data_WSB
# 
_chem_comp.id                                    WSB 
_chem_comp.name                                  "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H17 N2 O14 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-17 
_chem_comp.pdbx_modified_date                    2023-11-17 
_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                        482.168 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     WSB 
_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        8SQ9 
_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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
WSB N1    N1  N 0 1 N N N N N N 139.744 135.759 133.666 5.032  0.757  -0.578 N1    WSB 1  
WSB N3    N2  N 0 1 N N N N N N 138.990 134.613 131.797 5.766  2.216  1.101  N3    WSB 2  
WSB C4    C1  C 0 1 N N N N N N 140.218 134.048 131.518 6.446  2.945  0.193  C4    WSB 3  
WSB C5    C2  C 0 1 N N N N N N 141.264 134.406 132.431 6.423  2.558  -1.168 C5    WSB 4  
WSB C6    C3  C 0 1 N N N N N N 140.994 135.230 133.454 5.713  1.467  -1.529 C6    WSB 5  
WSB "C1'" C4  C 0 1 N N R N N N 139.489 136.657 134.807 4.263  -0.427 -0.968 "C1'" WSB 6  
WSB C2    C5  C 0 1 N N N N N N 138.686 135.459 132.832 5.067  1.133  0.714  C2    WSB 7  
WSB "C2'" C6  C 0 1 N N R N N N 138.970 135.947 136.052 4.822  -1.686 -0.271 "C2'" WSB 8  
WSB "C3'" C7  C 0 1 N N S N N N 140.239 135.696 136.851 3.566  -2.524 0.056  "C3'" WSB 9  
WSB C3A   C8  C 0 1 N N N N N N 144.412 133.743 136.630 -2.533 -0.139 -0.530 C3A   WSB 10 
WSB "C4'" C9  C 0 1 N N R N N N 141.069 136.930 136.524 2.396  -1.672 -0.484 "C4'" WSB 11 
WSB "C5'" C10 C 0 1 N N N N N N 142.565 136.777 136.649 1.186  -1.778 0.447  "C5'" WSB 12 
WSB O1A   O1  O 0 1 N N N N N N 145.051 135.027 134.355 -1.857 -2.345 0.880  O1A   WSB 13 
WSB O1B   O2  O 0 1 N N N N N N 144.538 135.231 138.865 -4.704 -1.512 0.598  O1B   WSB 14 
WSB O1G   O3  O 0 1 N N N N N N 146.959 131.948 137.998 -7.018 1.712  0.731  O1G   WSB 15 
WSB O2    O4  O 0 1 N N N N N N 137.561 135.911 132.997 4.459  0.484  1.543  O2    WSB 16 
WSB "O2'" O5  O 0 1 N N N N N N 138.057 136.785 136.729 5.688  -2.404 -1.152 "O2'" WSB 17 
WSB O2A   O6  O 0 1 N N N N N N 145.358 136.268 136.559 -1.229 -0.149 1.955  O2A   WSB 18 
WSB O2B   O7  O 0 1 N N N N N N 142.567 133.632 138.590 -4.043 0.737  1.536  O2B   WSB 19 
WSB O2G   O8  O 0 1 N N N N N N 146.646 131.631 140.467 -7.115 2.187  -1.746 O2G   WSB 20 
WSB "O3'" O9  O 0 1 N N N N N N 139.954 135.636 138.244 3.617  -3.785 -0.615 "O3'" WSB 21 
WSB O3B   O10 O 0 1 N N N N N N 144.883 132.754 139.119 -5.199 0.715  -0.708 O3B   WSB 22 
WSB O3G   O11 O 0 1 N N N N N N 147.035 133.931 139.536 -7.663 -0.199 -0.787 O3G   WSB 23 
WSB O4    O12 O 0 1 N N N N N N 140.333 133.304 130.545 7.079  3.926  0.542  O4    WSB 24 
WSB "O4'" O13 O 0 1 N N N N N N 140.724 137.268 135.162 2.901  -0.319 -0.499 "O4'" WSB 25 
WSB "O5'" O14 O 0 1 N N N N N N 143.053 135.890 135.612 0.080  -1.078 -0.127 "O5'" WSB 26 
WSB PA    P1  P 0 1 N N N N N N 144.530 135.322 135.734 -1.361 -0.982 0.584  PA    WSB 27 
WSB PB    P2  P 0 1 N N N N N N 144.036 133.891 138.403 -4.165 -0.030 0.275  PB    WSB 28 
WSB PG    P3  P 0 1 N N N N N N 146.472 132.553 139.289 -6.754 1.117  -0.598 PG    WSB 29 
WSB H1    H1  H 0 1 N N N N N N 138.241 134.380 131.177 5.781  2.473  2.036  H1    WSB 30 
WSB H2    H2  H 0 1 N N N N N N 142.262 134.015 132.296 6.961  3.130  -1.910 H2    WSB 31 
WSB H3    H3  H 0 1 N N N N N N 141.790 135.488 134.137 5.684  1.156  -2.562 H3    WSB 32 
WSB H4    H4  H 0 1 N N N N N N 138.760 137.425 134.510 4.282  -0.550 -2.051 H4    WSB 33 
WSB H5    H5  H 0 1 N N N N N N 138.508 134.989 135.771 5.350  -1.414 0.643  H5    WSB 34 
WSB H6    H6  H 0 1 N N N N N N 140.745 134.787 136.495 3.472  -2.668 1.132  H6    WSB 35 
WSB H7    H7  H 0 1 N N N N N N 143.617 133.144 136.162 -2.168 0.865  -0.748 H7    WSB 36 
