data_OJU
# 
_chem_comp.id                                    OJU 
_chem_comp.name                                  "2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxyethyl-[3-(2-chloranylethanoylamino)propyl]-dimethyl-azanium" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H33 Cl N5 O12 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Cytidine-diphosphate with a thiol-reactive chloroacetamide (cross-linker)" 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2022-09-13 
_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                        608.881 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     OJU 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8ALK 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
OJU C25 C1  C  0 1 N N N N N N -38.663 -13.717 -7.382  -5.911  0.014  -0.193 C25 OJU 1  
OJU P   P1  P  0 1 N N N N N N -40.634 -12.762 -1.980  -0.540  -3.848 -0.727 P   OJU 2  
OJU O1  O1  O  0 1 N N N N N N -40.328 -14.155 -1.587  -0.342  -5.301 -0.529 O1  OJU 3  
OJU O2  O2  O  0 1 N N N N N N -39.961 -12.452 -3.409  -1.990  -3.423 -0.173 O2  OJU 4  
OJU O3  O3  O  0 1 N N N N N N -40.063 -11.748 -0.875  -0.443  -3.502 -2.297 O3  OJU 5  
OJU C01 C2  C  0 1 N N N N N N -36.980 -13.906 -5.284  -4.657  -1.976 -1.794 C01 OJU 6  
OJU C03 C3  C  0 1 N N N N N N -36.249 -11.980 -6.441  -3.369  -1.232 0.088  C03 OJU 7  
OJU C04 C4  C  0 1 N N N N N N -38.556 -12.501 -6.444  -5.753  -1.435 0.270  C04 OJU 8  
OJU C05 C5  C  0 1 N N N N N N -37.492 -11.738 -4.445  -4.390  -3.403 0.115  C05 OJU 9  
OJU C06 C6  C  0 1 N N N N N N -38.602 -12.333 -3.567  -3.202  -4.043 -0.608 C06 OJU 10 
OJU C29 C7  C  0 1 N N N N N N -38.735 -13.216 -8.828  -7.172  0.614  0.432  C29 OJU 11 
OJU C32 C8  C  0 1 N N N N N N -36.571 -13.234 -10.123 -8.372  2.735  0.415  C32 OJU 12 
OJU C37 C9  C  0 1 N N N N N N -35.540 -13.983 -10.972 -8.528  4.163  -0.041 C37 OJU 13 
OJU N02 N1  N  1 1 N N N N N N -37.325 -12.545 -5.650  -4.542  -2.012 -0.330 N02 OJU 14 
OJU N31 N2  N  0 1 N N N N N N -37.755 -13.934 -9.633  -7.324  2.002  -0.012 N31 OJU 15 
OJU O36 O4  O  0 1 N N N N N N -36.407 -12.091 -9.861  -9.188  2.246  1.167  O36 OJU 16 
OJU H1  H1  H  0 1 N N N N N N -39.571 -14.290 -7.143  -5.041  0.592  0.117  H1  OJU 17 
OJU H2  H2  H  0 1 N N N N N N -37.780 -14.360 -7.257  -5.997  0.041  -1.280 H2  OJU 18 
OJU H3  H3  H  0 1 N N N N N N -39.639 -12.240 -0.182  -0.563  -2.565 -2.501 H3  OJU 19 
OJU H5  H5  H  0 1 N N N N N N -36.054 -13.903 -4.690  -3.759  -2.404 -2.240 H5  OJU 20 
OJU H6  H6  H  0 1 N N N N N N -37.795 -14.343 -4.689  -5.528  -2.554 -2.105 H6  OJU 21 
OJU H7  H7  H  0 1 N N N N N N -36.830 -14.504 -6.195  -4.771  -0.943 -2.125 H7  OJU 22 
OJU H8  H8  H  0 1 N N N N N N -35.315 -12.004 -5.861  -3.195  -1.382 1.153  H8  OJU 23 
