data_ZNT # _chem_comp.id ZNT _chem_comp.name "2'3'-cUA" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H23 N7 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "1-[(2R,5R,7R,8R,10S,12aR,14R,15R,15aS,16R)-14-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxooctahydro-2H,10H,12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-7-yl]pyrimidine-2,4(1H,3H)-dione" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-03-17 _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 635.372 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZNT _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 8GJX _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 ZNT C13 C1 C 0 1 N N R N N N -22.601 35.595 -1.475 2.767 0.363 0.834 C13 ZNT 1 ZNT C17 C2 C 0 1 N N N N N N -22.141 34.090 1.370 3.647 -1.616 -1.559 C17 ZNT 2 ZNT C20 C3 C 0 1 N N R N N N -23.092 36.755 -0.656 3.803 1.256 0.028 C20 ZNT 3 ZNT C22 C4 C 0 1 N N N N N N -22.581 39.133 -1.337 3.149 3.476 -0.594 C22 ZNT 4 ZNT C24 C5 C 0 1 N N N N N N -20.187 39.967 -0.734 1.715 3.892 -2.391 C24 ZNT 5 ZNT C26 C6 C 0 1 N N N N N N -20.844 37.615 -0.120 2.316 1.653 -1.835 C26 ZNT 6 ZNT C02 C7 C 0 1 N N R N N N -17.973 32.466 -2.125 -1.998 -1.300 -0.923 C02 ZNT 7 ZNT C03 C8 C 0 1 N N S N N N -19.349 32.963 -2.047 -0.620 -1.808 -0.419 C03 ZNT 8 ZNT C08 C9 C 0 1 N N R N N N -19.901 32.498 -3.341 -0.879 -2.312 1.070 C08 ZNT 9 ZNT C09 C10 C 0 1 N N N N N N -21.140 33.256 -3.709 0.104 -1.746 2.011 C09 ZNT 10 ZNT C14 C11 C 0 1 N N R N N N -23.108 34.409 -0.826 3.476 -1.046 0.795 C14 ZNT 11 ZNT C16 C12 C 0 1 N N R N N N -23.228 34.727 0.579 4.371 -0.993 -0.439 C16 ZNT 12 ZNT C25 C13 C 0 1 N N N N N N -19.853 38.683 -0.136 1.630 2.500 -2.632 C25 ZNT 13 ZNT C32 C14 C 0 1 N N R N N N -17.604 32.750 -3.550 -2.993 -1.642 0.289 C32 ZNT 14 ZNT C34 C15 C 0 1 Y N N N N N -15.716 34.254 -3.012 -4.933 -0.172 -0.155 C34 ZNT 15 ZNT C36 C16 C 0 1 Y N N N N N -13.663 33.994 -1.962 -6.750 -0.154 -1.563 C36 ZNT 16 ZNT C38 C17 C 0 1 Y N N N N N -14.197 36.115 -2.741 -6.548 1.618 -0.097 C38 ZNT 17 ZNT C40 C18 C 0 1 Y N N N N N -15.427 35.595 -3.204 -5.367 1.042 0.403 C40 ZNT 18 ZNT C42 C19 C 0 1 Y N N N N N -17.402 35.169 -4.051 -3.537 0.480 1.422 C42 ZNT 19 ZNT N21 N1 N 0 1 N N N N N N -22.171 37.812 -0.698 3.078 2.151 -0.813 N21 ZNT 20 ZNT N23 N2 N 0 1 N N N N N N -21.491 40.195 -1.313 2.476 4.343 -1.373 N23 ZNT 21 ZNT N33 N3 N 0 1 Y N N N N N -16.939 34.030 -3.555 -3.780 -0.503 0.510 N33 