data_U31
# 
_chem_comp.id                                    U31 
_chem_comp.name                                  
;2'-O-3-AMINOPROPYL 2'-DEOXYURIDINE-5'-MONOPHOSPHATE
;
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H20 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                     1999-12-02 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        381.276 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     U31 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1D9D 
_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 
U31 P      P    P 0 1 N N N 78.402 64.461 -7.570  -0.364 0.409  -4.758 P      U31 1  
U31 O1P    O1P  O 0 1 N N N 78.558 64.343 -9.021  0.544  -0.084 -5.992 O1P    U31 2  
U31 O2P    O2P  O 0 1 N N N 78.178 65.782 -6.991  0.051  1.771  -4.353 O2P    U31 3  
U31 O3P    O3P  O 0 1 N Y N 79.792 63.774 -6.963  -1.911 0.431  -5.206 O3P    U31 4  
U31 "O5'"  O5*  O 0 1 N N N 77.048 63.680 -7.374  -0.179 -0.599 -3.517 "O5'"  U31 5  
U31 "C5'"  C5*  C 0 1 N N N 76.037 64.180 -8.282  -1.006 -0.110 -2.460 "C5'"  U31 6  
U31 "C4'"  C4*  C 0 1 N N R 74.667 64.040 -7.819  -0.876 -1.029 -1.244 "C4'"  U31 7  
U31 "O4'"  O4*  O 0 1 N N N 73.973 65.225 -8.236  0.480  -1.026 -0.768 "O4'"  U31 8  
U31 "C3'"  C3*  C 0 1 N N R 73.998 62.921 -8.631  -1.764 -0.509 -0.097 "C3'"  U31 9  
U31 "O3'"  O3*  O 0 1 N N N 72.771 62.671 -7.865  -2.740 -1.488 0.265  "O3'"  U31 10 
U31 "C2'"  C2*  C 0 1 N N R 73.686 63.690 -9.947  -0.776 -0.271 1.070  "C2'"  U31 11 
U31 "O2'"  O2*  O 0 1 N N N 72.945 62.837 -10.824 -1.339 -0.701 2.311  "O2'"  U31 12 
U31 "C1'"  C1*  C 0 1 N N R 73.077 64.975 -9.289  0.424  -1.164 0.668  "C1'"  U31 13 
U31 N1     N1   N 0 1 N N N 72.832 66.313 -9.861  1.662  -0.678 1.281  N1     U31 14 
U31 C2     C2   C 0 1 N N N 72.445 67.406 -9.128  2.054  0.592  1.076  C2     U31 15 
U31 O2     O2   O 0 1 N N N 72.261 67.371 -7.986  1.371  1.325  0.387  O2     U31 16 
U31 N3     N3   N 0 1 N N N 72.178 68.568 -9.840  3.184  1.066  1.631  N3     U31 17 
U31 C4     C4   C 0 1 N N N 72.297 68.753 -11.149 3.952  0.266  2.398  C4     U31 18 
U31 O4     O4   O 0 1 N N N 71.987 69.831 -11.667 4.978  0.692  2.897  O4     U31 19 
U31 C5     C5   C 0 1 N N N 72.770 67.649 -11.795 3.555  -1.074 2.618  C5     U31 20 
U31 C6     C6   C 0 1 N N N 73.061 66.507 -11.147 2.413  -1.522 2.053  C6     U31 21 
U31 "CA'"  CA*  C 0 1 N N N 72.979 61.327 -10.725 -1.943 0.446  2.911  "CA'"  U31 22 
U31 "CB'"  CB*  C 0 1 N N N 73.674 60.562 -9.707  -2.568 0.051  4.250  "CB'"  U31 23 
U31 CC     CC   C 0 1 N N N 73.038 59.348 -9.386  -3.215 1.280  4.893  CC     U31 24 
U31 "ND'"  ND*  N 0 1 N N N 73.098 58.999 -8.017  -3.815 0.901  6.179  "ND'"  U31 25 
U31 H1P    H1P  H 0 1 N N N 78.703 63.483 -9.397  0.404  0.546  -6.712 H1P    U31 26 
U31 H3P    H3P  H 0 1 N N N 79.690 63.850 -6.021  -2.141 -0.472 -5.461 H3P    U31 27 
U31 "H5'1" 1H5* H 0 0 N N N 76.154 63.706 -9.285  -2.044 -0.090 -2.790 "H5'1" U31 28 
U31 "H5'2" 2H5* H 0 0 N N N 76.247 65.243 -8.542  -0.691 0.897  -2.189 "H5'2" U31 29 
U31 "H4'"  H4*  H 0 1 N N N 74.602 63.869 -6.719  -1.172 -2.043 -1.512 "H4'"  U31 30 
U31 "H3'"  H3*  H 0 1 N N N 74.637 62.018 -8.773  -2.250 0.423  -0.383 "H3'"  U31 31 
U31 HA     HA   H 0 1 N N N 72.357 61.979 -8.367  -3.326 -1.595 -0.496 HA     U31 32 
U31 "H2'"  H2*  H 0 1 N N N 74.648 63.962 -10.440 -0.481 0.777  1.121  "H2'"  U31 33 
U31 "H1'"  H1*  H 0 1 N N N 72.119 64.658 -8.815  0.240  -2.201 0.947  "H1'"  U31 34 
U31 H3     H3   H 0 1 N N N 71.854 69.368 -9.297  3.450  1.986  1.476  H3     U31 35 
U31 H5     H5   H 0 1 N N N 72.919 67.694 -12.887 4.157  -1.730 3.229  H5     U31 36 
U31 H6     H6   H 0 1 N N N 73.518 65.685 -11.723 2.094  -2.542 2.209  H6     U31 37 
U31 "HA'1" 1HA* H 0 0 N N N 73.347 60.953 -11.709 -2.717 0.836  2.250  "HA'1" U31 38 
U31 "HA'2" 2HA* H 0 0 N N N 71.917 60.987 -10.708 -1.185 1.211  3.075  "HA'2" U31 39 