OJU H9  H9  H  0 1 N N N N N N -36.124 -12.568 -7.362  -2.495  -1.562 -0.474 H9  OJU 24 
OJU H10 H10 H  0 1 N N N N N N -36.492 -10.939 -6.700  -3.548  -0.175 -0.106 H10 OJU 25 
OJU H11 H11 H  0 1 N N N N N N -38.560 -11.582 -7.048  -5.667  -1.462 1.357  H11 OJU 26 
OJU H12 H12 H  0 1 N N N N N N -39.421 -12.496 -5.764  -6.623  -2.014 -0.040 H12 OJU 27 
OJU H13 H13 H  0 1 N N N N N N -36.548 -11.726 -3.881  -5.298  -3.960 -0.116 H13 OJU 28 
OJU H14 H14 H  0 1 N N N N N N -37.763 -10.710 -4.729  -4.214  -3.423 1.190  H14 OJU 29 
OJU H15 H15 H  0 1 N N N N N N -38.316 -13.395 -3.587  -3.314  -3.905 -1.683 H15 OJU 30 
OJU H16 H16 H  0 1 N N N N N N -38.331 -11.899 -2.593  -3.168  -5.108 -0.379 H16 OJU 31 
OJU H17 H17 H  0 1 N N N N N N -38.515 -12.139 -8.855  -8.042  0.036  0.122  H17 OJU 32 
OJU H18 H18 H  0 1 N N N N N N -39.743 -13.395 -9.230  -7.087  0.588  1.519  H18 OJU 33 
OJU H19 H19 H  0 1 N N N N N N -34.739 -13.289 -11.266 -8.614  4.189  -1.128 H19 OJU 34 
OJU CL1 CL1 CL 0 0 N Y N N N N -36.002 -14.381 -11.851 -10.014 4.870  0.696  CL1 OJU 35 
OJU H21 H21 H  0 1 N N N N N N -35.113 -14.807 -10.381 -7.658  4.741  0.269  H21 OJU 36 
OJU H22 H22 H  0 1 N N N N N N -37.893 -14.901 -9.849  -6.672  2.393  -0.613 H22 OJU 37 
OJU O4  O5  O  0 1 N Y N N N N -42.224 -12.551 -2.090  0.599   -3.038 0.072  O4  OJU 38 
OJU P1  P2  P  0 1 N Y N N N N -42.667 -13.365 -1.881  2.193   -3.207 0.226  P1  OJU 39 
OJU O5  O6  O  0 1 N Y N N N N ?       ?       ?       2.792   -3.468 -1.103 O5  OJU 40 
OJU O6  O7  O  0 1 N Y N N N N ?       ?       ?       2.819   -1.858 0.841  O6  OJU 41 
OJU O7  O8  O  0 1 N Y N N N N ?       ?       ?       2.509   -4.443 1.209  O7  OJU 42 
OJU C1  C10 C  0 1 N Y N N N N ?       ?       ?       4.225   -1.655 1.001  C1  OJU 43 
OJU H20 H20 H  0 1 N Y N N N N ?       ?       ?       2.146   -4.340 2.099  H20 OJU 44 
OJU C2  C11 C  0 1 N Y N N N N ?       ?       ?       4.474   -0.273 1.611  C2  OJU 45 
OJU C3  C12 C  0 1 N Y N N N N ?       ?       ?       5.977   -0.081 1.910  C3  OJU 46 
OJU C4  C13 C  0 1 N Y N N N N ?       ?       ?       6.239   1.405  1.574  C4  OJU 47 
OJU C5  C14 C  0 1 N Y N N N N ?       ?       ?       4.863   1.934  1.113  C5  OJU 48 
OJU O8  O9  O  0 1 N Y N N N N ?       ?       ?       4.151   0.762  0.658  O8  OJU 49 
OJU H4  H4  H  0 1 N Y N N N N ?       ?       ?       4.629   -2.421 1.661  H4  OJU 50 
OJU H23 H23 H  0 1 N Y N N N N ?       ?       ?       4.714   -1.716 0.029  H23 OJU 51 
OJU H24 H24 H  0 1 N Y N N N N ?       ?       ?       3.887   -0.150 2.521  H24 OJU 52 
OJU H25 H25 H  0 1 N Y N N N N ?       ?       ?       6.186   -0.278 2.961  H25 OJU 53 
OJU O9  O10 O  0 1 N Y N N N N ?       ?       ?       6.766   -0.929 1.074  O9  OJU 54 
OJU H27 H27 H  0 1 N Y N N N N ?       ?       ?       6.577   1.942  2.460  H27 OJU 55 
