 60 Y6W HBB HBB H 0 1 N N N 25.470 -25.160 13.525 4.371 1.040 1.495 HBB Y6W 61 Y6W HBC HBC H 0 1 N N N 24.132 -26.290 15.291 5.091 3.330 1.929 HBC Y6W 62 Y6W HNBF HNBF H 0 0 N N N 27.653 -26.986 17.404 7.123 3.282 -1.712 HNBF Y6W 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 Y6W C2 C1 SING N N 1 Y6W C1 O5 SING N N 2 Y6W C1 CAK SING N N 3 Y6W C1 H1 SING N N 4 Y6W O2 C2 SING N N 5 Y6W C2 C3 SING N N 6 Y6W C2 H2 SING N N 7 Y6W O2 HO2 SING N N 8 Y6W O3 C3 SING N N 9 Y6W C3 C4 SING N N 10 Y6W C3 H3 SING N N 11 Y6W O3 HO3 SING N N 12 Y6W O4 C4 SING N N 13 Y6W C4 C5 SING N N 14 Y6W C4 H4 SING N N 15 Y6W O4 HO4 SING N N 16 Y6W O5 C5 SING N N 17 Y6W C5 C6 SING N N 18 Y6W C5 H5 SING N N 19 Y6W O6 C6 SING N N 20 Y6W C6 H6 SING N N 21 Y6W C6 H6A SING N N 22 Y6W O6 HO6 SING N N 23 Y6W "C2'" "C1'" SING N N 24 Y6W "O4'" "C1'" SING N N 25 Y6W "C1'" NAZ SING N N 26 Y6W "C1'" "H1'" SING N N 27 Y6W "C3'" "C2'" SING N N 28 Y6W "C2'" "O2'" SING N N 29 Y6W "C2'" "H2'" SING N N 30 Y6W "O2'" "HO2'" SING N N 31 Y6W "O3'" "C3'" SING N N 32 Y6W "C3'" "C4'" SING N N 33 Y6W "C3'" "H3'" SING N N 34 Y6W "O3'" "HO3'" SING N N 35 Y6W "C5'" "C4'" SING N N 36 Y6W "C4'" "O4'" SING N N 37 Y6W "C4'" "H4'" SING N N 38 Y6W "O5'" "C5'" SING N N 39 Y6W "C5'" "H5'" SING N N 40 Y6W "C5'" "H5'A" SING N N 41 Y6W "O5'" PAN SING N N 42 Y6W CAK CAL SING N N 43 Y6W CAK HAK SING N N 44 Y6W CAK HAKA SING N N 45 Y6W CAL CAM SING N N 46 Y6W CAL HAL SING N N 47 Y6W CAL HALA SING N N 48 Y6W CAM PAN SING N N 49 Y6W CAM HAM SING N N 50 Y6W CAM HAMA SING N N 51 Y6W OBH PAN DOUB N N 52 Y6W PAN OAO SING N N 53 Y6W OAO HOAO SING N N 54 Y6W CBB NAZ SING N N 55 Y6W NAZ CBA SING N N 56 Y6W CBA OBE DOUB N N 57 Y6W CBA NBF SING N N 58 Y6W CBB CBC DOUB N N 59 Y6W CBB HBB SING N N 60 Y6W CBC CBD SING N N 61 Y6W CBC HBC SING N N 62 Y6W CBD NBF SING N N 63 Y6W CBD OBG DOUB N N 64 Y6W NBF HNBF SING N N 65 # 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 Y6W SMILES ACDLabs 12.01 "C1(OC(C(C(C1O)O)O)CO)CCCP(OCC3C(C(C(N2C(=O)NC(C=C2)=O)O3)O)O)(O)=O" Y6W InChI InChI 1.03 "InChI=1S/C18H29N2O13P/c21-6-9-13(24)15(26)12(23)8(32-9)2-1-5-34(29,30)31-7-10-14(25)16(27)17(33-10)20-4-3-11(22)19-18(20)28/h3-4,8-10,12-17,21,23-27H,1-2,5-7H2,(H,29,30)(H,19,22,28)/t8-,9-,10-,12+,13+,14-,15-,16-,17-/m1/s1" Y6W InChIKey InChI 1.03 PDUJCKZVDKZKPQ-RUIRHDHUSA-N Y6W SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@H](CCC[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1O" Y6W SMILES CACTVS 3.385 "OC[CH]1O[CH](CCC[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O" Y6W SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CCC[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O)O" Y6W SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(CCCC3C(C(C(C(O3)CO)O)O)O)O)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 Y6W "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-{3-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]propyl}phosphonate (non-preferred name)" Y6W "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-[3-[(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]propyl]phosphinic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y6W "Create component" 2016-02-04 EBI Y6W "Initial release" 2016-03-09 RCSB #