data_UMC
# 
_chem_comp.id                                    UMC 
_chem_comp.name                                  
;2'-deoxy-5'-uridylic acid
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H15 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-08-03 
_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                        310.198 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UMC 
_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        ? 
_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 
UMC P      P    P 0 1 N N N N N N 111.030 23.670 31.307 4.002  -0.968 -0.034 P    UMC 1  
UMC N1     N1   N 0 1 N N N N N N 108.555 19.926 26.633 -2.553 0.335  -0.543 N1   UMC 2  
UMC C2     C2   C 0 1 N N N N N N 107.749 19.850 25.576 -2.582 -0.159 0.706  C2   UMC 3  
UMC O2     O2   O 0 1 N N N N N N 107.922 20.574 24.590 -1.701 0.147  1.485  O2   UMC 4  
UMC N3     N3   N 0 1 N N N N N N 106.746 18.957 25.611 -3.562 -0.981 1.115  N3   UMC 5  
UMC C4     C4   C 0 1 N N N N N N 106.589 18.026 26.567 -4.416 -1.533 0.233  C4   UMC 6  
UMC O4     O4   O 0 1 N N N N N N 105.668 17.202 26.485 -5.343 -2.208 0.628  O4   UMC 7  
UMC C5     C5   C 0 1 N N N N N N 107.565 17.951 27.714 -4.220 -1.311 -1.245 C5   UMC 8  
UMC C6     C6   C 0 1 N N N N N N 108.334 19.248 27.911 -3.658 0.094  -1.473 C6   UMC 9  
UMC "C1'"  C1*  C 0 1 N N R N N N 109.753 20.776 26.582 -1.403 1.131  -0.978 C1*  UMC 10 
UMC O1P    O1P  O 0 1 N N N N N N 112.246 24.415 31.810 3.539  -2.091 1.023  O1P  UMC 11 
UMC "C2'"  C2*  C 0 1 N N N N N N 109.530 22.263 26.854 -1.328 2.435  -0.160 C2*  UMC 12 
UMC O2P    O2P  O 0 1 N N N N N N 110.124 24.517 30.462 4.986  -0.065 0.605  O2P  UMC 13 
UMC "C3'"  C3*  C 0 1 N N S N N N 110.919 22.693 27.302 0.065  2.382  0.512  C3*  UMC 14 
UMC "O3'"  O3*  O 0 1 N N N N N N 111.800 22.856 26.183 0.693  3.665  0.488  O3*  UMC 15 
UMC O3P    O3P  O 0 1 N N N N N N 110.308 22.861 32.378 4.676  -1.679 -1.311 O3P  UMC 16 
UMC "C4'"  C4*  C 0 1 N N R N N N 111.369 21.509 28.135 0.824  1.377  -0.393 C4*  UMC 17 
UMC "O4'"  O4*  O 0 1 N N N N N N 110.714 20.374 27.562 -0.186 0.405  -0.737 O4*  UMC 18 
UMC "C5'"  C5*  C 0 1 N N N N N N 110.906 21.645 29.576 1.968  0.715  0.378  C5*  UMC 19 
UMC "O5'"  O5*  O 0 1 N N N N N N 111.701 22.590 30.300 2.721  -0.116 -0.508 O5*  UMC 20 
UMC H6     H6   H 0 1 N N N N N N 109.307 19.023 28.372 -4.443 0.831  -1.304 H6   UMC 21 
UMC "H2'"  H2*  H 0 1 N N N N N N 108.784 22.420 27.647 -1.403 3.302  -0.816 H2*  UMC 22 
UMC "H5'"  H5*  H 0 1 N N N N N N 109.858 21.980 29.584 2.618  1.485  0.795  H5*  UMC 23 
UMC "H2'A" H2*A H 0 0 N N N N N N 109.217 22.797 25.945 -2.115 2.457  0.595  H2*A UMC 24 
UMC "H5'A" H5*A H 0 0 N N N N N N 110.981 20.664 30.069 1.559  0.109  1.186  H5*A UMC 25 
UMC "H1'"  H1*  H 0 1 N N N N N N 110.202 20.683 25.582 -1.494 1.365  -2.039 H1*  UMC 26 
UMC "H3'"  H3*  H 0 1 N N N N N N 110.863 23.603 27.918 -0.009 2.006  1.533  H3*  UMC 27 
UMC "HO3'" HO3* H 0 0 N N N N N N 112.658 23.124 26.491 0.206  4.350  0.966  HO3* UMC 28 
UMC "H4'"  H4*  H 0 1 N N N N N N 112.464 21.408 28.095 1.202  1.875  -1.286 H4*  UMC 29 
UMC H5     H5   H 0 1 N N N N N N 108.283 17.142 27.514 -3.521 -2.051 -1.635 H5   UMC 30 
UMC H5A    H5A  H 0 1 N N N N N N 107.009 17.727 28.636 -5.177 -1.408 -1.758 H5A  UMC 31 