OJU O10 O11 O  0 1 N Y N N N N ?       ?       ?       7.198   1.519  0.521  O10 OJU 56 
OJU H29 H29 H  0 1 N Y N N N N ?       ?       ?       4.336   2.398  1.947  H29 OJU 57 
OJU N1  N3  N  0 1 N Y N N N N ?       ?       ?       5.026   2.890  0.015  N1  OJU 58 
OJU C8  C15 C  0 1 N Y N N N N ?       ?       ?       5.746   4.011  0.206  C8  OJU 59 
OJU N2  N4  N  0 1 N Y N N N N ?       ?       ?       5.911   4.897  -0.775 N2  OJU 60 
OJU C9  C16 C  0 1 N Y N N N N ?       ?       ?       5.367   4.696  -1.968 C9  OJU 61 
OJU C10 C17 C  0 1 N Y N N N N ?       ?       ?       4.607   3.532  -2.200 C10 OJU 62 
OJU C11 C18 C  0 1 N Y N N N N ?       ?       ?       4.453   2.637  -1.195 C11 OJU 63 
OJU N3  N5  N  0 1 N Y N N N N ?       ?       ?       5.543   5.619  -2.973 N3  OJU 64 
OJU O11 O12 O  0 1 N Y N N N N ?       ?       ?       6.256   4.219  1.294  O11 OJU 65 
OJU H26 H26 H  0 1 N Y N N N N ?       ?       ?       7.719   -0.849 1.219  H26 OJU 66 
OJU H28 H28 H  0 1 N Y N N N N ?       ?       ?       8.064   1.146  0.736  H28 OJU 67 
OJU H30 H30 H  0 1 N Y N N N N ?       ?       ?       4.157   3.354  -3.166 H30 OJU 68 
OJU H31 H31 H  0 1 N Y N N N N ?       ?       ?       3.876   1.738  -1.348 H31 OJU 69 
OJU H32 H32 H  0 1 N Y N N N N ?       ?       ?       6.066   6.419  -2.810 H32 OJU 70 
OJU H33 H33 H  0 1 N Y N N N N ?       ?       ?       5.144   5.469  -3.844 H33 OJU 71 
# 
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 
OJU C37 C32 SING N N 1  
OJU C32 O36 DOUB N N 2  
OJU C32 N31 SING N N 3  
OJU N31 C29 SING N N 4  
OJU C29 C25 SING N N 5  
OJU C25 C04 SING N N 6  
OJU C04 N02 SING N N 7  
OJU C03 N02 SING N N 8  
OJU N02 C01 SING N N 9  
OJU N02 C05 SING N N 10 
OJU C05 C06 SING N N 11 
OJU C06 O2  SING N N 12 
OJU O2  P   SING N N 13 
OJU P   O1  DOUB N N 14 
OJU P   O3  SING N N 15 
OJU C25 H1  SING N N 16 
OJU C25 H2  SING N N 17 
OJU O3  H3  SING N N 18 
OJU C01 H5  SING N N 19 
OJU C01 H6  SING N N 20 
OJU C01 H7  SING N N 21 
OJU C03 H8  SING N N 22 
OJU C03 H9  SING N N 23 
OJU C03 H10 SING N N 24 
OJU C04 H11 SING N N 25 
OJU C04 H12 SING N N 26 
OJU C05 H13 SING N N 27 
OJU C05 H14 SING N N 28 
OJU C06 H15 SING N N 29 
OJU C06 H16 SING N N 30 
OJU C29 H17 SING N N 31 
OJU C29 H18 SING N N 32 
OJU C37 H19 SING N N 33 
OJU C37 CL1 SING N N 34 
OJU C37 H21 SING N N 35 
OJU N31 H22 SING N N 36 
OJU P   O4  SING N N 37 
OJU O4  P1  SING N N 38 
OJU P1  O5  DOUB N N 39 
OJU P1  O6  SING N N 40 
OJU P1  O7  SING N N 41 
OJU O6  C1  SING N N 42 
OJU O7  H20 SING N N 43 
OJU C1  C2  SING N N 44 
OJU C2  C3  SING N N 45 
OJU C3  C4  SING N N 46 
OJU C4  C5  SING N N 47 
OJU C5  O8  SING N N 48 
OJU O8  C2  SING N N 49 
OJU C1  H4  SING N N 50 
OJU C1  H23 SING N N 51 
OJU C2  H24 SING N N 52 
OJU C3  H25 SING N N 53 
OJU C3  O9  SING N N 54 
OJU C4  H27 SING N N 55 
