data_UBB
# 
_chem_comp.id                                    UBB 
_chem_comp.name                                  "2',3'-DIDEOXY-URIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H13 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2003-02-13 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        292.182 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UBB 
_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        1NH3 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
UBB O1P    O1P  O 0 1 N N N N N N 122.486 -66.842 -8.186  1.132  -0.005 6.219 O1P    UBB 1  
UBB P      P    P 0 1 N N N N N N 121.262 -66.590 -8.991  1.672  1.380  5.584 P      UBB 2  
UBB O2P    O2P  O 0 1 N N N N N N 120.863 -67.561 -10.038 2.913  1.936  6.219 O2P    UBB 3  
UBB O3P    O3P  O 0 1 N N N N N N ?       ?       ?       0.379  2.348  5.648 O3P    UBB 4  
UBB "O5'"  O5*  O 0 1 N N N N N N 120.074 -66.390 -7.949  1.800  1.054  4.004 "O5'"  UBB 5  
UBB "C5'"  C5*  C 0 1 N N N N N N 120.267 -65.569 -6.792  0.670  0.525  3.329 "C5'"  UBB 6  
UBB "C4'"  C4*  C 0 1 N N S N N N 119.173 -65.814 -5.781  1.027  0.302  1.866 "C4'"  UBB 7  
UBB "O4'"  O4*  O 0 1 N N N N N N 117.955 -65.156 -6.202  2.097  -0.657 1.801 "O4'"  UBB 8  
UBB "C1'"  C1*  C 0 1 N N R N N N 116.900 -66.099 -6.260  1.600  -1.869 1.217 "C1'"  UBB 9  
UBB N1     N1   N 0 1 N N N N N N 115.977 -65.667 -7.322  2.073  -2.991 1.972 N1     UBB 10 
UBB C6     C6   C 0 1 N N N N N N 116.231 -65.885 -8.657  2.255  -2.839 3.341 C6     UBB 11 
UBB C5     C5   C 0 1 N N N N N N 115.440 -65.422 -9.633  2.689  -3.810 4.147 C5     UBB 12 
UBB C4     C4   C 0 1 N N N N N N 114.283 -64.672 -9.302  3.002  -5.136 3.577 C4     UBB 13 
UBB O4     O4   O 0 1 N N N N N N 113.596 -64.029 -10.089 3.404  -6.049 4.292 O4     UBB 14 
UBB N3     N3   N 0 1 N N N N N N 114.061 -64.533 -7.953  2.805  -5.238 2.209 N3     UBB 15 
UBB C2     C2   C 0 1 N N N N N N 114.845 -65.000 -6.928  2.350  -4.229 1.349 C2     UBB 16 
UBB O2     O2   O 0 1 N N N N N N 114.550 -64.833 -5.756  2.212  -4.436 0.142 O2     UBB 17 
UBB "C2'"  C2*  C 0 1 N N N N N N 117.566 -67.455 -6.424  0.087  -1.764 1.201 "C2'"  UBB 18 
UBB "C3'"  C3*  C 0 1 N N N N N N 118.818 -67.289 -5.581  -0.121 -0.277 1.054 "C3'"  UBB 19 
UBB H1P    H1P  H 0 1 N N N N N N 122.741 -66.219 -7.515  1.038  -0.076 7.193 H1P    UBB 20 
UBB H3P    H3P  H 0 1 N N N N N N -0.782  0.161   -0.514  0.141  2.766  6.503 H3P    UBB 21 
UBB "H5'1" 1H5* H 0 0 N N N N N N 121.280 -65.709 -6.348  0.386  -0.420 3.801 "H5'1" UBB 22 
UBB "H5'2" 2H5* H 0 0 N N N N N N 120.350 -64.489 -7.058  -0.158 1.234  3.416 "H5'2" UBB 23 
UBB "H4'"  H4*  H 0 1 N N N N N N 119.576 -65.413 -4.821  1.377  1.247  1.439 "H4'"  UBB 24 
UBB "H1'"  H1*  H 0 1 N N N N N N 116.258 -66.176 -5.351  2.006  -1.949 0.203 "H1'"  UBB 25 
UBB H6     H6   H 0 1 N N N N N N 117.119 -66.463 -8.962  2.019  -1.858 3.738 H6     UBB 26 
UBB H5     H5   H 0 1 N N N N N N 115.731 -65.650 -10.672 2.819  -3.655 5.211 H5     UBB 27 
UBB HN3    HN3  H 0 1 N N N N N N 113.218 -64.025 -7.681  3.012  -6.138 1.785 HN3    UBB 28 
UBB "H2'1" 1H2* H 0 0 N N N N N N 116.929 -68.330 -6.159  -0.342 -2.106 2.152 "H2'1" UBB 29 
