data_85Y # _chem_comp.id 85Y _chem_comp.name ;2'-deoxy-5-{[(naphthalen-2-yl)methyl]carbamoyl}uridine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C21 H22 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-01-06 _chem_comp.pdbx_modified_date 2018-08-13 _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 491.388 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 85Y _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 5UC6 _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 85Y C2 C1 C 0 1 N N N 97.496 53.780 116.098 1.219 -0.593 -1.228 C2 85Y 1 85Y C20 C2 C 0 1 N N N 99.031 50.662 113.748 -2.130 -0.994 1.288 C20 85Y 2 85Y C24 C3 C 0 1 Y N N 100.359 49.516 110.901 -5.639 0.168 1.194 C24 85Y 3 85Y C30 C4 C 0 1 Y N N 97.720 50.681 108.619 -8.521 -0.700 -0.930 C30 85Y 4 85Y C33 C5 C 0 1 Y N N 99.277 48.992 106.904 -8.925 2.044 -0.580 C33 85Y 5 85Y C4 C6 C 0 1 N N N 99.165 53.145 114.589 -1.073 -0.250 -0.923 C4 85Y 6 85Y C5 C7 C 0 1 N N N 98.591 51.775 114.622 -0.955 -0.856 0.413 C5 85Y 7 85Y C23 C8 C 0 1 N N N 100.780 49.704 112.323 -4.450 -0.495 1.840 C23 85Y 8 85Y C25 C9 C 0 1 Y N N 99.245 50.147 110.435 -6.501 -0.578 0.450 C25 85Y 9 85Y C26 C10 C 0 1 Y N N 98.874 50.046 109.095 -7.610 0.037 -0.154 C26 85Y 10 85Y O4 O1 O 0 1 N N N 100.204 53.448 113.955 -2.147 0.154 -1.330 O4 85Y 11 85Y N3 N1 N 0 1 N N N 98.602 54.077 115.348 0.036 -0.149 -1.685 N3 85Y 12 85Y O2 O2 O 0 1 N N N 96.941 54.706 116.780 2.202 -0.483 -1.935 O2 85Y 13 85Y C6 C11 C 0 1 N N N 97.398 51.518 115.350 0.289 -1.297 0.820 C6 85Y 14 85Y N1 N2 N 0 1 N N N 96.894 52.483 116.108 1.352 -1.149 -0.013 N1 85Y 15 85Y "C1'" C12 C 0 1 N N R 95.656 52.382 116.871 2.673 -1.607 0.424 "C1'" 85Y 16 85Y "O4'" O3 O 0 1 N N N 95.884 52.596 118.241 3.640 -0.542 0.302 "O4'" 85Y 17 85Y "C2'" C13 C 0 1 N N N 94.964 51.060 116.798 3.192 -2.721 -0.512 "C2'" 85Y 18 85Y "C3'" C14 C 0 1 N N S 94.032 51.118 117.987 4.709 -2.446 -0.617 "C3'" 85Y 19 85Y "O3'" O4 O 0 1 N N N 92.727 51.624 117.695 5.456 -3.554 -0.111 "O3'" 85Y 20 85Y "C4'" C15 C 0 1 N N R 94.752 52.059 118.953 4.926 -1.198 0.267 "C4'" 85Y 21 85Y "C5'" C16 C 0 1 N N N 95.278 51.290 120.191 5.977 -0.278 -0.359 "C5'" 85Y 22 85Y "O5'" O5 O 0 1 N N N 96.082 50.163 119.765 6.194 0.847 0.494 "O5'" 85Y 23 85Y P P1 P 0 1 N N N 96.927 49.283 120.868 7.238 2.023 0.147 PA 85Y 24 85Y OP3 O6 O 0 1 N Y N 96.044 49.013 122.005 6.746 2.805 -1.171 O1A 85Y 25 85Y OP2 O7 O 0 1 N N N 97.536 48.177 120.054 7.318 3.051 1.383 O2A 85Y 26 85Y O21 O8 O 0 1 N N N 98.728 49.402 114.235 -2.036 -1.593 2.342 