data_XSX
# 
_chem_comp.id                                    XSX 
_chem_comp.name                                  
;3-[(3R)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H20 N3 O11 P" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-12-07 
_chem_comp.pdbx_modified_date                    2023-09-01 
_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                        425.285 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     XSX 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8EVQ 
_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 
XSX "O5'"  O1  O 0 1 N N N 164.051 178.055 265.011 4.755  -0.172 -0.695 "O5'"  XSX 1  
XSX "C5'"  C1  C 0 1 N N N 163.351 179.249 265.328 4.232  0.681  0.326  "C5'"  XSX 2  
XSX "C4'"  C2  C 0 1 N N R 161.960 179.206 264.751 2.870  1.223  -0.111 "C4'"  XSX 3  
XSX "O4'"  O2  O 0 1 N N N 162.065 179.263 263.311 1.886  0.166  -0.119 "O4'"  XSX 4  
XSX "C3'"  C3  C 0 1 N N S 161.188 177.927 265.034 2.342  2.246  0.919  "C3'"  XSX 5  
XSX "O3'"  O3  O 0 1 N N N 160.469 178.005 266.253 2.609  3.580  0.483  "O3'"  XSX 6  
XSX "C2'"  C4  C 0 1 N N R 160.281 177.765 263.815 0.820  1.984  0.963  "C2'"  XSX 7  
XSX "O2'"  O4  O 0 1 N N N 159.064 178.472 264.000 0.100  3.148  0.554  "O2'"  XSX 8  
XSX "C1'"  C5  C 0 1 N N R 161.078 178.461 262.711 0.608  0.834  -0.047 "C1'"  XSX 9  
XSX C5     C6  C 0 1 N N N 163.682 176.265 261.190 -1.180 -1.612 2.058  C5     XSX 10 
XSX C6     C7  C 0 1 N N N 162.983 177.092 262.059 -0.229 -0.763 1.611  C6     XSX 11 
XSX N1     N1  N 0 1 N N N 161.756 177.543 261.765 -0.423 -0.087 0.438  N1     XSX 12 
XSX C2     C8  C 0 1 N N N 161.159 177.216 260.530 -1.551 -0.259 -0.275 C2     XSX 13 
XSX N3     N2  N 0 1 N N N 161.845 176.379 259.627 -2.515 -1.098 0.148  N3     XSX 14 
XSX C4     C9  C 0 1 N N N 163.124 175.903 259.974 -2.360 -1.788 1.296  C4     XSX 15 
XSX C1     C10 C 0 1 N N N 161.234 176.007 258.348 -3.732 -1.272 -0.649 C1     XSX 16 
XSX C3     C11 C 0 1 N N N 161.491 175.575 256.914 -4.786 -0.259 -0.197 C3     XSX 17 
XSX C7     C12 C 0 1 N N R 160.841 174.237 256.550 -6.057 -0.441 -1.029 C7     XSX 18 
XSX C9     C13 C 0 1 N N N 161.294 173.139 257.518 -7.050 0.634  -0.670 C9     XSX 19 
XSX N4     N3  N 0 1 N N N 161.212 173.847 255.163 -6.641 -1.760 -0.751 N4     XSX 20 
XSX O10    O5  O 0 1 N N N 160.421 172.640 258.257 -6.925 1.865  -1.191 O10    XSX 21 
XSX O11    O6  O 0 1 N N N 162.520 172.926 257.599 -7.959 0.388  0.087  O11    XSX 22 
XSX O2     O7  O 0 1 N N N 160.022 177.652 260.244 -1.702 0.352  -1.315 O2     XSX 23 
XSX O4     O8  O 0 1 N N N 163.758 175.159 259.197 -3.231 -2.547 1.679  O4     XSX 24 
XSX OP1    O9  O 0 1 N N N 166.107 176.610 265.220 7.235  0.079  -0.299 OP1    XSX 25 
XSX OP2    O10 O 0 1 N N N 166.024 178.670 263.618 6.119  -1.984 0.635  OP2    XSX 26 
XSX P      P1  P 0 1 N N N 165.640 178.013 264.920 6.176  -0.919 -0.571 P      XSX 27 
XSX H1     H1  H 0 1 N N N 163.892 180.110 264.908 4.118  0.114  1.250  H1     XSX 28 
XSX H2     H2  H 0 1 N N N 163.288 179.354 266.421 4.918  1.512  0.491  H2     XSX 29 
XSX H3     H3  H 0 1 N N N 161.384 180.066 265.124 2.944  1.682  -1.097 H3     XSX 30 
XSX H4     H4  H 0 1 N N N 161.895 177.085 265.062 2.790  2.068  1.897  H4     XSX 31 
XSX H5     H5  H 0 1 N N N 161.078 178.105 266.975 2.298  4.263  1.093  H5     XSX 32 
XSX H6     H6  H 0 1 N N N 160.124 176.702 263.578 0.514  1.678  1.963  H6     XSX 33 
XSX H7     H7  H 0 1 N N N 158.555 178.053 264.684 0.245  3.919  1.120  H7     XSX 34 
XSX H8     H8  H 0 1 N N N 160.383 179.097 262.142 0.333  1.233  -1.024 H8     XSX 35 
XSX H9     H9  H 0 1 N N N 164.662 175.903 261.462 -1.040 -2.153 2.983  H9     XSX 36 
XSX H10    H10 H 0 1 N N N 163.439 177.379 262.995 0.679  -0.619 2.178  H10    XSX 37 
XSX H11    H11 H 0 1 N N N 160.618 176.900 258.167 -3.502 -1.112 -1.702 H11    XSX 38 
XSX H12    H12 H 0 1 N N N 160.591 175.179 258.681 -4.116 -2.283 -0.510 H12    XSX 39 
XSX H13    H13 H 0 1 N N N 162.577 175.485 256.768 -5.015 -0.419 0.856  H13    XSX 40 