OJU C4  O10 SING N N 56 
OJU C5  H29 SING N N 57 
OJU C5  N1  SING N N 58 
OJU N1  C8  SING N N 59 
OJU C8  N2  SING N N 60 
OJU N2  C9  DOUB N N 61 
OJU C9  C10 SING N N 62 
OJU C10 C11 DOUB N N 63 
OJU C11 N1  SING N N 64 
OJU C9  N3  SING N N 65 
OJU C8  O11 DOUB N N 66 
OJU O9  H26 SING N N 67 
OJU O10 H28 SING N N 68 
OJU C10 H30 SING N N 69 
OJU C11 H31 SING N N 70 
OJU N3  H32 SING N N 71 
OJU N3  H33 SING N N 72 
# 
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 
OJU InChI            InChI                1.06    "InChI=1S/C18H32ClN5O12P2/c1-24(2,7-3-5-21-14(25)10-19)8-9-33-37(29,30)36-38(31,32)34-11-12-15(26)16(27)17(35-12)23-6-4-13(20)22-18(23)28/h4,6,12,15-17,26-27H,3,5,7-11H2,1-2H3,(H4-,20,21,22,25,28,29,30,31,32)/p+1" 
OJU InChIKey         InChI                1.06    WZACJIDOHFHVTD-UHFFFAOYSA-O                                                                                                                                                                                           
OJU SMILES_CANONICAL CACTVS               3.385   "C[N+](C)(CCCNC(=O)CCl)CCO[P](O)(=O)O[P](O)(=O)OCC1OC(C(O)C1O)N2C=CC(=NC2=O)N"                                                                                                                                        
OJU SMILES           CACTVS               3.385   "C[N+](C)(CCCNC(=O)CCl)CCO[P](O)(=O)O[P](O)(=O)OCC1OC(C(O)C1O)N2C=CC(=NC2=O)N"                                                                                                                                        
OJU SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C[N+](C)(CCCNC(=O)CCl)CCOP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O"                                                                                                                                          
OJU SMILES           "OpenEye OEToolkits" 3.1.0.0 "C[N+](C)(CCCNC(=O)CCl)CCOP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O"                                                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           OJU 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   3.1.0.0 
_pdbx_chem_comp_identifier.identifier        "2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxyethyl-[3-(2-chloranylethanoylamino)propyl]-dimethyl-azanium" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      OJU 
_pdbx_chem_comp_synonyms.name         "Cytidine-diphosphate with a thiol-reactive chloroacetamide (cross-linker)" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
OJU "Create component" 2022-09-13 PDBE 
OJU "Initial release"  2023-04-12 RCSB 
OJU "Modify PCM"       2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1 OJU CYS None Crosslinker "Amino-acid side chain" "Any position" C37 SG  ? ? 
2 OJU THR None Crosslinker "Amino-acid side chain" "Any position" P   OG1 ? ? 
# 
