data_UDP
# 
_chem_comp.id                                    UDP 
_chem_comp.name                                  "URIDINE-5'-DIPHOSPHATE" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H14 N2 O12 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_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                        404.161 
_chem_comp.one_letter_code                       N 
_chem_comp.three_letter_code                     UDP 
_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        1NAH 
_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 
UDP N1     N1     N 0 1 N N N N N N 15.861 15.192 39.665 -3.586 0.410  0.193  N1     UDP 1  
UDP C2     C2     C 0 1 N N N N N N 15.566 16.502 40.157 -4.585 0.798  1.007  C2     UDP 2  
UDP N3     N3     N 0 1 N N N N N N 16.683 17.291 40.382 -5.335 1.877  0.717  N3     UDP 3  
UDP C4     C4     C 0 1 N N N N N N 18.033 16.891 40.187 -5.094 2.591  -0.401 C4     UDP 4  
UDP C5     C5     C 0 1 N N N N N N 18.234 15.529 39.704 -4.045 2.195  -1.266 C5     UDP 5  
UDP C6     C6     C 0 1 N N N N N N 17.189 14.755 39.468 -3.309 1.107  -0.951 C6     UDP 6  
UDP O2     O2     O 0 1 N N N N N N 14.442 16.927 40.336 -4.815 0.163  2.019  O2     UDP 7  
UDP O4     O4     O 0 1 N N N N N N 18.907 17.729 40.403 -5.771 3.568  -0.665 O4     UDP 8  
UDP "C1'"  "C1'"  C 0 1 N N R N N N 14.733 14.256 39.447 -2.784 -0.766 0.539  "C1'"  UDP 9  
UDP "C2'"  "C2'"  C 0 1 N N R N N N 14.571 13.772 38.009 -2.990 -1.893 -0.505 "C2'"  UDP 10 
UDP "O2'"  "O2'"  O 0 1 N N N N N N 13.698 14.717 37.300 -4.127 -2.694 -0.174 "O2'"  UDP 11 
UDP "C3'"  "C3'"  C 0 1 N N S N N N 13.871 12.378 38.197 -1.681 -2.708 -0.366 "C3'"  UDP 12 
UDP "C4'"  "C4'"  C 0 1 N N R N N N 14.520 11.865 39.442 -0.691 -1.722 0.283  "C4'"  UDP 13 
UDP "O4'"  "O4'"  O 0 1 N N N N N N 14.969 13.076 40.161 -1.375 -0.468 0.438  "O4'"  UDP 14 
UDP "O3'"  "O3'"  O 0 1 N N N N N N 12.489 12.489 38.456 -1.885 -3.842 0.479  "O3'"  UDP 15 
UDP "C5'"  "C5'"  C 0 1 N N N N N N 15.675 10.964 39.264 0.530  -1.540 -0.621 "C5'"  UDP 16 
UDP "O5'"  "O5'"  O 0 1 N N N N N N 16.615 11.736 38.492 1.494  -0.718 0.040  "O5'"  UDP 17 
UDP PA     PA     P 0 1 N N N N N N 18.056 11.086 38.175 2.907  -0.318 -0.621 PA     UDP 18 
UDP O1A    O1A    O 0 1 N N N N N N 18.751 11.990 37.180 3.630  -1.546 -1.019 O1A    UDP 19 
UDP O2A    O2A    O 0 1 N N N N N N 18.899 10.824 39.383 2.651  0.599  -1.920 O2A    UDP 20 
UDP O3A    O3A    O 0 1 N N N N N N 17.921 9.607  37.471 3.787  0.501  0.449  O3A    UDP 21 
UDP PB     PB     P 0 1 N N N N N N 16.971 9.089  36.332 5.343  0.907  0.541  PB     UDP 22 
UDP O1B    O1B    O 0 1 N N N N N N 17.723 7.785  35.830 6.176  -0.227 0.081  O1B    UDP 23 
UDP O2B    O2B    O 0 1 N Y N N N N 16.843 10.179 35.297 5.619  2.189  -0.393 O2B    UDP 24 
UDP O3B    O3B    O 0 1 N N N N N N 15.643 8.680  36.921 5.716  1.263  2.066  O3B    UDP 25 
UDP HN3    HN3    H 0 1 N N N N N N 16.526 18.222 40.710 -6.052 2.143  1.314  HN3    UDP 26 
UDP H5     H5     H 0 1 N N N N N N 19.234 15.154 39.540 -3.837 2.754  -2.166 H5     UDP 27 
UDP H6     H6     H 0 1 N N N N N N 17.357 13.750 39.111 -2.506 0.790  -1.599 H6     UDP 28 
UDP "H1'"  "H1'"  H 0 1 N N N N N N 13.844 14.827 39.755 -3.034 -1.119 1.539  "H1'"  UDP 29 
UDP "H2'"  "H2'"  H 0 1 N N N N N N 15.504 13.699 37.430 -3.087 -1.480 -1.510 "H2'"  UDP 30 
UDP "HO2'" "HO2'" H 0 0 N N N N N N 13.585 14.431 36.401 -4.297 -3.412 -0.798 "HO2'" UDP 31 
UDP "H3'"  "H3'"  H 0 1 N N N N N N 13.971 11.753 37.297 -1.321 -3.021 -1.346 "H3'"  UDP 32 