XSX H14    H14 H 0 1 N N N 161.093 176.349 256.241 -4.402 0.751  -0.336 H14    XSX 41 
XSX H15    H15 H 0 1 N N N 159.748 174.343 256.620 -5.811 -0.369 -2.089 H15    XSX 42 
XSX H16    H16 H 0 1 N N N 160.783 172.973 254.936 -6.877 -1.852 0.226  H16    XSX 43 
XSX H17    H17 H 0 1 N N N 160.897 174.549 254.524 -7.445 -1.930 -1.336 H17    XSX 44 
XSX H19    H19 H 0 1 N N N 160.834 172.070 258.895 -7.586 2.521  -0.931 H19    XSX 45 
XSX H21    H21 H 0 1 N N N 166.555 178.072 263.106 5.446  -2.669 0.524  H21    XSX 46 
XSX OP3    OP3 O 0 1 N Y N 166.138 179.019 266.068 6.502  -1.685 -1.949 OP3    XSX 47 
XSX "HO3'" H18 H 0 0 N Y N 166.634 178.537 266.719 7.345  -2.158 -1.946 "HO3'" XSX 48 
# 
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 
XSX N4    C7     SING N N 1  
XSX C7    C3     SING N N 2  
XSX C7    C9     SING N N 3  
XSX C3    C1     SING N N 4  
XSX C9    O11    DOUB N N 5  
XSX C9    O10    SING N N 6  
XSX C1    N3     SING N N 7  
XSX O4    C4     DOUB N N 8  
XSX N3    C4     SING N N 9  
XSX N3    C2     SING N N 10 
XSX C4    C5     SING N N 11 
XSX O2    C2     DOUB N N 12 
XSX C2    N1     SING N N 13 
XSX C5    C6     DOUB N N 14 
XSX N1    C6     SING N N 15 
XSX N1    "C1'"  SING N N 16 
XSX "C1'" "O4'"  SING N N 17 
XSX "C1'" "C2'"  SING N N 18 
XSX "O4'" "C4'"  SING N N 19 
XSX OP2   P      SING N N 20 
XSX "C2'" "O2'"  SING N N 21 
XSX "C2'" "C3'"  SING N N 22 
XSX "C4'" "C3'"  SING N N 23 
XSX "C4'" "C5'"  SING N N 24 
XSX P     "O5'"  SING N N 25 
XSX P     OP1    DOUB N N 26 
XSX "O5'" "C5'"  SING N N 27 
XSX "C3'" "O3'"  SING N N 28 
XSX "C5'" H1     SING N N 29 
XSX "C5'" H2     SING N N 30 
XSX "C4'" H3     SING N N 31 
XSX "C3'" H4     SING N N 32 
XSX "O3'" H5     SING N N 33 
XSX "C2'" H6     SING N N 34 
XSX "O2'" H7     SING N N 35 
XSX "C1'" H8     SING N N 36 
XSX C5    H9     SING N N 37 
XSX C6    H10    SING N N 38 
XSX C1    H11    SING N N 39 
XSX C1    H12    SING N N 40 
XSX C3    H13    SING N N 41 
XSX C3    H14    SING N N 42 
XSX C7    H15    SING N N 43 
XSX N4    H16    SING N N 44 
XSX N4    H17    SING N N 45 
XSX O10   H19    SING N N 46 
XSX OP2   H21    SING N N 47 
XSX P     OP3    SING N N 48 
XSX OP3   "HO3'" SING N N 49 
# 
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 
XSX SMILES           ACDLabs              12.01 "O=C(O)C(N)CCN1C(=O)C=CN(C1=O)C1OC(COP(=O)(O)O)C(O)C1O"                                                                                                                                  
XSX InChI            InChI                1.06  "InChI=1S/C13H20N3O11P/c14-6(12(20)21)1-3-15-8(17)2-4-16(13(15)22)11-10(19)9(18)7(27-11)5-26-28(23,24)25/h2,4,6-7,9-11,18-19H,1,3,5,14H2,(H,20,21)(H2,23,24,25)/t6-,7-,9-,10-,11-/m1/s1" 
XSX InChIKey         InChI                1.06  CJKRCYMKRHIIKR-JBSYKWBFSA-N                                                                                                                                                              
XSX SMILES_CANONICAL CACTVS               3.385 "N[C@H](CCN1C(=O)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O)C(O)=O"                                                                                                          
XSX SMILES           CACTVS               3.385 "N[CH](CCN1C(=O)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O)C(O)=O"                                                                                                                 
XSX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N(C1=O)CC[C@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                                        
XSX SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N(C1=O)CCC(C(=O)O)N)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 
XSX "SYSTEMATIC NAME" ACDLabs              12.01 
;3-[(3R)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate)
;
XSX "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-2-azanyl-4-[3-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic 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 
XSX "Create component" 2022-12-07 RCSB 
XSX "Initial release"  2023-09-06 RCSB 
# 