U31 "HB'1" 1HB* H 0 0 N N N 73.835 61.178 -8.791  -1.794 -0.339 4.911  "HB'1" U31 40 
U31 "HB'2" 2HB* H 0 0 N N N 74.735 60.386 -10.001 -3.326 -0.714 4.086  "HB'2" U31 41 
U31 HCC1   1HCC H 0 0 N N N 73.440 58.521 -10.016 -3.989 1.671  4.232  HCC1   U31 42 
U31 HCC2   2HCC H 0 0 N N N 71.980 59.359 -9.738  -2.457 2.046  5.057  HCC2   U31 43 
U31 "HD'1" 1HD* H 0 0 N N N 73.093 59.786 -7.368  -4.227 1.738  6.564  "HD'1" U31 44 
U31 "HD'2" 2HD* H 0 0 N N N 73.994 58.625 -7.704  -4.576 0.273  5.970  "HD'2" U31 45 
# 
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 
U31 P     O1P    SING N N 1  
U31 P     O2P    DOUB N N 2  
U31 P     O3P    SING N N 3  
U31 P     "O5'"  SING N N 4  
U31 O1P   H1P    SING N N 5  
U31 O3P   H3P    SING N N 6  
U31 "O5'" "C5'"  SING N N 7  
U31 "C5'" "C4'"  SING N N 8  
U31 "C5'" "H5'1" SING N N 9  
U31 "C5'" "H5'2" SING N N 10 
U31 "C4'" "O4'"  SING N N 11 
U31 "C4'" "C3'"  SING N N 12 
U31 "C4'" "H4'"  SING N N 13 
U31 "O4'" "C1'"  SING N N 14 
U31 "C3'" "O3'"  SING N N 15 
U31 "C3'" "C2'"  SING N N 16 
U31 "C3'" "H3'"  SING N N 17 
U31 "O3'" HA     SING N N 18 
U31 "C2'" "O2'"  SING N N 19 
U31 "C2'" "C1'"  SING N N 20 
U31 "C2'" "H2'"  SING N N 21 
U31 "O2'" "CA'"  SING N N 22 
U31 "C1'" N1     SING N N 23 
U31 "C1'" "H1'"  SING N N 24 
U31 N1    C2     SING N N 25 
U31 N1    C6     SING N N 26 
U31 C2    O2     DOUB N N 27 
U31 C2    N3     SING N N 28 
U31 N3    C4     SING N N 29 
U31 N3    H3     SING N N 30 
U31 C4    O4     DOUB N N 31 
U31 C4    C5     SING N N 32 
U31 C5    C6     DOUB N N 33 
U31 C5    H5     SING N N 34 
U31 C6    H6     SING N N 35 
U31 "CA'" "CB'"  SING N N 36 
U31 "CA'" "HA'1" SING N N 37 
U31 "CA'" "HA'2" SING N N 38 
U31 "CB'" CC     SING N N 39 
U31 "CB'" "HB'1" SING N N 40 
U31 "CB'" "HB'2" SING N N 41 
U31 CC    "ND'"  SING N N 42 
U31 CC    HCC1   SING N N 43 
U31 CC    HCC2   SING N N 44 
U31 "ND'" "HD'1" SING N N 45 
U31 "ND'" "HD'2" SING N N 46 
# 
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 
U31 SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2OCCCN)COP(=O)(O)O"                                                                                                                                         
U31 InChI            InChI                1.02b "InChI=1/C12H20N3O9P/c13-3-1-5-22-10-9(17)7(6-23-25(19,20)21)24-11(10)15-4-2-8(16)14-12(15)18/h2,4,7,9-11,17H,1,3,5-6,13H2,(H,14,16,18)(H2,19,20,21)/t7-,9-,10-,11-/m1/s1/f/h14,19-20H" 
U31 InChIKey         InChI                1.02b BYBLQLKEQYUZOM-LMFIAKJTDJ                                                                                                                                                               
U31 SMILES_CANONICAL CACTVS               3.341 "NCCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O"                                                                                                                       
U31 SMILES           CACTVS               3.341 "NCCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O"                                                                                                                             
U31 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)OCCCN"                                                                                                                     
U31 SMILES           "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCCN"                                                                                                                                       
# 
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 
U31 "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-O-(3-aminopropyl)uridine 5'-(dihydrogen phosphate)
;
U31 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-4-(3-aminopropoxy)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