WSB H8    H8  H 0 1 N N N N N N 145.374 133.220 136.528 -2.622 -0.703 -1.458 H8    WSB 37 
WSB H9    H9  H 0 1 N N N N N N 140.748 137.745 137.190 2.127  -1.990 -1.491 H9    WSB 38 
WSB H10   H10 H 0 1 N N N N N N 142.808 136.355 137.635 0.922  -2.827 0.582  H10   WSB 39 
WSB H11   H11 H 0 1 N N N N N N 143.044 137.762 136.543 1.432  -1.338 1.414  H11   WSB 40 
WSB H12   H12 H 0 1 N N N N N N 143.816 135.734 139.222 -4.808 -2.072 -0.184 H12   WSB 41 
WSB H13   H13 H 0 1 N N N N N N 137.734 136.341 137.505 6.067  -3.205 -0.765 H13   WSB 42 
WSB H14   H14 H 0 1 N N N N N N 146.116 136.545 136.058 -0.908 0.756  1.836  H14   WSB 43 
WSB H15   H15 H 0 1 N N N N N N 147.040 130.817 140.177 -8.038 2.474  -1.740 H15   WSB 44 
WSB H16   H16 H 0 1 N N N N N N 140.758 135.479 138.726 4.368  -4.337 -0.358 H16   WSB 45 
WSB H17   H17 H 0 1 N N N N N N 147.607 134.173 138.817 -7.542 -0.641 -1.638 H17   WSB 46 
# 
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 
WSB O4    C4    DOUB N N 1  
WSB C4    N3    SING N N 2  
WSB C4    C5    SING N N 3  
WSB N3    C2    SING N N 4  
WSB C5    C6    DOUB N N 5  
WSB C2    O2    DOUB N N 6  
WSB C2    N1    SING N N 7  
WSB C6    N1    SING N N 8  
WSB N1    "C1'" SING N N 9  
WSB O1A   PA    DOUB N N 10 
WSB "C1'" "O4'" SING N N 11 
WSB "C1'" "C2'" SING N N 12 
WSB "O4'" "C4'" SING N N 13 
WSB "O5'" PA    SING N N 14 
WSB "O5'" "C5'" SING N N 15 
WSB PA    O2A   SING N N 16 
WSB PA    C3A   SING N N 17 
WSB "C2'" "O2'" SING N N 18 
WSB "C2'" "C3'" SING N N 19 
WSB "C4'" "C5'" SING N N 20 
WSB "C4'" "C3'" SING N N 21 
WSB C3A   PB    SING N N 22 
WSB "C3'" "O3'" SING N N 23 
WSB O1G   PG    DOUB N N 24 
WSB PB    O2B   DOUB N N 25 
WSB PB    O1B   SING N N 26 
WSB PB    O3B   SING N N 27 
WSB O3B   PG    SING N N 28 
WSB PG    O3G   SING N N 29 
WSB PG    O2G   SING N N 30 
WSB N3    H1    SING N N 31 
WSB C5    H2    SING N N 32 
WSB C6    H3    SING N N 33 
WSB "C1'" H4    SING N N 34 
WSB "C2'" H5    SING N N 35 
WSB "C3'" H6    SING N N 36 
WSB C3A   H7    SING N N 37 
WSB C3A   H8    SING N N 38 
WSB "C4'" H9    SING N N 39 
WSB "C5'" H10   SING N N 40 
WSB "C5'" H11   SING N N 41 
WSB O1B   H12   SING N N 42 
WSB "O2'" H13   SING N N 43 
WSB O2A   H14   SING N N 44 
WSB O2G   H15   SING N N 45 
WSB "O3'" H16   SING N N 46 
WSB O3G   H17   SING N N 47 
# 
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 
WSB SMILES           ACDLabs              12.01 "O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC1OC(N2C=CC(=O)NC2=O)C(O)C1O"                                                                                                                                        
WSB InChI            InChI                1.06  "InChI=1S/C10H17N2O14P3/c13-6-1-2-12(10(16)11-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H,11,13,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1" 
WSB InChIKey         InChI                1.06  UJLGWNDCUWVLAK-ZOQUXTDFSA-N                                                                                                                                                                        
WSB SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                               
WSB SMILES           CACTVS               3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                      
WSB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O"                                                                                                                  
WSB SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(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 
WSB "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine"                                                                                   
WSB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic 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 
WSB "Create component" 2023-05-17 RCSB 
WSB "Initial release"  2023-11-22 RCSB 
# 
