data_URU
# 
_chem_comp.id                                    URU 
_chem_comp.name                                  
"((2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-(2- ((((2R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)- 3,4-dihydroxytetrahydrofuran-2-yl)methyl)amino)-2-oxoethyl)-4- hydroxytetrahydrofuran-2-yl)methyl phosphate" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C20 H26 N5 O14 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-01-07 
_chem_comp.pdbx_modified_date                    2014-07-03 
_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                        591.419 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     URU 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        4O41 
_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 
URU P     P     P 0 1 N N N 8.858  -1.049 9.850  -5.936 3.625  0.733  P     URU 1  
URU OP1   OP1   O 0 1 N N N 9.016  0.138  8.973  -6.589 3.395  -0.575 OP1   URU 2  
URU "O5'" "O5'" O 0 1 N N N 7.303  -1.392 10.016 -4.976 2.380  1.080  "O5'" URU 3  
URU "C5'" "C5'" C 0 1 N N N 6.408  -1.433 8.886  -3.943 1.925  0.204  "C5'" URU 4  
URU "C4'" "C4'" C 0 1 N N S 5.039  -1.832 9.363  -3.227 0.730  0.837  "C4'" URU 5  
URU "C3'" "C3'" C 0 1 N N S 4.442  -1.058 10.531 -2.091 0.223  -0.086 "C3'" URU 6  
URU "C6'" "C6'" C 0 1 N N N 3.887  0.313  10.144 -0.795 0.997  0.166  "C6'" URU 7  
URU "C2'" "C2'" C 0 1 N N R 3.442  -2.055 11.096 -1.946 -1.253 0.357  "C2'" URU 8  
URU "O2'" "O2'" O 0 1 N N N 2.245  -2.012 10.296 -0.868 -1.394 1.284  "O2'" URU 9  
URU "C1'" "C1'" C 0 1 N N R 4.209  -3.373 10.920 -3.291 -1.576 1.038  "C1'" URU 10 
URU "O4'" "O4'" O 0 1 N N N 5.100  -3.202 9.858  -4.116 -0.404 0.932  "O4'" URU 11 
URU N1    N1    N 0 1 N N N 4.942  -3.681 12.156 -3.936 -2.702 0.358  N1    URU 12 
URU C6    C6    C 0 1 N N N 6.284  -3.423 12.301 -4.120 -3.882 1.027  C6    URU 13 
URU C5    C5    C 0 1 N N N 6.953  -3.690 13.433 -4.714 -4.920 0.400  C5    URU 14 
URU C4    C4    C 0 1 N N N 6.257  -4.269 14.544 -5.137 -4.764 -0.942 C4    URU 15 
URU N3    N3    N 0 1 N N N 4.921  -4.486 14.311 -4.937 -3.585 -1.566 N3    URU 16 
URU C2    C2    C 0 1 N N N 4.221  -4.222 13.192 -4.346 -2.565 -0.916 C2    URU 17 
URU O2    O2    O 0 1 N N N 3.034  -4.448 13.090 -4.177 -1.507 -1.489 O2    URU 18 
URU O4    O4    O 0 1 N N N 6.779  -4.545 15.614 -5.675 -5.686 -1.528 O4    URU 19 
URU OP2   OP2   O 0 1 N N N 9.421  -1.049 11.228 -5.060 4.974  0.664  OP2   URU 20 
URU C     C     C 0 1 N N N 3.263  0.997  11.337 0.250  0.565  -0.830 C     URU 21 
URU O3    O3    O 0 1 N N N 3.511  0.720  12.501 -0.014 -0.280 -1.659 O3    URU 22 
URU "NZ'" "NZ'" N 0 1 N N N 2.330  1.996  11.027 1.479  1.117  -0.798 "NZ'" URU 23 
URU "CZ'" "CZ'" C 0 1 N N N 1.656  2.802  12.030 2.496  0.696  -1.766 "CZ'" URU 24 
URU "CY'" "CY'" C 0 1 N N R 0.190  2.339  12.049 3.791  1.471  -1.514 "CY'" URU 25 
URU "CX'" "CX'" C 0 1 N N S -0.502 2.774  13.335 4.833  1.115  -2.592 "CX'" URU 26 
URU "OX'" "OX'" O 0 1 N N N -0.849 4.136  13.211 5.218  2.283  -3.321 "OX'" URU 27 
URU "CW'" "CW'" C 0 1 N N R -1.617 1.746  13.448 6.033  0.557  -1.791 "CW'" URU 28 
URU "OW'" "OW'" O 0 1 N N N -2.634 2.136  12.569 7.270  1.029  -2.329 "OW'" URU 29 
URU "CV'" "CV'" C 0 1 N N R -0.964 0.463  12.928 5.783  1.145  -0.379 "CV'" URU 30 
URU "OY'" "OY'" O 0 1 N N N 0.101  0.871  12.106 4.346  1.095  -0.243 "OY'" URU 31 