UMC HN3    HN3  H 0 1 N N N N N N 106.070 18.987 24.875 -3.656 -1.181 2.059  HN3  UMC 32 
UMC H6A    H6A  H 0 1 N N N N N N 107.759 19.910 28.575 -3.295 0.179  -2.497 H6A  UMC 33 
UMC HO1P   HO1P H 0 0 N N N N N N 112.222 25.311 31.495 2.893  -2.719 0.672  HO1P UMC 34 
UMC HO3P   HO3P H 0 0 N N N N N N 109.375 23.033 32.330 5.456  -2.210 -1.100 HO3P UMC 35 
# 
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 
UMC "O5'"  P      SING N N 1  
UMC O2P    P      DOUB N N 2  
UMC P      O1P    SING N N 3  
UMC P      O3P    SING N N 4  
UMC C2     N1     SING N N 5  
UMC "C1'"  N1     SING N N 6  
UMC N1     C6     SING N N 7  
UMC O2     C2     DOUB N N 8  
UMC C2     N3     SING N N 9  
UMC HN3    N3     SING N N 10 
UMC N3     C4     SING N N 11 
UMC O4     C4     DOUB N N 12 
UMC C4     C5     SING N N 13 
UMC H5A    C5     SING N N 14 
UMC C5     C6     SING N N 15 
UMC C5     H5     SING N N 16 
UMC C6     H6     SING N N 17 
UMC C6     H6A    SING N N 18 
UMC "H1'"  "C1'"  SING N N 19 
UMC "C1'"  "C2'"  SING N N 20 
UMC "C1'"  "O4'"  SING N N 21 
UMC O1P    HO1P   SING N N 22 
UMC "H2'A" "C2'"  SING N N 23 
UMC "C2'"  "C3'"  SING N N 24 
UMC "C2'"  "H2'"  SING N N 25 
UMC "O3'"  "C3'"  SING N N 26 
UMC "C3'"  "H3'"  SING N N 27 
UMC "C3'"  "C4'"  SING N N 28 
UMC "HO3'" "O3'"  SING N N 29 
UMC O3P    HO3P   SING N N 30 
UMC "O4'"  "C4'"  SING N N 31 
UMC "H4'"  "C4'"  SING N N 32 
UMC "C4'"  "C5'"  SING N N 33 
UMC "C5'"  "H5'"  SING N N 34 
UMC "C5'"  "H5'A" SING N N 35 
UMC "C5'"  "O5'"  SING N N 36 
# 
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 
UMC SMILES           ACDLabs              12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)CC1)CC2O"                                                                                                   
UMC InChI            InChI                1.03  "InChI=1S/C9H15N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h5-6,8,12H,1-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" 
UMC InChIKey         InChI                1.03  WQQZADPPRABIFU-SHYZEUOFSA-N                                                                                                               
UMC SMILES_CANONICAL CACTVS               3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O"                                                                                     
UMC SMILES           CACTVS               3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O"                                                                                          
UMC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                    
UMC SMILES           "OpenEye OEToolkits" 1.7.6 "C1CN(C(=O)NC1=O)C2CC(C(O2)COP(=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 
UMC "SYSTEMATIC NAME" ACDLabs              12.01 
;2'-deoxy-5'-uridylic acid
;
UMC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-3-oxidanyl-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 
UMC "Create component"   2012-08-03 RCSB 
UMC "Other modification" 2012-08-07 RCSB 
UMC "Initial release"    2012-08-24 RCSB 
UMC "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            UMC 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_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               C6 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