O21 85Y 27 85Y N22 N3 N 0 1 N N N 100.248 50.859 113.068 -3.310 -0.456 0.921 N22 85Y 28 85Y C27 C17 C 0 1 Y N N 99.629 49.131 108.228 -7.815 1.429 0.023 C27 85Y 29 85Y C28 C18 C 0 1 Y N N 100.753 48.470 108.765 -6.904 2.166 0.799 C28 85Y 30 85Y C29 C19 C 0 1 Y N N 101.143 48.689 110.059 -5.843 1.535 1.372 C29 85Y 31 85Y C31 C20 C 0 1 Y N N 97.356 50.433 107.279 -9.585 -0.070 -1.499 C31 85Y 32 85Y C32 C21 C 0 1 Y N N 98.134 49.639 106.434 -9.786 1.298 -1.325 C32 85Y 33 85Y H1 H1 H 0 1 N N N 97.134 51.332 109.251 -8.378 -1.761 -1.074 H1 85Y 34 85Y H2 H2 H 0 1 N N N 99.878 48.390 106.238 -9.094 3.103 -0.454 H2 85Y 35 85Y H3 H3 H 0 1 N N N 100.482 48.799 112.872 -4.194 0.033 2.759 H3 85Y 36 85Y H4 H4 H 0 1 N N N 101.876 49.792 112.328 -4.694 -1.531 2.072 H4 85Y 37 85Y H5 H5 H 0 1 N N N 98.642 50.733 111.112 -6.332 -1.637 0.323 H5 85Y 38 85Y H6 H6 H 0 1 N N N 98.987 55.000 115.372 -0.021 0.248 -2.569 H6 85Y 39 85Y H7 H7 H 0 1 N N N 96.911 50.556 115.287 0.416 -1.751 1.791 H7 85Y 40 85Y H8 H8 H 0 1 N N N 94.959 53.148 116.500 2.629 -1.963 1.453 H8 85Y 41 85Y H9 H9 H 0 1 N N N 94.404 50.955 115.857 3.012 -3.703 -0.073 H9 85Y 42 85Y H10 H10 H 0 1 N N N 95.680 50.230 116.893 2.721 -2.648 -1.492 H10 85Y 43 85Y H11 H11 H 0 1 N N N 93.963 50.119 118.443 4.988 -2.236 -1.650 H11 85Y 44 85Y H12 H12 H 0 1 N N N 92.204 51.629 118.488 5.310 -4.380 -0.593 H12 85Y 45 85Y H13 H13 H 0 1 N N N 94.069 52.859 119.276 5.229 -1.493 1.271 H13 85Y 46 85Y H14 H14 H 0 1 N N N 95.892 51.965 120.806 6.911 -0.826 -0.483 H14 85Y 47 85Y H15 H15 H 0 1 N N N 94.426 50.927 120.784 5.625 0.066 -1.332 H15 85Y 48 85Y HOP3 H16 H 0 0 N Y N 96.315 49.539 122.748 5.874 3.214 -1.084 H16 85Y 49 85Y HOP2 H17 H 0 0 N N N 98.445 48.382 119.870 7.930 3.787 1.243 H17 85Y 50 85Y H18 H18 H 0 1 N N N 100.726 51.737 113.089 -3.404 -0.043 0.048 H18 85Y 51 85Y H19 H19 H 0 1 N N N 101.313 47.783 108.148 -7.048 3.227 0.942 H19 85Y 52 85Y H20 H20 H 0 1 N N N 102.046 48.233 110.437 -5.144 2.104 1.968 H20 85Y 53 85Y H21 H21 H 0 1 N N N 96.447 50.871 106.894 -10.283 -0.639 -2.095 H21 85Y 54 85Y H22 H22 H 0 1 N N N 97.846 49.524 105.399 -10.639 1.773 -1.788 H22 85Y 55 85Y OP1 O9 O 0 1 N N N 98.045 50.287 121.060 8.575 1.438 -0.097 O1 85Y 56 # 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 85Y C32 C33 DOUB Y N 1 85Y C32 C31 SING Y N 2 85Y C33 C27 SING Y N 3 85Y C31 C30 DOUB Y N 4 85Y C27 C28 DOUB Y N 5 85Y C27 C26 SING Y N 6 85Y C30 C26 SING Y N 7 85Y C28 C29 SING Y N 8 85Y C26 C25 DOUB Y N 9 85Y C29 C24 DOUB Y N 10 85Y C25 C24 SING Y N 11 85Y C24 C23 