UBB "H2'2" 2H2* H 0 0 N N N N N N 117.743 -67.771 -7.478  -0.371 -2.351 0.399 "H2'2" UBB 30 
UBB "H3'1" 1H3* H 0 0 N N N N N N 119.640 -68.002 -5.822  -0.001 0.001  0.000 "H3'1" UBB 31 
UBB "H3'2" 2H3* H 0 0 N N N N N N 118.707 -67.601 -4.516  -1.108 0.062  1.383 "H3'2" UBB 32 
# 
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 
UBB O1P   P      SING N N 1  
UBB O1P   H1P    SING N N 2  
UBB P     O2P    DOUB N N 3  
UBB P     O3P    SING N N 4  
UBB P     "O5'"  SING N N 5  
UBB O3P   H3P    SING N N 6  
UBB "O5'" "C5'"  SING N N 7  
UBB "C5'" "C4'"  SING N N 8  
UBB "C5'" "H5'1" SING N N 9  
UBB "C5'" "H5'2" SING N N 10 
UBB "C4'" "O4'"  SING N N 11 
UBB "C4'" "C3'"  SING N N 12 
UBB "C4'" "H4'"  SING N N 13 
UBB "O4'" "C1'"  SING N N 14 
UBB "C1'" N1     SING N N 15 
UBB "C1'" "C2'"  SING N N 16 
UBB "C1'" "H1'"  SING N N 17 
UBB N1    C6     SING N N 18 
UBB N1    C2     SING N N 19 
UBB C6    C5     DOUB N N 20 
UBB C6    H6     SING N N 21 
UBB C5    C4     SING N N 22 
UBB C5    H5     SING N N 23 
UBB C4    O4     DOUB N N 24 
UBB C4    N3     SING N N 25 
UBB N3    C2     SING N N 26 
UBB N3    HN3    SING N N 27 
UBB C2    O2     DOUB N N 28 
UBB "C2'" "C3'"  SING N N 29 
UBB "C2'" "H2'1" SING N N 30 
UBB "C2'" "H2'2" SING N N 31 
UBB "C3'" "H3'1" SING N N 32 
UBB "C3'" "H3'2" SING N N 33 
# 
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 
UBB SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1)C2OC(CC2)COP(=O)(O)O"                                                                                             
UBB SMILES_CANONICAL CACTVS               3.341 "O[P](O)(=O)OC[C@@H]1CC[C@@H](O1)N2C=CC(=O)NC2=O"                                                                                   
UBB SMILES           CACTVS               3.341 "O[P](O)(=O)OC[CH]1CC[CH](O1)N2C=CC(=O)NC2=O"                                                                                       
UBB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@@H](O[C@@H]1COP(=O)(O)O)N2C=CC(=O)NC2=O"                                                                                     
UBB SMILES           "OpenEye OEToolkits" 1.5.0 "C1CC(OC1COP(=O)(O)O)N2C=CC(=O)NC2=O"                                                                                               
UBB InChI            InChI                1.03  "InChI=1S/C9H13N2O7P/c12-7-3-4-11(9(13)10-7)8-2-1-6(18-8)5-17-19(14,15)16/h3-4,6,8H,1-2,5H2,(H,10,12,13)(H2,14,15,16)/t6-,8+/m0/s1" 
UBB InChIKey         InChI                1.03  YHPMDBWWRCBXNU-POYBYMJQSA-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 
UBB "SYSTEMATIC NAME" ACDLabs              10.04 "[(2S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate" 
UBB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,5R)-5-(2,4-dioxopyrimidin-1-yl)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 
UBB "Create component"  2003-02-13 RCSB 
UBB "Modify descriptor" 2011-06-04 RCSB 
UBB "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            UBB 
_pdbx_chem_comp_pcm.modified_residue_id                PTR 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               "C3'" 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   O3P 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
