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 ? ? #