URU N11   N11   N 0 1 N N N -0.428 -0.373 14.026 6.427  0.320  0.646  N11   URU 32 
URU C16   C16   C 0 1 N N N 0.925  -0.569 14.218 7.452  0.840  1.389  C16   URU 33 
URU C15   C15   C 0 1 N N N 1.370  -1.394 15.192 8.045  0.079  2.334  C15   URU 34 
URU C14   C14   C 0 1 N N N 0.453  -2.060 16.050 7.592  -1.247 2.536  C14   URU 35 
URU N13   N13   N 0 1 N N N -0.882 -1.810 15.795 6.580  -1.722 1.783  N13   URU 36 
URU C12   C12   C 0 1 N N N -1.366 -0.998 14.816 6.003  -0.940 0.851  C12   URU 37 
URU O12   O12   O 0 1 N N N -2.584 -0.837 14.661 5.088  -1.380 0.183  O12   URU 38 
URU O14   O14   O 0 1 N N N 0.681  -2.835 16.975 8.112  -1.952 3.382  O14   URU 39 
URU H2    H2    H 0 1 N N N 6.772  -2.168 8.153  -4.380 1.623  -0.748 H2    URU 40 
URU H3    H3    H 0 1 N N N 6.360  -0.439 8.417  -3.228 2.730  0.037  H3    URU 41 
URU H4    H4    H 0 1 N N N 4.340  -1.781 8.515  -2.837 0.995  1.820  H4    URU 42 
URU H5    H5    H 0 1 N N N 5.233  -0.906 11.280 -2.383 0.287  -1.134 H5    URU 43 
URU H6    H6    H 0 1 N N N 4.706  0.938  9.758  -0.983 2.065  0.054  H6    URU 44 
URU H7    H7    H 0 1 N N N 3.124  0.185  9.362  -0.441 0.794  1.176  H7    URU 45 
URU H8    H8    H 0 1 N N N 3.242  -1.856 12.159 -1.792 -1.898 -0.508 H8    URU 46 
URU H9    H9    H 0 1 N N N 1.612  -2.631 10.639 -0.732 -2.300 1.595  H9    URU 47 
URU H10   H10   H 0 1 N N N 3.491  -4.177 10.703 -3.126 -1.822 2.087  H10   URU 48 
URU H11   H11   H 0 1 N N N 6.821  -2.988 11.471 -3.791 -3.983 2.050  H11   URU 49 
URU H12   H12   H 0 1 N N N 8.008  -3.470 13.506 -4.866 -5.857 0.916  H12   URU 50 
URU H13   H13   H 0 1 N N N 4.404  -4.890 15.066 -5.224 -3.471 -2.485 H13   URU 51 
URU H14   H14   H 0 1 N N N 9.851  -0.218 11.395 -4.602 5.188  1.489  H14   URU 52 
URU H15   H15   H 0 1 N N N 2.117  2.163  10.064 1.691  1.792  -0.135 H15   URU 53 
URU H16   H16   H 0 1 N N N 2.117  2.645  13.016 2.684  -0.371 -1.655 H16   URU 54 
URU H17   H17   H 0 1 N N N 1.715  3.868  11.763 2.142  0.900  -2.777 H17   URU 55 
URU H18   H18   H 0 1 N N N -0.345 2.735  11.173 3.591  2.542  -1.528 H18   URU 56 
URU H19   H19   H 0 1 N N N 0.194  2.634  14.175 4.438  0.356  -3.268 H19   URU 57 
URU H20   H20   H 0 1 N Y N -1.283 4.426  14.005 5.872  2.117  -4.013 H20   URU 58 
URU H21   H21   H 0 1 N N N -1.956 1.631  14.488 6.012  -0.533 -1.767 H21   URU 59 
URU H22   H22   H 0 1 N N N -3.042 2.932  12.889 7.429  0.760  -3.244 H22   URU 60 
URU H23   H23   H 0 1 N N N -1.706 -0.110 12.352 6.140  2.173  -0.323 H23   URU 61 
URU H24   H24   H 0 1 N N N 1.635  -0.058 13.584 7.784  1.854  1.221  H24   URU 62 
URU H25   H25   H 0 1 N N N 2.431  -1.548 15.319 8.856  0.477  2.927  H25   URU 63 
URU H26   H26   H 0 1 N N N -1.551 -2.266 16.382 6.264  -2.629 1.915  H26   URU 64 
URU OP3   OP3   O 0 1 N Y N ?      ?      ?      -7.060 3.772  1.876  OP3   URU 65 
URU H1    H1    H 0 1 N Y N ?      ?      ?      -7.674 4.505  1.731  H1    URU 66 
# 
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 
URU "C5'" "C4'" SING N N 1  
URU "C5'" "O5'" SING N N 2  
URU OP1   P     DOUB N N 3  
URU "C4'" "O4'" SING N N 4  
URU "C4'" "C3'" SING N N 5  
URU P     "O5'" SING N N 6  
URU P     OP2   SING N N 7  
URU "O4'" "C1'" SING N N 8  
URU "C6'" "C3'" SING N N 9  
URU "C6'" C     SING N N 10 
URU "O2'" "C2'" SING N N 11 
URU "C3'" "C2'" SING N N 12 
URU "C1'" "C2'" SING N N 13 
