data_UMP
# 
_chem_comp.id                                    UMP 
_chem_comp.name                                  
;2'-DEOXYURIDINE 5'-MONOPHOSPHATE
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H13 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         DUMP 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_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                        308.182 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     UMP 
_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 
UMP N1     N1     N 0 1 N N N N N N 20.447 12.689 18.071 -2.460 0.157  -0.225 N1     UMP 1  
UMP C2     C2     C 0 1 N N N N N N 20.926 11.704 17.241 -3.508 -0.069 -1.038 C2     UMP 2  
UMP N3     N3     N 0 1 N N N N N N 20.589 10.398 17.525 -4.527 -0.860 -0.650 N3     UMP 3  
UMP C4     C4     C 0 1 N N N N N N 19.824 10.026 18.595 -4.510 -1.441 0.567  C4     UMP 4  
UMP C5     C5     C 0 1 N N N N N N 19.350 11.064 19.418 -3.413 -1.211 1.432  C5     UMP 5  
UMP C6     C6     C 0 1 N N N N N N 19.707 12.367 19.148 -2.406 -0.414 1.018  C6     UMP 6  
UMP O2     O2     O 0 1 N N N N N N 21.632 11.940 16.243 -3.536 0.448  -2.138 O2     UMP 7  
UMP O4     O4     O 0 1 N N N N N N 19.562 8.808  18.746 -5.431 -2.156 0.919  O4     UMP 8  
UMP "C1'"  "C1'"  C 0 1 N N R N N N 20.790 14.106 17.813 -1.364 1.017  -0.677 "C1'"  UMP 9  
UMP "C2'"  "C2'"  C 0 1 N N N N N N 19.576 14.957 17.530 -1.299 2.285  0.197  "C2'"  UMP 10 
UMP "C3'"  "C3'"  C 0 1 N N S N N N 19.269 15.668 18.818 0.127  2.258  0.798  "C3'"  UMP 11 
UMP "C4'"  "C4'"  C 0 1 N N R N N N 20.644 15.747 19.476 0.878  1.327  -0.187 "C4'"  UMP 12 
UMP "O3'"  "O3'"  O 0 1 N N N N N N 18.640 16.944 18.641 0.703  3.566  0.803  "O3'"  UMP 13 
UMP "O4'"  "O4'"  O 0 1 N N N N N N 21.395 14.611 19.000 -0.110 0.331  -0.528 "O4'"  UMP 14 
UMP "C5'"  "C5'"  C 0 1 N N N N N N 20.680 15.746 20.969 2.083  0.678  0.497  "C5'"  UMP 15 
UMP "O5'"  "O5'"  O 0 1 N N N N N N 20.080 14.578 21.461 2.823  -0.082 -0.461 "O5'"  UMP 16 
UMP P      P      P 0 1 N N N N N N 19.859 14.370 23.016 4.157  -0.901 -0.088 P      UMP 17 
UMP OP1    O1P    O 0 1 N N N N N N 19.304 12.981 23.168 5.136  0.011  0.544  OP1    UMP 18 
UMP OP2    O2P    O 0 1 N N N N N N 21.183 14.526 23.710 3.790  -2.088 0.936  OP2    UMP 19 
UMP OP3    O3P    O 0 1 N Y N N N N 18.841 15.373 23.449 4.794  -1.527 -1.428 OP3    UMP 20 
UMP HN3    HN3    H 0 1 N N N N N N 20.923 9.681  16.913 -5.275 -1.012 -1.248 HN3    UMP 21 
UMP H5     H5     H 0 1 N N N N N N 18.709 10.840 20.258 -3.383 -1.668 2.410  H5     UMP 22 
UMP H6     H6     H 0 1 N N N N N N 19.385 13.150 19.818 -1.561 -0.228 1.664  H6     UMP 23 
UMP "H1'"  "H1'"  H 0 1 N N N N N N 21.488 14.172 16.965 -1.516 1.294  -1.720 "H1'"  UMP 24 
UMP "H2'"  "H2'1" H 0 1 N N N N N N 19.794 15.683 16.733 -1.439 3.177  -0.414 "H2'"  UMP 25 
UMP "H2''" "H2'2" H 0 0 N N N N N N 18.727 14.326 17.228 -2.048 2.242  0.988  "H2''" UMP 26 
UMP "H3'"  "H3'"  H 0 1 N N N N N N 18.626 15.021 19.433 0.118  1.835  1.803  "H3'"  UMP 27 
UMP "H4'"  "H4'"  H 0 1 N N N N N N 21.132 16.667 19.123 1.189  1.878  -1.074 "H4'"  UMP 28 
UMP "HO3'" "HO3'" H 0 0 N Y N N N N 18.475 17.337 19.490 0.215  4.209  1.335  "HO3'" UMP 29 
