data_9BJ # _chem_comp.id 9BJ _chem_comp.name "3',3'-cdUMP" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H24 N4 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "1-{(2R,6R,8R,10aR,12R,13R,13aS)-6-[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-1,2-dihydroxyethyl]-2,8,13-trihydroxy-2,8-dioxohexahydro-2H,4H,8H,10H-2lambda~5~,8lambda~5~-furo[3,2-d][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-12-yl}pyrimidine-2,4(1H,3H)-dione" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-04-17 _chem_comp.pdbx_modified_date 2021-03-13 _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 614.348 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9BJ _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 5VDS _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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.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 9BJ C10 C1 C 0 1 N N R -23.383 3.050 27.610 -4.914 -0.093 0.845 C10 9BJ 1 9BJ C13 C2 C 0 1 N N N -21.400 1.644 24.530 -8.146 1.396 -0.132 C13 9BJ 2 9BJ C21 C3 C 0 1 N N R -27.502 -1.528 25.373 2.395 -0.822 0.719 C21 9BJ 3 9BJ C22 C4 C 0 1 N N N -28.719 -1.237 25.628 2.056 -2.233 1.206 C22 9BJ 4 9BJ O01 O1 O 0 1 N N N -24.272 -2.466 26.300 1.168 1.700 -0.116 O01 9BJ 5 9BJ P02 P1 P 0 1 N N N -25.392 -1.766 27.043 1.054 1.407 1.330 P02 9BJ 6 9BJ O03 O2 O 0 1 N N N -25.202 -0.103 27.159 -0.481 1.087 1.693 O03 9BJ 7 9BJ C04 C5 C 0 1 N N N -25.564 0.547 28.383 -1.524 1.065 0.716 C04 9BJ 8 9BJ C05 C6 C 0 1 N N R -25.173 1.876 28.344 -2.602 0.068 1.143 C05 9BJ 9 9BJ C06 C7 C 0 1 N N S -25.581 2.575 26.943 -2.790 -0.997 0.052 C06 9BJ 10 9BJ O07 O3 O 0 1 N N N -27.000 3.058 26.989 -2.225 -2.241 0.468 O07 9BJ 11 9BJ C08 C8 C 0 1 N N R -24.791 3.529 26.842 -4.315 -1.131 -0.116 C08 9BJ 12 9BJ O09 O4 O 0 1 N N N -25.341 4.726 27.506 -4.741 -2.446 0.246 O09 9BJ 13 9BJ N11 N1 N 0 1 N N N -22.451 2.963 26.456 -5.912 0.716 0.141 N11 9BJ 14 9BJ C12 C9 C 0 1 N N N -22.343 1.726 25.694 -7.226 0.650 0.517 C12 9BJ 15 9BJ C14 C10 C 0 1 N N N -20.569 2.832 24.159 -7.728 2.235 -1.193 C14 9BJ 16 9BJ N15 N2 N 0 1 N N N -20.682 4.062 24.928 -6.423 2.273 -1.532 N15 9BJ 17 9BJ C16 C11 C 0 1 N N N -21.621 4.141 26.082 -5.528 1.518 -0.869 C16 9BJ 18 9BJ O17 O5 O 0 1 N N N -21.706 5.148 26.703 -4.355 1.562 -1.186 O17 9BJ 19 9BJ O18 O6 O 0 1 N N N -19.818 2.770 23.238 -8.539 2.917 -1.793 O18 9BJ 20 9BJ O19 O7 O 0 1 N N N -23.674 2.010 28.378 -3.852 0.743 1.307 O19 9BJ 21 9BJ O20 O8 O 0 1 N N N -26.909 -2.246 26.539 1.969 0.133 1.693 O20 9BJ 22 9BJ C23 C12 C 0 1 N N N -28.819 0.169 26.176 1.431 -3.031 0.061 C23 9BJ 23 9BJ O24 O9 O 0 1 N N N -28.061 1.048 25.338 0.113 -3.443 0.431 O24 9BJ 24 9BJ P25 P2 P 0 1 N N N -27.987 2.690 25.692 -1.194 -3.083 -0.438 P25 9BJ 25 9BJ O26 O10 O 0 1 N N N -27.736 3.554 24.473 -0.798 -2.276 -1.614 O26 9BJ 26 9BJ O27 O11 O 0 1 N N N -29.376 3.078 26.144 -1.900 -4.443 -0.932 O27 9BJ 27 9BJ O28 O12 O 0 1 N N N -29.554 -1.379 24.190 3.925 1.654 1.050 O28 9BJ 28 9BJ C29 C13 C 0 1 N N R -28.772 -1.940 23.318 4.245 0.708 0.028 C29 9BJ 29 9BJ N30 N3 N 0 1 N N N -28.111 -1.161 22.228 5.674 0.788 -0.282 N30 9BJ 30 9BJ C31 C14 C 0 1 N N N -27.748 -1.820 20.941 6.071 1.001 -1.550 C31 9BJ 31 9BJ N32 N4 N 0 1 N N N -27.108 -1.026 19.850 7.378 1.079 -1.862 N32 9BJ 32 9BJ C33 C15 C 0 1 N N N -26.839 0.394 20.035 8.315 0.943 -0.903 C33 9BJ 33 9BJ C34 C16 C 0 1 N N N -27.207 1.061 21.323 7.912 0.719 0.436 C34 9BJ 34 9BJ C35 C17 C 0 1 N N N -27.849 0.259 22.414 6.594 0.650 0.722 C35 9BJ 35 9BJ O36 O13 O 0 1 N N N -26.327 1.027 19.168 9.498 1.013 -1.185 O36 9BJ 36 9BJ O37 O14 O 0 1 N N N -27.966 -2.977 20.782 5.236 1.125 -2.425 O37 9BJ 37 9BJ C38 C18 C 0 1 N N R -27.568 -2.485 24.129 3.906 -0.702 0.515 C38 9BJ 38 9BJ O39 O15 O 0 1 N N N -27.814 -3.734 24.529 4.332 -1.658 -0.459 O39 9BJ 39 9BJ O40 O16 O 0 1 N N N -25.308 -2.273 28.460 1.551 2.683 2.177 O40 9BJ 40 9BJ H1 H1 H 0 1 N N N -23.074 3.904 28.230 -5.379 -0.598 1.691 H1 9BJ 41 9BJ H2 H2 H 0 1 N N N -21.321 0.729 23.961 -9.187 1.349 0.151 H2 9BJ 42 9BJ H3 H3 H 0 1 N N N -26.886 -0.653 25.118 1.884 -0.631 -0.225 H3 9BJ 43 9BJ H4 H4 H 0 1 N N N -29.311 -1.309 24.703 2.967 -2.730 1.541 H4 9BJ 44 9BJ H5 H5 H 0 1 N N N -29.113 -1.945 26.372 1.350 -2.171 2.034 H5 9BJ 45 9BJ H6 H6 H 0 1 N N N -26.654 0.491 28.517 -1.963 2.059 0.631 H6 9BJ 46 9BJ H7 H7 H 0 1 N N N -25.065 0.044 29.225 -1.113 0.765 -0.248 H7 9BJ 47 9BJ H8 H8 H 0 1 N N N -25.619 2.456 29.165 -2.316 -0.409 2.080 H8 9BJ 48 9BJ H9 H9 H 0 1 N N N -25.474 1.825 26.145 -2.335 -0.667 -0.882 H9 9BJ 49 9BJ H10 H10 H 0 1 N N N -24.528 3.772 25.802 -4.604 -0.908 -1.143 H10 9BJ 50 9BJ H11 H11 H 0 1 N N N -26.140 4.994 27.067 -5.699 -2.575 0.203 H11 9BJ 51 9BJ H12 H12 H 0 1 N N N -22.941 0.869 25.967 -7.526 0.004 1.328 H12 9BJ 52 9BJ H13 H13 H 0 1 N N N -20.128 4.857 