ZNT 22 ZNT N35 N4 N 0 1 Y N N N N N -14.813 33.480 -2.389 -5.649 -0.729 -1.127 N35 ZNT 23 ZNT N37 N5 N 0 1 Y N N N N N -13.361 35.279 -2.134 -7.197 0.987 -1.071 N37 ZNT 24 ZNT N39 N6 N 0 1 N N N N N N -13.861 37.522 -2.926 -7.024 2.813 0.413 N39 ZNT 25 ZNT N41 N7 N 0 1 Y N N N N N -16.489 36.127 -3.848 -4.470 1.386 1.358 N41 ZNT 26 ZNT O01 O1 O 0 1 N N N N N N -17.938 31.070 -1.873 -2.422 -2.019 -2.096 O01 ZNT 27 ZNT O04 O2 O 0 1 N N N N N N -20.017 32.384 -0.912 -0.146 -2.849 -1.221 O04 ZNT 28 ZNT O06 O3 O 0 1 N N N N N N -19.706 32.197 1.738 2.016 -4.181 -0.330 O06 ZNT 29 ZNT O07 O4 O 0 1 N N N N N N -18.456 33.807 0.482 1.705 -3.663 -2.790 O07 ZNT 30 ZNT O10 O5 O 0 1 N N N N N N -20.787 34.590 -3.990 0.138 -0.352 1.982 O10 ZNT 31 ZNT O12 O6 O 0 1 N N N N N N -23.092 35.674 -2.820 2.516 0.823 2.127 O12 ZNT 32 ZNT O15 O7 O 0 1 N N N N N N -24.435 34.054 -1.365 4.325 -1.158 1.985 O15 ZNT 33 ZNT O18 O8 O 0 1 N N N N N N -20.864 34.408 0.818 2.290 -1.721 -1.338 O18 ZNT 34 ZNT O19 O9 O 0 1 N N N N N N -23.172 36.230 0.712 4.668 0.379 -0.776 O19 ZNT 35 ZNT O27 O10 O 0 1 N N N N N N -19.382 40.833 -0.747 1.105 4.676 -3.096 O27 ZNT 36 ZNT O28 O11 O 0 1 N N N N N N -23.650 39.316 -1.810 3.828 3.897 0.323 O28 ZNT 37 ZNT O29 O12 O 0 1 N N N N N N -21.460 37.146 -4.307 0.382 2.004 3.175 O29 ZNT 38 ZNT O30 O13 O 0 1 N N N N N N -22.788 35.419 -5.288 1.363 -0.154 4.185 O30 ZNT 39 ZNT O31 O14 O 0 1 N N N N N N -18.822 32.781 -4.292 -2.168 -1.972 1.422 O31 ZNT 40 ZNT P05 P1 P 0 1 N N N N N N -19.814 33.144 0.564 1.438 -3.080 -1.440 P05 ZNT 41 ZNT P11 P2 P 0 1 N N N N N N -21.983 35.754 -4.051 1.143 0.516 2.834 P11 ZNT 42 ZNT H1 H1 H 0 1 N N N N N N -21.501 35.587 -1.471 1.811 0.242 0.196 H1 ZNT 43 ZNT H2 H2 H 0 1 N N N N N N -22.187 34.455 2.407 3.825 -1.067 -2.499 H2 ZNT 44 ZNT H3 H3 H 0 1 N N N N N N -22.278 32.999 1.359 4.154 -2.663 -1.787 H3 ZNT 45 ZNT H4 H4 H 0 1 N N N N N N -24.086 37.071 -1.007 4.340 1.774 0.747 H4 ZNT 46 ZNT H5 H5 H 0 1 N N N N N N -20.594 36.664 0.326 2.265 0.587 -2.004 H5 ZNT 47 ZNT H6 H6 H 0 1 N N N N N N -17.315 33.020 -1.439 -2.018 -0.211 -1.046 H6 ZNT 48 ZNT H7 H7 H 0 1 N N N N N N -19.363 34.062 -1.996 0.090 -0.931 -0.377 H7 ZNT 49 ZNT H8 H8 H 0 1 N N N N N N -20.113 31.419 -3.303 -0.865 -3.432 1.024 H8 ZNT 50 ZNT H9 H9 H 0 1 N N N N N N -21.852 33.230 -2.871 -0.103 -2.075 2.962 H9 ZNT 51 ZNT H10 H10 H 0 1 N N N N N N -21.602 32.801 -4.597 1.083 -2.168 1.752 H10 ZNT 52 ZNT H11 H11 H 0 1 N N N N N N -22.411 33.570 -0.968 2.794 -1.891 0.792 H11 ZNT 53 ZNT H12 H12 H 0 1 N N N N N N -24.200 34.375 0.956 5.381 -1.524 -0.227 H12 ZNT 54 ZNT H13 H13 H 0 1 N N N N N N -18.875 38.523 0.294 1.025 2.120 -3.442 H13 ZNT 55 ZNT H14 H14 H 0 1 N N N N N N -16.934 31.963 -3.927 -3.550 -2.466 -0.038 H14 ZNT 56 ZNT H15 H15 H 0 1 N N N N N N -12.954 33.351 -1.462 -7.308 -0.632 -2.354 H15 ZNT 57 ZNT H16 H16 H 0 1 N N N N N N -18.357 35.302 -4.538 -2.696 0.504 2.099 H16 ZNT 58 ZNT H17 H17 H 0 1 N N N N N N -21.686 41.089 -1.715 2.539 5.296 -1.202 H17 ZNT 59 ZNT H18 H18 H 0 1 N N N N N N -12.958 37.703 -2.537 -7.841 3.200 0.060 H18 ZNT 60 ZNT H19 H19 H 0 1 N N N N N N -13.853 37.737 -3.903 -6.541 3.263 1.123 H19 ZNT 61 ZNT H20 H20 H 0 1 N N N N N N -18.174 30.905 -0.968 -3.278 -1.734 -2.444 H20 ZNT 62 ZNT H21 H21 H 0 1 N N N N N N -18.836 32.258 2.115 2.963 -4.360 -0.412 H21 ZNT 63 ZNT H22 H22 H 0 1 N N N N N N -24.756 33.273 -0.929 4.804 -1.995 2.049 H22 ZNT 64 ZNT H23 H23 H 0 1 N N N N N N -21.762 37.447 -5.156 -0.467 1.917 3.629 H23 ZNT 65 # 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 ZNT O30 P11 DOUB N N 1 ZNT O29 P11 SING N N 2 ZNT O31 C32 SING N N 3 ZNT O31 C08 SING N N 4 ZNT P11 O10 SING N N 5 ZNT P11 O12 SING N N 6 ZNT C42 N41 DOUB Y N 7 ZNT C42 N33 SING Y N 8 ZNT O10 C09 SING N N 9 ZNT N41 C40 SING Y N 10 ZNT C09 C08 SING N N 11 ZNT N33 C32 SING N N 12 ZNT N33 C34 SING Y N 13 ZNT C32 C02 SING N N 14 ZNT C08 C03 SING N N 15 ZNT C40 C34 DOUB Y N 16 ZNT C40 C38 SING Y N 17 ZNT C34 N35 SING Y N 18 ZNT N39 C38 SING N N 19 ZNT O12 C13 SING N N 20 ZNT C38 N37 DOUB Y N 21 ZNT N35 C36 DOUB Y N 22 ZNT N37 C36 SING Y N 23 ZNT C02 C03 SING N N 24 ZNT C02 O01 SING N N 25 ZNT C03 O04 SING N N 26 ZNT O28 C22 DOUB N N 27 ZNT C13 C14 SING N N 28 ZNT C13 C20 SING N N 29 ZNT O15 C14 SING N N 30 ZNT C22 N23 SING N N 31 ZNT C22 N21 SING N N 32 ZNT N23 C24 SING N N 33 ZNT O04 P05 SING N N 34 ZNT C14 C16 SING N N 35 ZNT O27 C24 DOUB N N 36 ZNT C24 C25 SING N N 37 ZNT N21 C20 SING N N 38 ZNT N21 C26 SING N N 39 ZNT C20 O19 SING N N 40 ZNT C25 C26 DOUB N N 41 ZNT O07 P05 DOUB N N 42 ZNT P05 O18 SING N N 43 ZNT P05 O06 SING N N 44 ZNT C16 O19 SING N N 45 ZNT C16 C17 SING N N 46 ZNT O18 C17 SING N N 47 ZNT C13 H1 SING N N 48 ZNT C17 H2 SING N N 49 ZNT C17 H3 SING N N 50 ZNT C20 H4 SING N N 51 ZNT C26 H5 SING N N 52 ZNT C02 H6 SING N N 53 ZNT C03 H7 SING N N 54 ZNT C08 H8 SING N N 55 ZNT C09 H9 SING N N 56 ZNT C09 H10 SING N N 57 ZNT C14 H11 