UMP "H5'"  "H5'1" H 0 1 N N N N N N 21.725 15.790 21.308 2.723  1.454  0.918  "H5'"  UMP 30 
UMP "H5''" "H5'2" H 0 0 N N N N N N 20.135 16.623 21.347 1.738  0.020  1.294  "H5''" UMP 31 
UMP HOP2   HOP2   H 0 0 N N N N N N 21.424 13.704 24.121 3.152  -2.725 0.587  HOP2   UMP 32 
UMP HOP3   HOP3   H 0 0 N N N N N N 18.053 14.924 23.731 5.603  -2.035 -1.279 HOP3   UMP 33 
# 
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 
UMP N1    C2     SING N N 1  
UMP N1    C6     SING N N 2  
UMP N1    "C1'"  SING N N 3  
UMP C2    N3     SING N N 4  
UMP C2    O2     DOUB N N 5  
UMP N3    C4     SING N N 6  
UMP N3    HN3    SING N N 7  
UMP C4    C5     SING N N 8  
UMP C4    O4     DOUB N N 9  
UMP C5    C6     DOUB N N 10 
UMP C5    H5     SING N N 11 
UMP C6    H6     SING N N 12 
UMP "C1'" "C2'"  SING N N 13 
UMP "C1'" "O4'"  SING N N 14 
UMP "C1'" "H1'"  SING N N 15 
UMP "C2'" "C3'"  SING N N 16 
UMP "C2'" "H2'"  SING N N 17 
UMP "C2'" "H2''" SING N N 18 
UMP "C3'" "C4'"  SING N N 19 
UMP "C3'" "O3'"  SING N N 20 
UMP "C3'" "H3'"  SING N N 21 
UMP "C4'" "O4'"  SING N N 22 
UMP "C4'" "C5'"  SING N N 23 
UMP "C4'" "H4'"  SING N N 24 
UMP "O3'" "HO3'" SING N N 25 
UMP "C5'" "O5'"  SING N N 26 
UMP "C5'" "H5'"  SING N N 27 
UMP "C5'" "H5''" SING N N 28 
UMP "O5'" P      SING N N 29 
UMP P     OP1    DOUB N N 30 
UMP P     OP2    SING N N 31 
UMP P     OP3    SING N N 32 
UMP OP2   HOP2   SING N N 33 
UMP OP3   HOP3   SING N N 34 
# 
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 
UMP SMILES           ACDLabs              12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O"                                                                                                      
UMP InChI            InChI                1.03  "InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" 
UMP InChIKey         InChI                1.03  JSRLJPSBLDHEIO-SHYZEUOFSA-N                                                                                                                   
UMP SMILES_CANONICAL CACTVS               3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                        
UMP SMILES           CACTVS               3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                             
UMP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O"                                                                                         
UMP SMILES           "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=CC(=O)NC2=O)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 
UMP "SYSTEMATIC NAME" ACDLabs              12.01 
;2'-deoxy-5'-uridylic acid
;
UMP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-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 
UMP "Create component"    1999-07-08 RCSB 
UMP "Modify descriptor"   2011-06-04 RCSB 
UMP "Modify linking type" 2012-05-02 RCSB 
UMP "Modify synonyms"     2020-06-05 PDBE 
UMP "Modify PCM"          2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      UMP 
_pdbx_chem_comp_synonyms.name         DUMP 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            UMP 
_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      ? 
# 