URU "C1'" N1    SING N N 14 
URU "NZ'" C     SING N N 15 
URU "NZ'" "CZ'" SING N N 16 
URU C     O3    DOUB N N 17 
URU "CZ'" "CY'" SING N N 18 
URU "CY'" "OY'" SING N N 19 
URU "CY'" "CX'" SING N N 20 
URU "OY'" "CV'" SING N N 21 
URU N1    C6    SING N N 22 
URU N1    C2    SING N N 23 
URU C6    C5    DOUB N N 24 
URU "OW'" "CW'" SING N N 25 
URU "CV'" "CW'" SING N N 26 
URU "CV'" N11   SING N N 27 
URU O2    C2    DOUB N N 28 
URU C2    N3    SING N N 29 
URU "OX'" "CX'" SING N N 30 
URU "CX'" "CW'" SING N N 31 
URU C5    C4    SING N N 32 
URU N11   C16   SING N N 33 
URU N11   C12   SING N N 34 
URU C16   C15   DOUB N N 35 
URU N3    C4    SING N N 36 
URU C4    O4    DOUB N N 37 
URU O12   C12   DOUB N N 38 
URU C12   N13   SING N N 39 
URU C15   C14   SING N N 40 
URU N13   C14   SING N N 41 
URU C14   O14   DOUB N N 42 
URU "C5'" H2    SING N N 43 
URU "C5'" H3    SING N N 44 
URU "C4'" H4    SING N N 45 
URU "C3'" H5    SING N N 46 
URU "C6'" H6    SING N N 47 
URU "C6'" H7    SING N N 48 
URU "C2'" H8    SING N N 49 
URU "O2'" H9    SING N N 50 
URU "C1'" H10   SING N N 51 
URU C6    H11   SING N N 52 
URU C5    H12   SING N N 53 
URU N3    H13   SING N N 54 
URU OP2   H14   SING N N 55 
URU "NZ'" H15   SING N N 56 
URU "CZ'" H16   SING N N 57 
URU "CZ'" H17   SING N N 58 
URU "CY'" H18   SING N N 59 
URU "CX'" H19   SING N N 60 
URU "OX'" H20   SING N N 61 
URU "CW'" H21   SING N N 62 
URU "OW'" H22   SING N N 63 
URU "CV'" H23   SING N N 64 
URU C16   H24   SING N N 65 
URU C15   H25   SING N N 66 
URU N13   H26   SING N N 67 
URU P     OP3   SING N N 68 
URU OP3   H1    SING N N 69 
# 
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 
URU SMILES           ACDLabs              12.01 "O=P(O)(O)OCC2OC(N1C=CC(=O)NC1=O)C(O)C2CC(=O)NCC4OC(N3C(=O)NC(=O)C=C3)C(O)C4O" 
URU InChI            InChI                1.03  
;InChI=1S/C20H26N5O14P/c26-11-1-3-24(19(32)22-11)17-14(29)8(10(39-17)7-37-40(34,35)36)5-13(28)21-6-9-15(30)16(31)18(38-9)25-4-2-12(27)23-20(25)33/h1-4,8-10,14-18,29-31H,5-7H2,(H,21,28)(H,22,26,32)(H,23,27,33)(H2,34,35,36)/t8-,9-,10-,14-,15-,16-,17-,18-/m1/s1
;
URU InChIKey         InChI                1.03  WKTKVGCYUSOTBH-VKGBBMGNSA-N 
URU SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CNC(=O)C[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO[P](O)(O)=O)N3C=CC(=O)NC3=O)N4C=CC(=O)NC4=O" 
URU SMILES           CACTVS               3.385 "O[CH]1[CH](O)[CH](O[CH]1CNC(=O)C[CH]2[CH](O)[CH](O[CH]2CO[P](O)(O)=O)N3C=CC(=O)NC3=O)N4C=CC(=O)NC4=O" 
URU 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)(O)O)CC(=O)NC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)O" 
URU SMILES           "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)CC(=O)NCC3C(C(C(O3)N4C=CC(=O)NC4=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 
URU "SYSTEMATIC NAME" ACDLabs              12.01 
;{(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-[2-({[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}amino)-2-oxoethyl]-4-hydroxytetrahydrofuran-2-yl}methyl dihydrogen phosphate (non-preferred name)
;
URU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 
"[(2S,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-[2-[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]-4-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 
URU "Create component" 2014-01-07 RCSB 
URU "Initial release"  2014-07-08 RCSB 
# 
