data_1RN
# 
_chem_comp.id                                    1RN 
_chem_comp.name                                  "(E)-N-{[4-oxo-1-(5-O-phosphono-beta-D-arabinofuranosyl)-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl]methylidene}glycine" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H16 N3 O10 P S" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2013-05-09 
_chem_comp.pdbx_modified_date                    2013-05-24 
_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                        425.308 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     1RN 
_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        4JYZ 
_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 
1RN N1    N1    N 0 1 N N N 62.348 17.067 -13.404 0.606  1.747  0.408  N1    1RN 1  
1RN C2    C2    C 0 1 N N N 62.900 18.147 -14.068 1.477  2.752  0.593  C2    1RN 2  
1RN S2    S2    S 0 1 N N N 62.434 19.284 -14.003 0.889  4.359  0.646  S2    1RN 3  
1RN N3    N3    N 0 1 N N N 64.018 17.848 -14.812 2.796  2.537  0.739  N3    1RN 4  
1RN C4    C4    C 0 1 N N N 64.619 16.607 -14.959 3.292  1.282  0.702  C4    1RN 5  
1RN O4    O4    O 0 1 N N N 65.626 16.500 -15.656 4.485  1.082  0.834  O4    1RN 6  
1RN C5    C5    C 0 1 N N N 63.980 15.546 -14.252 2.359  0.162  0.500  C5    1RN 7  
1RN C6    C6    C 0 1 N N N 62.899 15.805 -13.512 1.016  0.452  0.358  C6    1RN 8  
1RN "C1'" "C1'" C 0 1 N N R 61.159 17.304 -12.579 -0.819 2.053  0.264  "C1'" 1RN 9  
1RN "O2'" "O2'" O 0 1 N N N 60.352 15.651 -13.979 -0.407 1.570  -2.107 "O2'" 1RN 10 
1RN "C2'" "C2'" C 0 1 N N S 59.881 16.649 -13.097 -1.158 2.391  -1.211 "C2'" 1RN 11 
1RN "O3'" "O3'" O 0 1 N N N 58.602 17.568 -11.134 -3.454 3.232  -1.128 "O3'" 1RN 12 
1RN "C3'" "C3'" C 0 1 N N S 59.122 16.438 -11.816 -2.667 2.050  -1.283 "C3'" 1RN 13 
1RN "C4'" "C4'" C 0 1 N N R 60.224 15.875 -10.937 -2.895 1.091  -0.098 "C4'" 1RN 14 
1RN "O4'" "O4'" O 0 1 N N N 61.363 16.729 -11.292 -1.620 0.883  0.534  "O4'" 1RN 15 
1RN "C5'" "C5'" C 0 1 N N N 60.591 14.441 -11.213 -3.447 -0.242 -0.607 "C5'" 1RN 16 
1RN "O5'" "O5'" O 0 1 N N N 59.507 13.585 -10.892 -3.764 -1.081 0.505  "O5'" 1RN 17 
1RN P     P     P 0 1 N N N 58.956 12.540 -11.959 -4.370 -2.564 0.340  P     1RN 18 
1RN OP1   OP1   O 0 1 N N N 59.777 12.650 -13.190 -5.833 -2.474 -0.326 OP1   1RN 19 
1RN OP2   OP2   O 0 1 N N N 58.817 11.221 -11.287 -3.481 -3.366 -0.529 OP2   1RN 20 
1RN C3    C3    C 0 1 N N N 64.484 14.247 -14.333 2.842  -1.225 0.451  C3    1RN 21 
1RN N2    N2    N 0 1 N N N 63.701 13.290 -13.799 4.106  -1.477 0.587  N2    1RN 22 
1RN C7    C7    C 0 1 N N N 64.114 12.133 -13.848 4.587  -2.859 0.539  C7    1RN 23 
1RN C1    C1    C 0 1 N N N 63.580 11.333 -14.735 5.472  -3.041 -0.668 C1    1RN 24 
1RN O2    O2    O 0 1 N N N 64.039 10.169 -14.799 5.678  -2.112 -1.411 O2    1RN 25 
1RN O1    O1    O 0 1 N N N 62.723 11.824 -15.503 6.029  -4.237 -0.917 O1    1RN 26 
1RN H1    H1    H 0 1 N N N 62.435 14.992 -12.974 0.299  -0.342 0.209  H1    1RN 27 
1RN H2    H2    H 0 1 N N N 60.987 18.387 -12.486 -1.103 2.876  0.921  H2    1RN 28 
1RN H3    H3    H 0 1 N N N 59.614 15.185 -14.354 -0.584 1.744  -3.042 H3    1RN 29 
1RN H4    H4    H 0 1 N N N 59.340 17.408 -13.681 -0.987 3.447  -1.417 H4    1RN 30 
1RN H5    H5    H 0 1 N N N 58.151 17.284 -10.348 -3.307 3.896  -1.815 H5    1RN 31 
1RN H6    H6    H 0 1 N N N 58.344 15.675 -11.966 -2.902 1.557  -2.226 H6    1RN 32 
1RN H7    H7    H 0 1 N N N 59.960 16.001 -9.877  -3.592 1.537  0.611  H7    1RN 33 
1RN H8    H8    H 0 1 N N N 60.839 14.329 -12.279 -4.347 -0.062 -1.194 H8    1RN 34 
1RN H9    H9    H 0 1 N N N 61.464 14.166 -10.603 -2.699 -0.731 -1.230 H9    1RN 35 
1RN H10   H10   H 0 1 N N N 60.137 11.798 -13.408 -6.470 -1.962 0.191  H10   1RN 36 
1RN H12   H12   H 0 1 N N N 65.436 14.025 -14.792 2.143  -2.035 0.302  H12   1RN 37 
1RN H13   H13   H 0 1 N N N 65.194 12.178 -14.054 5.156  -3.078 1.442  H13   1RN 38 
1RN H14   H14   H 0 1 N N N 63.948 11.683 -12.858 3.737  -3.538 0.472  H14   1RN 39 