24.681 -6.129 2.845 -2.258 H13 9BJ 53 9BJ H14 H14 H 0 1 N N N -29.872 0.487 26.188 1.380 -2.407 -0.831 H14 9BJ 54 9BJ H15 H15 H 0 1 N N N -28.416 0.196 27.199 2.042 -3.910 -0.145 H15 9BJ 55 9BJ H16 H16 H 0 1 N N N -29.724 3.745 25.564 -1.336 -5.001 -1.485 H16 9BJ 56 9BJ H17 H17 H 0 1 N N N -29.875 -2.036 24.797 4.405 1.515 1.878 H17 9BJ 57 9BJ H18 H18 H 0 1 N N N -29.269 -2.806 22.857 3.666 0.932 -0.868 H18 9BJ 58 9BJ H19 H19 H 0 1 N N N -26.863 -1.471 18.989 7.646 1.232 -2.782 H19 9BJ 59 9BJ H20 H20 H 0 1 N N N -27.011 2.114 21.465 8.648 0.608 1.218 H20 9BJ 60 9BJ H21 H21 H 0 1 N N N -28.119 0.737 23.344 6.267 0.483 1.738 H21 9BJ 61 9BJ H22 H22 H 0 1 N N N -26.644 -2.390 23.539 4.417 -0.893 1.459 H22 9BJ 62 9BJ H23 H23 H 0 1 N N N -27.853 -4.307 23.773 3.918 -1.548 -1.325 H23 9BJ 63 9BJ H24 H24 H 0 1 N N N -24.590 -2.891 28.534 1.043 3.489 2.008 H24 9BJ 64 # # 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 9BJ C10 C08 SING N N 1 9BJ C10 N11 SING N N 2 9BJ C10 O19 SING N N 3 9BJ C13 C12 DOUB N N 4 9BJ C13 C14 SING N N 5 9BJ C21 C22 SING N N 6 9BJ C21 O20 SING N N 7 9BJ C21 C38 SING N N 8 9BJ C22 C23 SING N N 9 9BJ O01 P02 DOUB N N 10 9BJ P02 O03 SING N N 11 9BJ P02 O20 SING N N 12 9BJ P02 O40 SING N N 13 9BJ O03 C04 SING N N 14 9BJ C04 C05 SING N N 15 9BJ C05 C06 SING N N 16 9BJ C05 O19 SING N N 17 9BJ C06 O07 SING N N 18 9BJ C06 C08 SING N N 19 9BJ O07 P25 SING N N 20 9BJ C08 O09 SING N N 21 9BJ N11 C12 SING N N 22 9BJ N11 C16 SING N N 23 9BJ C14 N15 SING N N 24 9BJ C14 O18 DOUB N N 25 9BJ N15 C16 SING N N 26 9BJ C16 O17 DOUB N N 27 9BJ C23 O24 SING N N 28 9BJ O24 P25 SING N N 29 9BJ P25 O26 DOUB N N 30 9BJ P25 O27 SING N N 31 9BJ O28 C29 SING N N 32 9BJ C29 N30 SING N N 33 9BJ C29 C38 SING N N 34 9BJ N30 C31 SING N N 35 9BJ N30 C35 SING N N 36 9BJ C31 N32 SING N N 37 9BJ C31 O37 DOUB N N 38 9BJ N32 C33 SING N N 39 9BJ C33 C34 SING N N 40 9BJ C33 O36 DOUB N N 41 9BJ C34 C35 DOUB N N 42 9BJ C38 O39 SING N N 43 9BJ C10 H1 SING N N 44 9BJ C13 H2 SING N N 45 9BJ C21 H3 SING N N 46 9BJ C22 H4 SING N N 47 9BJ C22 H5 SING N N 48 9BJ C04 H6 SING N N 49 9BJ C04 H7 SING N N 50 9BJ C05 H8 SING N N 51 9BJ C06 H9 SING N N 52 9BJ C08 H10 SING N N 53 9BJ O09 H11 SING N N 54 9BJ C12 H12 SING N N 55 9BJ N15 H13 SING N N 56 9BJ C23 H14 SING N N 57 9BJ C23 H15 SING N N 58 9BJ O27 H16 SING N N 59 9BJ O28 H17 SING N N 60 9BJ C29 H18 SING N N 61 9BJ N32 H19 SING N N 62 9BJ C34 H20 