SING N N 58 ZNT C16 H12 SING N N 59 ZNT C25 H13 SING N N 60 ZNT C32 H14 SING N N 61 ZNT C36 H15 SING N N 62 ZNT C42 H16 SING N N 63 ZNT N23 H17 SING N N 64 ZNT N39 H18 SING N N 65 ZNT N39 H19 SING N N 66 ZNT O01 H20 SING N N 67 ZNT O06 H21 SING N N 68 ZNT O15 H22 SING N N 69 ZNT O29 H23 SING N N 70 # 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 ZNT SMILES ACDLabs 12.01 "Nc1ncnc2c1ncn2C1OC2COP(=O)(O)OC3C(OC(COP(=O)(O)OC2C1O)C3O)N1C=CC(=O)NC1=O" ZNT InChI InChI 1.06 "InChI=1S/C19H23N7O14P2/c20-15-10-16(22-5-21-15)26(6-23-10)17-12(29)13-8(38-17)4-36-42(33,34)40-14-11(28)7(3-35-41(31,32)39-13)37-18(14)25-2-1-9(27)24-19(25)30/h1-2,5-8,11-14,17-18,28-29H,3-4H2,(H,31,32)(H,33,34)(H2,20,21,22)(H,24,27,30)/t7-,8-,11-,12-,13-,14-,17-,18-/m1/s1" ZNT InChIKey InChI 1.06 QFSRDWZEQDGHEV-KPKSGTNCSA-N ZNT SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@@H]5[C@H](O)[C@@H](CO[P](O)(=O)O[C@H]4[C@H]3O)O[C@H]5N6C=CC(=O)NC6=O" ZNT SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](CO[P](O)(=O)O[CH]4[CH]3O)O[CH]5N6C=CC(=O)NC6=O" ZNT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)COP(=O)(O[C@@H]5[C@@H]([C@@H](COP(=O)(O4)O)O[C@H]5N6C=CC(=O)NC6=O)O)O)O)N" ZNT SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(C(COP(=O)(O4)O)OC5N6C=CC(=O)NC6=O)O)O)O)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 ZNT "SYSTEMATIC NAME" ACDLabs 12.01 "1-[(2R,5R,7R,8R,10S,12aR,14R,15R,15aS,16R)-14-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxooctahydro-2H,10H,12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-7-yl]pyrimidine-2,4(1H,3H)-dione" ZNT "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[(1~{R},6~{R},8~{R},9~{R},10~{S},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-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 ZNT "Create component" 2023-03-17 RCSB ZNT "Modify name" 2023-04-13 RCSB ZNT "Initial release" 2023-07-05 RCSB ZNT "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id ZNT _pdbx_chem_comp_synonyms.name "1-[(2R,5R,7R,8R,10S,12aR,14R,15R,15aS,16R)-14-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxooctahydro-2H,10H,12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-7-yl]pyrimidine-2,4(1H,3H)-dione" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id ZNT _pdbx_chem_comp_pcm.modified_residue_id ARG _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 O29 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NH1 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #