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 
# 
