data_U25
# 
_chem_comp.id                                    U25 
_chem_comp.name                                  "URIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H13 N2 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                     2002-08-23 
_chem_comp.pdbx_modified_date                    2009-01-07 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   OBS 
_chem_comp.pdbx_replaced_by                      U5P 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        324.181 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     U25 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        2F8E 
_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 
U25 OP3    O3P  O 0 1 N Y N ?      ?      ?      -4.767 -0.595 -1.309 OP3    U25 1  
U25 P      P    P 0 1 N N N 17.132 25.835 16.671 -4.127 -0.814 0.152  P      U25 2  
U25 OP1    O1P  O 0 1 N N N 15.885 26.284 17.394 -4.550 0.286  1.047  OP1    U25 3  
U25 OP2    O2P  O 0 1 N N N 18.064 26.872 16.088 -4.631 -2.220 0.754  OP2    U25 4  
U25 "O5'"  O5*  O 0 1 N N N 17.987 24.893 17.665 -2.521 -0.824 0.038  "O5'"  U25 5  
U25 "C5'"  C5*  C 0 1 N N N 17.515 24.586 18.977 -2.128 0.482  -0.387 "C5'"  U25 6  
U25 "C4'"  C4*  C 0 1 N N R 18.666 24.632 19.975 -0.605 0.540  -0.516 "C4'"  U25 7  
U25 "O4'"  O4*  O 0 1 N N N 19.311 25.909 19.948 0.021  0.402  0.778  "O4'"  U25 8  
U25 "C3'"  C3*  C 0 1 N N S 18.184 24.404 21.403 -0.150 1.945  -0.989 "C3'"  U25 9  
U25 "O3'"  O3*  O 0 1 N N N 18.800 23.230 21.937 -0.957 2.967  -0.400 "O3'"  U25 10 
U25 "C2'"  C2*  C 0 1 N N R 18.630 25.621 22.189 1.302  2.012  -0.456 "C2'"  U25 11 
U25 "O2'"  O2*  O 0 1 N N N 19.201 25.262 23.452 1.583  3.312  0.066  "O2'"  U25 12 
U25 "C1'"  C1*  C 0 1 N N R 19.671 26.263 21.285 1.341  0.959  0.668  "C1'"  U25 13 
U25 N1     N1   N 0 1 N N N 19.789 27.715 21.485 2.300  -0.096 0.328  N1     U25 14 
U25 C2     C2   C 0 1 N N N 18.791 28.593 21.223 3.619  0.134  0.462  C2     U25 15 
U25 O2     O2   O 0 1 N N N 17.679 28.218 20.784 4.000  1.214  0.868  O2     U25 16 
U25 N3     N3   N 0 1 N N N 18.979 29.920 21.436 4.521  -0.819 0.162  N3     U25 17 
U25 C4     C4   C 0 1 N N N 20.159 30.388 21.909 4.113  -2.023 -0.289 C4     U25 18 
U25 O4     O4   O 0 1 N N N 20.323 31.610 22.103 4.929  -2.884 -0.566 O4     U25 19 
U25 C5     C5   C 0 1 N N N 21.191 29.501 22.181 2.729  -2.276 -0.439 C5     U25 20 
U25 C6     C6   C 0 1 N N N 20.970 28.149 21.954 1.845  -1.304 -0.126 C6     U25 21 
U25 HOP3   3HOP H 0 0 N N N ?      ?      ?      -4.467 -1.331 -1.859 HOP3   U25 22 
U25 HOP2   2HOP H 0 0 N N N 18.260 27.528 16.746 -5.596 -2.171 0.806  HOP2   U25 23 
U25 "H5'"  1H5* H 0 1 N N N 16.753 25.323 19.269 -2.459 1.217  0.347  "H5'"  U25 24 
U25 "H5''" 2H5* H 0 0 N N N 17.081 23.575 18.975 -2.583 0.702  -1.352 "H5''" U25 25 
U25 "H4'"  H4*  H 0 1 N N N 19.362 23.833 19.680 -0.247 -0.229 -1.199 "H4'"  U25 26 
U25 "H3'"  H3*  H 0 1 N N N 17.094 24.267 21.450 -0.170 2.015  -2.076 "H3'"  U25 27 
U25 "HO'3" 3HO* H 0 0 N N N 18.937 22.599 21.240 -0.568 3.814  -0.658 "HO'3" U25 28 
U25 "H2'"  H2*  H 0 1 N N N 17.793 26.291 22.434 2.009  1.758  -1.245 "H2'"  U25 29 
U25 "HO2'" 2HO* H 0 0 N N N 20.143 25.182 23.363 1.486  3.935  -0.667 "HO2'" U25 30 
U25 "H1'"  H1*  H 0 1 N N N 20.677 25.890 21.526 1.624  1.431  1.608  "H1'"  U25 31 
U25 H3     H3   H 0 1 N N N 18.237 30.561 21.241 5.468  -0.638 0.267  H3     U25 32 
U25 H5     H5   H 0 1 N N N 22.140 29.852 22.559 2.383  -3.234 -0.799 H5     U25 33 
U25 H6     H6   H 0 1 N N N 21.757 27.438 22.157 0.785  -1.479 -0.234 H6     U25 34 
# 
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 
U25 OP3   P      SING N N 1  
U25 OP3   HOP3   SING N N 2  
U25 P     OP1    DOUB N N 3  
U25 P     OP2    SING N N 4  
U25 P     "O5'"  SING N N 5  
U25 OP2   HOP2   SING N N 6  
U25 "O5'" "C5'"  SING N N 7  
U25 "C5'" "C4'"  SING N N 8  
U25 "C5'" "H5'"  SING N N 9  
U25 "C5'" "H5''" SING N N 10 
U25 "C4'" "O4'"  SING N N 11 
U25 "C4'" "C3'"  SING N N 12 
U25 "C4'" "H4'"  SING N N 13 
U25 "O4'" "C1'"  SING N N 14 
U25 "C3'" "O3'"  SING N N 15 
U25 "C3'" "C2'"  SING N N 16 
U25 "C3'" "H3'"  SING N N 17 
U25 "O3'" "HO'3" SING N N 18 
U25 "C2'" "O2'"  SING N N 19 
U25 "C2'" "C1'"  SING N N 20 
U25 "C2'" "H2'"  SING N N 21 
U25 "O2'" "HO2'" SING N N 22 
U25 "C1'" N1     SING N N 23 
U25 "C1'" "H1'"  SING N N 24 
U25 N1    C2     SING N N 25 
U25 N1    C6     SING N N 26 
U25 C2    O2     DOUB N N 27 
U25 C2    N3     SING N N 28 
U25 N3    C4     SING N N 29 
U25 N3    H3     SING N N 30 
U25 C4    O4     DOUB N N 31 
U25 C4    C5     SING N N 32 
U25 C5    C6     DOUB N N 33 
U25 C5    H5     SING N N 34 
U25 C6    H6     SING N N 35 
# 
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 
U25 SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O"                                                                                                                     
U25 InChI            InChI                1.02b "InChI=1/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1/f/h10,16-17H" 
U25 InChIKey         InChI                1.02b DJJCXFVJDGTHFX-UUVCVCPKDX                                                                                                                                       
U25 SMILES_CANONICAL CACTVS               3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                  
U25 SMILES           CACTVS               3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                         
U25 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                                 
U25 SMILES           "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=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 
U25 "SYSTEMATIC NAME" ACDLabs              10.04 
;5'-uridylic acid
;
U25 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