SING N N 12 85Y C23 N22 SING N N 13 85Y N22 C20 SING N N 14 85Y C20 O21 DOUB N N 15 85Y C20 C5 SING N N 16 85Y O4 C4 DOUB N N 17 85Y C4 C5 SING N N 18 85Y C4 N3 SING N N 19 85Y C5 C6 DOUB N N 20 85Y N3 C2 SING N N 21 85Y C6 N1 SING N N 22 85Y C2 N1 SING N N 23 85Y C2 O2 DOUB N N 24 85Y N1 "C1'" SING N N 25 85Y "C2'" "C1'" SING N N 26 85Y "C2'" "C3'" SING N N 27 85Y "C1'" "O4'" SING N N 28 85Y "O3'" "C3'" SING N N 29 85Y "C3'" "C4'" SING N N 30 85Y "O4'" "C4'" SING N N 31 85Y "C4'" "C5'" SING N N 32 85Y "O5'" "C5'" SING N N 33 85Y "O5'" P SING N N 34 85Y OP2 P SING N N 35 85Y P OP3 SING N N 36 85Y C30 H1 SING N N 37 85Y C33 H2 SING N N 38 85Y C23 H3 SING N N 39 85Y C23 H4 SING N N 40 85Y C25 H5 SING N N 41 85Y N3 H6 SING N N 42 85Y C6 H7 SING N N 43 85Y "C1'" H8 SING N N 44 85Y "C2'" H9 SING N N 45 85Y "C2'" H10 SING N N 46 85Y "C3'" H11 SING N N 47 85Y "O3'" H12 SING N N 48 85Y "C4'" H13 SING N N 49 85Y "C5'" H14 SING N N 50 85Y "C5'" H15 SING N N 51 85Y OP3 HOP3 SING N N 52 85Y OP2 HOP2 SING N N 53 85Y N22 H18 SING N N 54 85Y C28 H19 SING N N 55 85Y C29 H20 SING N N 56 85Y C31 H21 SING N N 57 85Y C32 H22 SING N N 58 85Y P OP1 DOUB N N 59 # 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 85Y SMILES ACDLabs 12.01 "C3(N(C=C(C(=O)NCc2cc1ccccc1cc2)C(N3)=O)C4OC(C(C4)O)COP(O)(=O)O)=O" 85Y InChI InChI 1.03 "InChI=1S/C21H22N3O9P/c25-16-8-18(33-17(16)11-32-34(29,30)31)24-10-15(20(27)23-21(24)28)19(26)22-9-12-5-6-13-3-1-2-4-14(13)7-12/h1-7,10,16-18,25H,8-9,11H2,(H,22,26)(H,23,27,28)(H2,29,30,31)/t16-,17+,18+/m0/s1" 85Y InChIKey InChI 1.03 OIDHQCJPEWHGIY-RCCFBDPRSA-N 85Y SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3ccc4ccccc4c3)C(=O)NC2=O" 85Y SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3ccc4ccccc4c3)C(=O)NC2=O" 85Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc2cc(ccc2c1)CNC(=O)C3=CN(C(=O)NC3=O)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O" 85Y SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc2cc(ccc2c1)CNC(=O)C3=CN(C(=O)NC3=O)C4CC(C(O4)COP(=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 85Y "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-5-{[(naphthalen-2-yl)methyl]carbamoyl}uridine 5'-(dihydrogen phosphate) ; 85Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[5-(naphthalen-2-ylmethylcarbamoyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 85Y "Create component" 2017-01-06 RCSB 85Y "Initial release" 2017-10-11 RCSB 85Y "Modify atom id" 2017-10-11 RCSB 85Y "Modify atom id" 2017-08-13 RCSB 85Y "Modify leaving atom flag" 2017-08-13 RCSB #