data_UBD
# 
_chem_comp.id                                    UBD 
_chem_comp.name                                  
;URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE)
;
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H14 N2 O12 P2" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2007-06-07 
_chem_comp.pdbx_modified_date                    2013-03-22 
_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                        404.161 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     UBD 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        "Corina V3.40" 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_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 
UBD C2     C2   C 0 1 N N N -2.797 -2.735 35.357 3.856  0.081  0.934  C2     UBD 1  
UBD C4     C4   C 0 1 N N N -5.039 -3.615 35.597 5.218  -1.194 -0.472 C4     UBD 2  
UBD C5     C5   C 0 1 N N N -4.498 -4.893 36.033 4.096  -1.469 -1.292 C5     UBD 3  
UBD C6     C6   C 0 1 N N N -3.153 -5.055 36.117 2.894  -0.955 -0.953 C6     UBD 4  
UBD N1     N1   N 0 1 N N N -2.271 -4.016 35.793 2.781  -0.177 0.167  N1     UBD 5  
UBD O2     O2   O 0 1 N N N -2.038 -1.797 35.061 3.732  0.775  1.924  O2     UBD 6  
UBD P1     P1   P 0 1 N N N -2.005 -7.397 39.337 -3.000 -3.307 0.054  P1     UBD 7  
UBD O1P    O1P  O 0 1 N N N -1.124 -6.983 40.506 -3.177 -4.363 1.257  O1P    UBD 8  
UBD O2P    O2P  O 0 1 N N N -3.432 -6.951 39.536 -2.356 -4.049 -1.221 O2P    UBD 9  
UBD O3P    O3P  O 0 1 N Y N -2.022 -9.011 39.134 -4.321 -2.752 -0.313 O3P    UBD 10 
UBD "O5'"  O5*  O 0 1 N N N -1.454 -6.805 37.943 -2.029 -2.113 0.527  "O5'"  UBD 11 
UBD "C5'"  C5*  C 0 1 N N N -0.170 -7.206 37.437 -1.757 -0.965 -0.279 "C5'"  UBD 12 
UBD "C4'"  C4*  C 0 1 N N R 0.502  -6.092 36.634 -0.801 -0.032 0.467  "C4'"  UBD 13 
UBD "O4'"  O4*  O 0 1 N N N -0.364 -5.545 35.560 0.482  -0.663 0.613  "O4'"  UBD 14 
UBD "C3'"  C3*  C 0 1 N N S 0.890  -4.885 37.481 -0.586 1.258  -0.348 "C3'"  UBD 15 
UBD "O3'"  O3*  O 0 1 N N N 2.159  -4.399 36.971 -1.009 2.399  0.403  "O3'"  UBD 16 
UBD "C2'"  C2*  C 0 1 N N R -0.213 -3.863 37.265 0.942  1.305  -0.590 "C2'"  UBD 17 
UBD "O2'"  O2*  O 0 1 N N N 0.273  -2.533 37.359 1.442  2.635  -0.437 "O2'"  UBD 18 
UBD "C1'"  C1*  C 0 1 N N R -0.774 -4.200 35.880 1.477  0.380  0.534  "C1'"  UBD 19 
UBD N3     N3   N 0 1 N N N -4.177 -2.565 35.269 5.064  -0.423 0.623  N3     UBD 20 
UBD O4     O4   O 0 1 N N N -6.275 -3.453 35.515 6.311  -1.651 -0.754 O4     UBD 21 
UBD P2     P2   P 0 1 N N N 3.440  -4.139 37.937 -2.168 3.398  -0.098 P2     UBD 22 
UBD O4P    O4P  O 0 1 N N N 3.860  -2.691 37.835 -1.688 4.149  -1.439 O4P    UBD 23 
UBD O5P    O5P  O 0 1 N N N 4.568  -5.025 37.490 -3.398 2.624  -0.381 O5P    UBD 24 
UBD O6P    O6P  O 0 1 N N N 3.060  -4.482 39.451 -2.471 4.486  1.048  O6P    UBD 25 
UBD H5     H5   H 0 1 N N N -5.161 -5.706 36.288 4.200  -2.084 -2.173 H5     UBD 26 
UBD H6     H6   H 0 1 N N N -2.754 -6.005 36.441 2.027  -1.153 -1.566 H6     UBD 27 
UBD HO1P   HO1P H 0 0 N N N -0.225 -6.897 40.211 -3.750 -5.111 1.042  HO1P   UBD 28 
UBD HO2P   HO2P H 0 0 N N N -3.608 -6.857 40.465 -1.487 -4.438 -1.052 HO2P   UBD 29 
UBD "H5'1" 1H5* H 0 0 N N N 0.477  -7.466 38.287 -1.300 -1.280 -1.217 "H5'1" UBD 30 
UBD "H5'2" 2H5* H 0 0 N N N -0.320 -8.066 36.768 -2.689 -0.439 -0.488 "H5'2" UBD 31 
UBD "H4'"  H4*  H 0 1 N N N 1.391  -6.591 36.221 -1.209 0.210  1.448  "H4'"  UBD 32 
UBD "H3'"  H3*  H 0 1 N N N 0.999  -5.106 38.553 -1.123 1.206  -1.295 "H3'"  UBD 33 
UBD "H2'"  H2*  H 0 1 N N N -0.994 -3.912 38.038 1.192  0.907  -1.573 "H2'"  UBD 34 