UDP "H4'"  "H4'"  H 0 1 N N N N N N 13.783 11.242 39.970 -0.380 -2.098 1.258  "H4'"  UDP 33 
UDP "HO3'" "HO3'" H 0 0 N N N N N N 12.115 11.622 38.561 -2.544 -4.467 0.146  "HO3'" UDP 34 
UDP "H5'1" "H5'1" H 0 0 N N N N N N 16.103 10.670 40.234 0.970  -2.514 -0.837 "H5'1" UDP 35 
UDP "H5'2" "H5'2" H 0 0 N N N N N N 15.385 10.045 38.734 0.225  -1.064 -1.553 "H5'2" UDP 36 
UDP HOA2   HOA2   H 0 0 N N N N N N 19.727 11.282 39.297 2.179  1.422  -1.733 HOA2   UDP 37 
UDP HOB2   HOB2   H 0 0 N N N N N N 17.248 9.895  34.486 5.105  2.971  -0.148 HOB2   UDP 38 
UDP HOB3   HOB3   H 0 0 N N N N N N 15.547 7.737  36.863 6.640  1.517  2.196  HOB3   UDP 39 
# 
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 
UDP N1    C2     SING N N 1  
UDP N1    C6     SING N N 2  
UDP N1    "C1'"  SING N N 3  
UDP C2    N3     SING N N 4  
UDP C2    O2     DOUB N N 5  
UDP N3    C4     SING N N 6  
UDP N3    HN3    SING N N 7  
UDP C4    C5     SING N N 8  
UDP C4    O4     DOUB N N 9  
UDP C5    C6     DOUB N N 10 
UDP C5    H5     SING N N 11 
UDP C6    H6     SING N N 12 
UDP "C1'" "C2'"  SING N N 13 
UDP "C1'" "O4'"  SING N N 14 
UDP "C1'" "H1'"  SING N N 15 
UDP "C2'" "O2'"  SING N N 16 
UDP "C2'" "C3'"  SING N N 17 
UDP "C2'" "H2'"  SING N N 18 
UDP "O2'" "HO2'" SING N N 19 
UDP "C3'" "C4'"  SING N N 20 
UDP "C3'" "O3'"  SING N N 21 
UDP "C3'" "H3'"  SING N N 22 
UDP "C4'" "O4'"  SING N N 23 
UDP "C4'" "C5'"  SING N N 24 
UDP "C4'" "H4'"  SING N N 25 
UDP "O3'" "HO3'" SING N N 26 
UDP "C5'" "O5'"  SING N N 27 
UDP "C5'" "H5'1" SING N N 28 
UDP "C5'" "H5'2" SING N N 29 
UDP "O5'" PA     SING N N 30 
UDP PA    O1A    DOUB N N 31 
UDP PA    O2A    SING N N 32 
UDP PA    O3A    SING N N 33 
UDP O2A   HOA2   SING N N 34 
UDP O3A   PB     SING N N 35 
UDP PB    O1B    DOUB N N 36 
UDP PB    O2B    SING N N 37 
UDP PB    O3B    SING N N 38 
UDP O2B   HOB2   SING N N 39 
UDP O3B   HOB3   SING N N 40 
# 
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 
UDP SMILES           ACDLabs              12.01 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O"                                                                                                                       
UDP SMILES_CANONICAL CACTVS               3.370 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                  
UDP SMILES           CACTVS               3.370 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                         
UDP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O"                                                                                               
UDP SMILES           "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                     
UDP InChI            InChI                1.03  "InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" 
UDP InChIKey         InChI                1.03  XCCTYIAWTASOJW-XVFCMESISA-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 
UDP "SYSTEMATIC NAME" ACDLabs              12.01 
;uridine 5'-(trihydrogen diphosphate)
;
UDP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen 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 
UDP "Create component"  1999-07-08 RCSB 
UDP "Modify descriptor" 2011-06-04 RCSB 
UDP "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            UDP 
_pdbx_chem_comp_pcm.modified_residue_id                SRZ 
_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               O3B 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   CZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