SING N N 63 9BJ C35 H21 SING N N 64 9BJ C38 H22 SING N N 65 9BJ O39 H23 SING N N 66 9BJ O40 H24 SING N N 67 # # 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 9BJ SMILES ACDLabs 12.01 "C3(C(C1C(COP(=O)(OC(CCOP(O1)(=O)O)C(C(O)N2C(NC(C=C2)=O)=O)O)O)O3)O)N4C=CC(NC4=O)=O" 9BJ InChI InChI 1.03 "InChI=1S/C18H24N4O16P2/c23-10-1-4-21(17(28)19-10)15(27)12(25)8-3-6-34-39(30,31)38-14-9(7-35-40(32,33)37-8)36-16(13(14)26)22-5-2-11(24)20-18(22)29/h1-2,4-5,8-9,12-16,25-27H,3,6-7H2,(H,30,31)(H,32,33)(H,19,23,28)(H,20,24,29)/t8-,9-,12-,13-,14-,15-,16-/m1/s1" 9BJ InChIKey InChI 1.03 SDBXSRQCWCPJQL-WXFFCYTBSA-N 9BJ SMILES_CANONICAL CACTVS 3.385 "O[C@@H]([C@@H](O)N1C=CC(=O)NC1=O)[C@H]2CCO[P](O)(=O)O[C@H]3[C@@H](O)[C@@H](O[C@@H]3CO[P](O)(=O)O2)N4C=CC(=O)NC4=O" 9BJ SMILES CACTVS 3.385 "O[CH]([CH](O)N1C=CC(=O)NC1=O)[CH]2CCO[P](O)(=O)O[CH]3[CH](O)[CH](O[CH]3CO[P](O)(=O)O2)N4C=CC(=O)NC4=O" 9BJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1COP(=O)(O[C@@H]2[C@@H](COP(=O)(O[C@H]1[C@H]([C@H](N3C=CC(=O)NC3=O)O)O)O)O[C@H]([C@@H]2O)N4C=CC(=O)NC4=O)O" 9BJ SMILES "OpenEye OEToolkits" 2.0.6 "C1COP(=O)(OC2C(COP(=O)(OC1C(C(N3C=CC(=O)NC3=O)O)O)O)OC(C2O)N4C=CC(=O)NC4=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 9BJ "SYSTEMATIC NAME" ACDLabs 12.01 "1-{(2R,6R,8R,10aR,12R,13R,13aS)-6-[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-1,2-dihydroxyethyl]-2,8,13-trihydroxy-2,8-dioxohexahydro-2H,4H,8H,10H-2lambda~5~,8lambda~5~-furo[3,2-d][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-12-yl}pyrimidine-2,4(1H,3H)-dione" 9BJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "1-[(1~{S},7~{R},12~{R},14~{R},15~{R})-7-[(1~{R},2~{R})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-1,2-bis(oxidanyl)ethyl]-3,9,15-tris(oxidanyl)-3,9-bis(oxidanylidene)-2,4,8,10,13-pentaoxa-3$l^{5},9$l^{5}-diphosphabicyclo[10.3.0]pentadecan-14-yl]pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 9BJ "Create component" 2017-04-17 RCSB 9BJ "Initial release" 2017-09-27 RCSB 9BJ "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 9BJ _pdbx_chem_comp_synonyms.name "1-{(2R,6R,8R,10aR,12R,13R,13aS)-6-[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-1,2-dihydroxyethyl]-2,8,13-trihydroxy-2,8-dioxohexahydro-2H,4H,8H,10H-2lambda~5~,8lambda~5~-furo[3,2-d][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-12-yl}pyrimidine-2,4(1H,3H)-dione" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##