UBD "HO2'" HO2* H 0 0 N N N 0.382  -2.299 38.273 2.396  2.715  -0.579 "HO2'" UBD 35 
UBD "H1'"  H1*  H 0 1 N N N -0.369 -3.497 35.137 1.543  0.920  1.479  "H1'"  UBD 36 
UBD HN3    HN3  H 0 1 N N N -4.552 -1.688 34.970 5.828  -0.230 1.189  HN3    UBD 37 
UBD HO4P   HO4P H 0 0 N N N 3.948  -2.324 38.707 -0.885 4.677  -1.327 HO4P   UBD 38 
UBD HO6P   HO6P H 0 0 N N N 3.853  -4.550 39.969 -3.161 5.122  0.814  HO6P   UBD 39 
# 
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 
UBD C2    O2     DOUB N N 1  
UBD C2    N3     SING N N 2  
UBD C2    N1     SING N N 3  
UBD C4    N3     SING N N 4  
UBD C4    O4     DOUB N N 5  
UBD C4    C5     SING N N 6  
UBD C5    C6     DOUB N N 7  
UBD C5    H5     SING N N 8  
UBD C6    N1     SING N N 9  
UBD C6    H6     SING N N 10 
UBD N1    "C1'"  SING N N 11 
UBD P1    "O5'"  SING N N 12 
UBD P1    O3P    DOUB N N 13 
UBD P1    O2P    SING N N 14 
UBD P1    O1P    SING N N 15 
UBD O1P   HO1P   SING N N 16 
UBD O2P   HO2P   SING N N 17 
UBD "O5'" "C5'"  SING N N 18 
UBD "C5'" "C4'"  SING N N 19 
UBD "C5'" "H5'1" SING N N 20 
UBD "C5'" "H5'2" SING N N 21 
UBD "C4'" "O4'"  SING N N 22 
UBD "C4'" "C3'"  SING N N 23 
UBD "C4'" "H4'"  SING N N 24 
UBD "O4'" "C1'"  SING N N 25 
UBD "C3'" "O3'"  SING N N 26 
UBD "C3'" "C2'"  SING N N 27 
UBD "C3'" "H3'"  SING N N 28 
UBD "O3'" P2     SING N N 29 
UBD "C2'" "C1'"  SING N N 30 
UBD "C2'" "O2'"  SING N N 31 
UBD "C2'" "H2'"  SING N N 32 
UBD "O2'" "HO2'" SING N N 33 
UBD "C1'" "H1'"  SING N N 34 
UBD N3    HN3    SING N N 35 
UBD P2    O5P    DOUB N N 36 
UBD P2    O4P    SING N N 37 
UBD P2    O6P    SING N N 38 
UBD O4P   HO4P   SING N N 39 
UBD O6P   HO6P   SING N N 40 
# 
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 
UBD SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1)C2OC(C(OP(=O)(O)O)C2O)COP(=O)(O)O"                                                                                                                        
UBD SMILES_CANONICAL CACTVS               3.341 "O[C@@H]1[C@H](O[P](O)(O)=O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O"                                                                                                    
UBD SMILES           CACTVS               3.341 "O[CH]1[CH](O[P](O)(O)=O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O"                                                                                                          
UBD 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)OP(=O)(O)O)O"                                                                                                    
UBD SMILES           "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)OP(=O)(O)O)O"                                                                                                                      
UBD InChI            InChI                1.03  "InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(14)10-5)8-6(13)7(23-25(18,19)20)4(22-8)3-21-24(15,16)17/h1-2,4,6-8,13H,3H2,(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1" 
UBD InChIKey         InChI                1.03  ZPVPRWPOZBXDKD-XVFCMESISA-N                                                                                                                                                 
# 
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 
UBD "SYSTEMATIC NAME" ACDLabs              10.04 
;uridine 3',5'-bis(dihydrogen phosphate)
;
UBD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-4-hydroxy-3-phosphonooxy-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 
UBD "Create component"  2007-06-07 RCSB 
UBD "Modify descriptor" 2011-06-04 RCSB 
UBD "Initial release"   2013-03-27 RCSB 
# 