1RN H15   H15   H 0 1 N N N 62.468 11.176 -16.150 6.589  -4.305 -1.703 H15   1RN 40 
1RN H16   H16   H 0 1 N N N 64.444 18.609 -15.301 3.395  3.288  0.871  H16   1RN 41 
1RN OP3   OP3   O 0 1 N Y N ?      ?      ?       -4.480 -3.263 1.786  OP3   1RN 42 
1RN H18   H18   H 0 1 N N N ?      ?      ?       -4.838 -4.161 1.763  H18   1RN 43 
# 
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 
1RN N1    C2    SING N N 1  
1RN N1    C6    SING N N 2  
1RN N1    "C1'" SING N N 3  
1RN C2    S2    DOUB N N 4  
1RN C2    N3    SING N N 5  
1RN N3    C4    SING N N 6  
1RN C4    O4    DOUB N N 7  
1RN C4    C5    SING N N 8  
1RN C5    C6    DOUB N N 9  
1RN C5    C3    SING N N 10 
1RN "C1'" "C2'" SING N N 11 
1RN "C1'" "O4'" SING N N 12 
1RN "O2'" "C2'" SING N N 13 
1RN "C2'" "C3'" SING N N 14 
1RN "O3'" "C3'" SING N N 15 
1RN "C3'" "C4'" SING N N 16 
1RN "C4'" "O4'" SING N N 17 
1RN "C4'" "C5'" SING N N 18 
1RN "C5'" "O5'" SING N N 19 
1RN "O5'" P     SING N N 20 
1RN P     OP1   SING N N 21 
1RN P     OP2   DOUB N N 22 
1RN C3    N2    DOUB N N 23 
1RN N2    C7    SING N N 24 
1RN C7    C1    SING N N 25 
1RN C1    O2    DOUB N N 26 
1RN C1    O1    SING N N 27 
1RN C6    H1    SING N N 28 
1RN "C1'" H2    SING N N 29 
1RN "O2'" H3    SING N N 30 
1RN "C2'" H4    SING N N 31 
1RN "O3'" H5    SING N N 32 
1RN "C3'" H6    SING N N 33 
1RN "C4'" H7    SING N N 34 
1RN "C5'" H8    SING N N 35 
1RN "C5'" H9    SING N N 36 
1RN OP1   H10   SING N N 37 
1RN C3    H12   SING N N 38 
1RN C7    H13   SING N N 39 
1RN C7    H14   SING N N 40 
1RN O1    H15   SING N N 41 
1RN N3    H16   SING N N 42 
1RN P     OP3   SING N N 43 
1RN OP3   H18   SING N N 44 
# 
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 
1RN SMILES           ACDLabs              12.01 "O=C(O)C/N=C/C=1C(=O)NC(=S)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O"                                                                                                                                      
1RN InChI            InChI                1.03  "InChI=1S/C12H16N3O10PS/c16-7(17)2-13-1-5-3-15(12(27)14-10(5)20)11-9(19)8(18)6(25-11)4-24-26(21,22)23/h1,3,6,8-9,11,18-19H,2,4H2,(H,16,17)(H,14,20,27)(H2,21,22,23)/b13-1+/t6-,8-,9+,11-/m1/s1" 
1RN InChIKey         InChI                1.03  OIOFJGQNCGWJPT-PDCDXKGCSA-N                                                                                                                                                                     
1RN SMILES_CANONICAL CACTVS               3.370 "O[C@H]1[C@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C=NCC(O)=O)C(=O)NC2=S"                                                                                                                       
1RN SMILES           CACTVS               3.370 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C=NCC(O)=O)C(=O)NC2=S"                                                                                                                             
1RN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=C(C(=O)NC(=S)N1[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)/C=N/CC(=O)O"                                                                                                                    
1RN SMILES           "OpenEye OEToolkits" 1.7.6 "C1=C(C(=O)NC(=S)N1C2C(C(C(O2)COP(=O)(O)O)O)O)C=NCC(=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 
1RN "SYSTEMATIC NAME" ACDLabs              12.01 "(E)-N-{[4-oxo-1-(5-O-phosphono-beta-D-arabinofuranosyl)-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl]methylidene}glycine"                                       
1RN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "2-[(E)-[1-[(2R,3S,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-4-oxidanylidene-2-sulfanylidene-pyrimidin-5-yl]methylideneamino]ethanoic 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 
1RN "Create component"    2013-05-09 RCSB 
1RN "Modify linking type" 2013-05-22 RCSB 
1RN "Initial release"     2013-05-29 RCSB 
# 
